Microsatellite genome-wide database development for the commercial blackhead seabream (Acanthopagrus schlegelii). Genes (Basel) 14:620, 2023. Pubmed reference: 36980892. DOI: 10.3390/genes14030620.

Acestrorhynchus altus :

2023

Yang, X., Song, Y., Zhang, R., Yu, M., Guo, X., Guo, H., Du, X., Sun, S., Li, C., Mao, X., Fan, G., Liu, X. :

Unraveling the genomic features, phylogeny and genetic basis of tooth ontogenesis in characiformes through analysis of four genomes. DNA Res , 2023. Pubmed reference: 37788574. DOI: 10.1093/dnares/dsad022.

Acinonyx jubatus (cheetah) :

2023

Winter, S., Meißner, R., Greve, C., Ben Hamadou, A., Horin, P., Prost, S., Burger, P.A. :

A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus). J Hered , 2023. Pubmed reference: 36869783. DOI: 10.1093/jhered/esad015.

Acomys cahirinus (Egyptian spiny mouse) :

2023

Nguyen, E.D., Fard, V.N., Kim, B.Y., Collins, S., Galey, M., Nelson, B.R., Wakenight, P., Gable, S.M., McKenna, A., Bammler, T.K., MacDonald, J., Okamura, D.M., Shendure, J., Beier, D.R., Ramirez, J.M., Majesky, M.W., Millen, K.J., Tollis, M., Miller, D.E. :

GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). bioRxiv , 2023. Pubmed reference: 37066261. DOI: 10.1101/2023.04.03.535372.

GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3 (Bethesda) , 2023. Pubmed reference: 37552705. DOI: 10.1093/g3journal/jkad177.

Acridotheres tristis (common myna) :

2024

Stuart, K.C., Johnson, R.N., Major, R., Atsawawaranunt, K., Ewart, K.M., Rollins, L.A., Santure, A.W., Whibley, A. :

The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res :dsae005, 2024. Pubmed reference: 38366840. DOI: 10.1093/dnares/dsae005.

Acrossocheilus fasciatus :

2024

Zheng, J., Jiang, J., Rui, Q., Li, F., Liu, S., Cheng, S., Chi, M., Jiang, W. :

Chromosome-level genome assembly of Acrossocheilus fasciatus using PacBio sequencing and Hi-C technology. Sci Data 11:166, 2024. Pubmed reference: 38310107. DOI: 10.1038/s41597-024-02999-6.

Actinemys marmorata (Pacific pond turtle) :

2022

Todd, B.D., Jenkinson, T.S., Escalona, M., Beraut, E., Nguyen, O., Sahasrabudhe, R., Scott, P.A., Toffelmier, E., Wang, I.J., Shaffer, H.B. :

Reference genome of the northwestern pond turtle, Actinemys marmorata. J Hered 113:624-631, 2022. Pubmed reference: 35665811. DOI: 10.1093/jhered/esac021.

Agapornis roseicollis (peach-faced lovebird) :

2018

van der Zwan, H., van der Westhuizen, F., Visser, C., van der Sluis, R. :

Draft de novo genome sequence of Agapornis roseicollis for application in avian breeding. Anim Biotechnol 29:241-246, 2018. Pubmed reference: 29035135. DOI: 10.1080/10495398.2017.1367692.

Agelaius tricolor (tricolored blackbird) :

2022

Ballare, K.M., Escalona, M., Barr, K., Seligmann, W., Sacco, S., Sahasrabudhe, R.M., Nguyen, O., Wyckoff, C., Smith, T.B., Shapiro, B. :

A reference genome assembly of the declining tricolored blackbird, Agelaius tricolor. J Hered , 2022. Pubmed reference: 36099176. DOI: 10.1093/jhered/esac053.

Ahaetulla prasina (Asian vine snakes) :

2023

Tang, C.Y., Zhang, X., Xu, X., Sun, S., Peng, C., Song, M.H., Yan, C., Sun, H., Liu, M., Xie, L., Luo, S.J., Li, J.T. :

Genetic mapping and molecular mechanism behind color variation in the Asian vine snake. Genome Biol 24:46, 2023. Pubmed reference: 36895044. DOI: 10.1186/s13059-023-02887-z.

Ailuropoda melanoleuca (giant panda) :

2024

Guan, D., Sun, S., Song, L., Zhao, P., Nie, Y., Huang, X., Zhou, W., Yan, L., Lei, Y., Hu, Y., Wei, F. :

Taking a color photo: A homozygous 25-bp deletion in Bace2 may cause brown-and-white coat color in giant pandas. Proc Natl Acad Sci U S A 121:e2317430121, 2024. Pubmed reference: 38437540. DOI: 10.1073/pnas.2317430121.

2023

Ma, S., Zhu, Y., Wu, H. :

Development and validation of SNP markers for giant panda using a kompetitive allele specific PCR approach. Anim Genet , 2023. Pubmed reference: 37580020. DOI: 10.1111/age.13350.

Yang, S., Lan, T., Wei, R., Zhang, L., Lin, L., Du, H., Huang, Y., Zhang, G., Huang, S., Shi, M., Wang, C., Wang, Q., Li, R., Han, L., Tang, D., Li, H., Zhang, H., Cui, J., Lu, H., Huang, J., Luo, Y., Li, D., Wan, Q.H., Liu, H., Fang, S.G. :

Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism. BMC Biol 21:222, 2023. Pubmed reference: 37858133. DOI: 10.1186/s12915-023-01691-2.

Akarotaxis nudiceps :

2023

Bista, I., Wood, J.M.D., Desvignes, T., McCarthy, S.A., Matschiner, M., Ning, Z., Tracey, A., Torrance, J., Sims, Y., Chow, W., Smith, M., Oliver, K., Haggerty, L., Salzburger, W., Postlethwait, J.H., Howe, K., Clark, M.S., William Detrich, H., Christina Cheng, C.H., Miska, E.A., Durbin, R. :

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Albula glossodonta (roundjaw bonefish) :

2022

Pickett, B.D., Talma, S., Glass, J.R., Ence, D., Johnson, T.P., Cowley, P.D., Ridge, P.G., Kauwe, J.S.K. :

Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish. GigaByte 2022:gigabyte44, 2022. Pubmed reference: 36968794. DOI: 10.46471/gigabyte.44.

Alectoris chukar (chukar partridge) :

2024

Zhou, H., Huang, X., Liu, J., Ding, J., Xu, K., Zhu, W., He, C., Yang, L., Zhu, J., Han, C., Qin, C., Luo, H., Chen, K., Jiang, S., Shi, Y., Zeng, J., Weng, Z., Xu, Y., Wang, Q., Zhong, M., Du, B., Song, S., Meng, H. :

De novo phased genome assembly, annotation and population genotyping of Alectoris chukar. Sci Data 11:162, 2024. Pubmed reference: 38307880. DOI: 10.1038/s41597-024-02991-0.

Alectoris magna (Przewalski's partridge) :

2023

Wang, X., Xia, W., Teng, X., Lin, W., Xing, Z., Wang, S., Liu, X., Qu, J., Zhao, W., Wang, L. :

Chromosome-level genome assembly of Przevalski's partridge (Alectoris magna). Sci Data 10:829, 2023. Pubmed reference: 38007538. DOI: 10.1038/s41597-023-02655-5.

Alligator mississippiensis (American alligator) :

2017

Rice, E.S., Kohno, S., John, J.S., Pham, S., Howard, J., Lareau, L.F., O'Connell, B.L., Hickey, G., Armstrong, J., Deran, A., Fiddes, I., Platt, R.N., Gresham, C., McCarthy, F., Kern, C., Haan, D., Phan, T., Schmidt, C., Sanford, J.R., Ray, D.A., Paten, B., Guillette, L.J., Green, R.E. :

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res , 2017. Pubmed reference: 28137821. DOI: 10.1101/gr.213595.116.

2014

Green, R.E., Braun, E.L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M.W., St John, J.A., Capella-Gutiérrez, S., Castoe, T.A., Kern, C., Fujita, M.K., Opazo, J.C., Jurka, J., Kojima, K.K., Caballero, J., Hubley, R.M., Smit, A.F., Platt, R.N., Lavoie, C.A., Ramakodi, M.P., Finger, J.W., Suh, A., Isberg, S.R., Miles, L., Chong, A.Y., Jaratlerdsiri, W., Gongora, J., Moran, C., Iriarte, A., McCormack, J., Burgess, S.C., Edwards, S.V., Lyons, E., Williams, C., Breen, M., Howard, J.T., Gresham, C.R., Peterson, D.G., Schmitz, J., Pollock, D.D., Haussler, D., Triplett, E.W., Zhang, G., Irie, N., Jarvis, E.D., Brochu, C.A., Schmidt, C.J., McCarthy, F.M., Faircloth, B.C., Hoffmann, F.G., Glenn, T.C., Gabaldón, T., Paten, B., Ray, D.A. :

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449, 2014. Pubmed reference: 25504731. DOI: 10.1126/science.1254449.

Amazona aestiva (blue-fronted amazon) :

2018

Wirthlin, M., Lima, N.C.B., Guedes, R.L.M., Soares, A.E.R., Almeida, L.G.P., Cavaleiro, N.P., Loss de Morais, G., Chaves, A.V., Howard, J.T., Teixeira, M.M., Schneider, P.N., Santos, F.R., Schatz, M.C., Felipe, M.S., Miyaki, C.Y., Aleixo, A., Schneider, M.P.C., Jarvis, E.D., Vasconcelos, A.T.R., Prosdocimi, F., Mello, C.V. :

Parrot genomes and the evolution of heightened longevity and cognition. Curr Biol 28:4001-4008.e7, 2018. Pubmed reference: 30528582. DOI: 10.1016/j.cub.2018.10.050.

Amazona vittata (Puerto Rican parrot) :

2012

Oleksyk, T.K., Pombert, J.F., Siu, D., Mazo-Vargas, A., Ramos, B., Guiblet, W., Afanador, Y., Ruiz-Rodriguez, C.T., Nickerson, M.L., Logue, D.M., Dean, M., Figueroa, L., Valentin, R., Martinez-Cruzado, J.C. :

A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education. Gigascience 1:14, 2012. Pubmed reference: 23587420. DOI: 10.1186/2047-217X-1-14.

Amblyraja radiata (thorny skate) :

2021

Rhie, A., McCarthy, S.A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., Lee, C., Ko, B.J., Chaisson, M., Gedman, G.L., Cantin, L.J., Thibaud-Nissen, F., Haggerty, L., Bista, I., Smith, M., Haase, B., Mountcastle, J., Winkler, S., Paez, S., Howard, J., Vernes, S.C., Lama, T.M., Grutzner, F., Warren, W.C., Balakrishnan, C.N., Burt, D., George, J.M., Biegler, M.T., Iorns, D., Digby, A., Eason, D., Robertson, B., Edwards, T., Wilkinson, M., Turner, G., Meyer, A., Kautt, A.F., Franchini, P., Detrich, H.W., Svardal, H., Wagner, M., Naylor, G.J.P., Pippel, M., Malinsky, M., Mooney, M., Simbirsky, M., Hannigan, B.T., Pesout, T., Houck, M., Misuraca, A., Kingan, S.B., Hall, R., Kronenberg, Z., Sović, I., Dunn, C., Ning, Z., Hastie, A., Lee, J., Selvaraj, S., Green, R.E., Putnam, N.H., Gut, I., Ghurye, J., Garrison, E., Sims, Y., Collins, J., Pelan, S., Torrance, J., Tracey, A., Wood, J., Dagnew, R.E., Guan, D., London, S.E., Clayton, D.F., Mello, C.V., Friedrich, S.R., Lovell, P.V., Osipova, E., Al-Ajli, F.O., Secomandi, S., Kim, H., Theofanopoulou, C., Hiller, M., Zhou, Y., Harris, R.S., Makova, K.D., Medvedev, P., Hoffman, J., Masterson, P., Clark, K., Martin, F., Howe, K., Flicek, P., Walenz, B.P., Kwak, W., Clawson, H., Diekhans, M., Nassar, L., Paten, B., Kraus, R.H.S., Crawford, A.J., Gilbert, M.T.P., Zhang, G., Venkatesh, B., Murphy, R.W., Koepfli, K.P., Shapiro, B., Johnson, W.E., Di Palma, F., Marques-Bonet, T., Teeling, E.C., Warnow, T., Graves, J.M., Ryder, O.A., Haussler, D., O'Brien, S.J., Korlach, J., Lewin, H.A., Howe, K., Myers, E.W., Durbin, R., Phillippy, A.M., Jarvis, E.D. :

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Amia calva (bowfin) :

2021

Thompson, A.W., Hawkins, M.B., Parey, E., Wcisel, D.J., Ota, T., Kawasaki, K., Funk, E., Losilla, M., Fitch, O.E., Pan, Q., Feron, R., Louis, A., Montfort, J., Milhes, M., Racicot, B.L., Childs, K.L., Fontenot, Q., Ferrara, A., David, S.R., McCune, A.R., Dornburg, A., Yoder, J.A., Guiguen, Y., Roest Crollius, H., Berthelot, C., Harris, M.P., Braasch, I. :

The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat Genet 53:1373-84, 2021. Pubmed reference: 34462605. DOI: 10.1038/s41588-021-00914-y.

Amphilophus citrinellus (Midas cichlid) :

2022

Kratochwil, C.F., Kautt, A.F., Nater, A., Härer, A., Liang, Y., Henning, F., Meyer, A. :

An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes. Nat Commun 13:296, 2022. Pubmed reference: 35027541. DOI: 10.1038/s41467-021-27685-8.

Amphiprion bicinctus (twoband anemonefish) :

2018

Casas, L., Saenz-Agudelo, P., Irigoien, X. :

High-throughput sequencing and linkage mapping of a clownfish genome provide insights on the distribution of molecular players involved in sex change. Sci Rep 8:4073, 2018. Pubmed reference: 29511241. DOI: 10.1038/s41598-018-22282-0.

Amphiprion percula (orange clownfish) :

2019

Lehmann, R., Lightfoot, D.J., Schunter, C., Michell, C.T., Ohyanagi, H., Mineta, K., Foret, S., Berumen, M.L., Miller, D.J., Aranda, M., Gojobori, T., Munday, P.L., Ravasi, T. :

Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Mol Ecol Resour 19:570-585, 2019. Pubmed reference: 30203521. DOI: 10.1111/1755-0998.12939.

Anas platyrhynchos (Mallard) :

2024

Li, L., Quan, J., Liu, H., Yu, H., Chen, H., Xia, C., Zhao, S., Gao, C. :

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing. BMC Genomics 25:17, 2024. Pubmed reference: 38166615. DOI: 10.1186/s12864-023-09928-8.

Hu, J., Song, L., Ning, M., Niu, X., Han, M., Gao, C., Feng, X., Cai, H., Li, T., Li, F., Li, H., Gong, D., Song, W., Liu, L., Pu, J., Liu, J., Smith, J., Sun, H., Huang, Y. :

A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families. BMC Biol 22:31, 2024. Pubmed reference: 38317190. DOI: 10.1186/s12915-024-01817-0.

2023

Yu, S., Liu, Z., Li, M., Zhou, D., Hua, P., Cheng, H., Fan, W., Xu, Y., Liu, D., Liang, S., Zhang, Y., Xie, M., Tang, J., Jiang, Y., Hou, S., Zhou, Z. :

Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection. Gigascience 12, 2023. Pubmed reference: 36971291. DOI: 10.1093/gigascience/giad016.

Lavretsky, P., Hernández, F., Swale, T., Mohl, J.E. :

Chromosomal-level reference genome of a wild North American mallard (Anas platyrhynchos). G3 (Bethesda) , 2023. Pubmed reference: 37523777. DOI: 10.1093/g3journal/jkad171.

Gu, H., Wen, J., Zhao, X., Zhang, X., Ren, X., Cheng, H., Qu, L. :

Evolution, inheritance, and strata formation of the W chromosome in duck (Anas platyrhynchos). Genome Biol Evol 15, 2023. Pubmed reference: 37931036. DOI: 10.1093/gbe/evad183.

2021

Zhu, F., Yin, Z.T., Wang, Z., Smith, J., Zhang, F., Martin, F., Ogeh, D., Hincke, M., Lin, F.B., Burt, D.W., Zhou, Z.K., Hou, S.S., Zhao, Q.S., Li, X.Q., Ding, S.R., Li, G.S., Yang, F.X., Hao, J.P., Zhang, Z., Lu, L.Z., Yang, N., Hou, Z.C. :

Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. Nat Commun 12:5932, 2021. Pubmed reference: 34635656. DOI: 10.1038/s41467-021-26272-1.

2013

Huang, Y., Li, Y., Burt, D.W., Chen, H., Zhang, Y., Qian, W., Kim, H., Gan, S., Zhao, Y., Li, J., Yi, K., Feng, H., Zhu, P., Li, B., Liu, Q., Fairley, S., Magor, K.E., Du, Z., Hu, X., Goodman, L., Tafer, H., Vignal, A., Lee, T., Kim, K.W., Sheng, Z., An, Y., Searle, S., Herrero, J., Groenen, M.A., Crooijmans, R.P., Faraut, T., Cai, Q., Webster, R.G., Aldridge, J.R., Warren, W.C., Bartschat, S., Kehr, S., Marz, M., Stadler, P.F., Smith, J., Kraus, R.H., Zhao, Y., Ren, L., Fei, J., Morisson, M., Kaiser, P., Griffin, D.K., Rao, M., Pitel, F., Wang, J., Li, N. :

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet 45:776-83, 2013. Pubmed reference: 23749191. DOI: 10.1038/ng.2657.

Andrias davidianus (Chinese giant salamander) :

2021

Hu, Q., Liu, Y., Liao, X., Tian, H., Ji, X., Zhu, J., Xiao, H. :

A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander. BMC Genomics 22:230, 2021. Pubmed reference: 33794798. DOI: 10.1186/s12864-021-07550-0.

Anolis apletophallus (slender anole) :

2023

Pirani, R.M., Arias, C.F., Charles, K., Chung, A.K., Curlis, J.D., Nicholson, D.J., Vargas, M., Cox, C.L., McMillan, W.O., Logan, M.L. :

A high-quality genome for the slender anole (Anolis apletophallus), an emerging model for field-studies of tropical ecology and evolution. G3 (Bethesda) , 2023. Pubmed reference: 37875105. DOI: 10.1093/g3journal/jkad248.

Anoplopoma fimbria (sablefish) :

2023

Flores, A.M., Christensen, K.A., Campbell, B., Koop, B.F., Taylor, J.S. :

Sablefish (Anoplopoma fimbria) chromosome-level genome assembly. G3 (Bethesda) , 2023. Pubmed reference: 37097026. DOI: 10.1093/g3journal/jkad089.

Anser anser (domestic goose) :

2023

Gao, G., Zhang, H., Ni, J., Zhao, X., Zhang, K., Wang, J., Kong, X., Wang, Q. :

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis. J Anim Sci Biotechnol 14:150, 2023. Pubmed reference: 38001525. DOI: 10.1186/s40104-023-00944-y.

Anser cygnoides (swan goose) :

2023

Ni, H., Zhang, Y., Yang, Y., Yin, Y., Xie, H., Zheng, J., Dong, L., Diao, J., Wei, M., Lv, Z., Yan, S., Li, Y., Sun, H., Sun, X. :

Whole genome sequencing of a wild swan goose population. Front Genet 14:1038606, 2023. Pubmed reference: 36911404. DOI: 10.3389/fgene.2023.1038606.

2022

Zhang, Y., Ni, H., Xie, H., Yin, Y., Zheng, J., Dong, L., Diao, J., Yan, S., Yang, Y., Sun, H., Sun, X. :

De novo assembly of a wild swan goose (Anser cygnoides) genome. Anim Genet 53:878-880, 2022. Pubmed reference: 36086875. DOI: 10.1111/age.13262.

2015

Lu, L., Chen, Y., Wang, Z., Li, X., Chen, W., Tao, Z., Shen, J., Tian, Y., Wang, D., Li, G., Chen, L., Chen, F., Fang, D., Yu, L., Sun, Y., Ma, Y., Li, J., Wang, J. :

The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver. Genome Biol 16:89, 2015. Pubmed reference: 25943208. DOI: 10.1186/s13059-015-0652-y.

Aphelocoma californica (Western scrub-jay) :

2023

DeRaad, D.A., Escalona, M., Benham, P., Marimuthu, M.P.A., Sahasrabudhe, R.M., Nguyen, O., Chumchim, N., Beraut, E., Fairbairn, C.W., Seligmann, W., Bowie, R.C.K., Cicero, C., McCormack, J.E., Wayne, R.K. :

De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica. J Hered , 2023. Pubmed reference: 37589384. DOI: 10.1093/jhered/esad047.

Apis mellifera (honey bee) :

2023

Parejo, M., Talenti, A., Richardson, M., Vignal, A., Barnett, M., Wragg, D. :

AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap. Sci Data 10:198, 2023. Pubmed reference: 37037860. DOI: 10.1038/s41597-023-02097-z.

Duhan, N., Kaur, S., Kaundal, R. :

ranchSATdb: A genome-wide simple sequence repeat (SSR) markers database of livestock species for mutant germplasm characterization and improving farm animal health. Genes (Basel) 14, 2023. Pubmed reference: 37510385. DOI: 10.3390/genes14071481.

Ara macao (scarlet macaw) :

2013

Seabury, C.M., Dowd, S.E., Seabury, P.M., Raudsepp, T., Brightsmith, D.J., Liboriussen, P., Halley, Y., Fisher, C.A., Owens, E., Viswanathan, G., Tizard, I.R. :

A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao). PLoS One 8:e62415, 2013. Pubmed reference: 23667475. DOI: 10.1371/journal.pone.0062415.

Aratinga solstitialis (sun parakeet) :

2020

Gelabert, P., Sandoval-Velasco, M., Serres, A., de Manuel, M., Renom, P., Margaryan, A., Stiller, J., de-Dios, T., Fang, Q., Feng, S., Mañosa, S., Pacheco, G., Ferrando-Bernal, M., Shi, G., Hao, F., Chen, X., Petersen, B., Olsen, R.A., Navarro, A., Deng, Y., Dalén, L., Marquès-Bonet, T., Zhang, G., Antunes, A., Gilbert, M.T.P., Lalueza-Fox, C. :

Evolutionary history, genomic adaptation to toxic diet, and extinction of the Carolina parakeet. Curr Biol 30:108-114.e5, 2020. Pubmed reference: 31839456. DOI: 10.1016/j.cub.2019.10.066.

Archilochus colubris :

2023

Gershman, A., Hauck, Q., Dick, M., Jamison, J.M., Tassia, M., Agirrezabala, X., Muhammad, S., Ali, R., Workman, R.E., Valle, M., Wong, G.W., Welch, K.C., Timp, W. :

Genomic insights into metabolic flux in hummingbirds. Genome Res , 2023. Pubmed reference: 37156619. DOI: 10.1101/gr.276779.122.

Archocentrus centrarchus (flier cichlid) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Arizona elegans occidentalis :

2022

Wood, D.A., Richmond, J.Q., Escalona, M., Marimuthu, M.P.A., Nguyen, O., Sacco, S., Beraut, E., Westphal, M., Fisher, R.N., Vandergast, A.G., Toffelmier, E., Wang, I.J., Shaffer, H.B. :

Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California species of special concern. J Hered 113:632-640, 2022. Pubmed reference: 35939354. DOI: 10.1093/jhered/esac040.

Aselliscus stoliczkanus (Stoliczka's Asian trident bat) :

2023

Lan, L., Zhang, X., Yang, S., Li, L., Mao, X. :

Chromosome-level genome assembly of the Stoliczka's Asian trident bat (Aselliscus stoliczkanus). Sci Data 10:902, 2023. Pubmed reference: 38102156. DOI: 10.1038/s41597-023-02838-0.

Astatotilapia calliptera (eastern happy) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Astyanax mexicanus (Mexican tetra) :

2023

Warren, W.C., Rice, E.S., Maggs, X., Roback, E., Keene, A., Martin, F., Ogeh, D., Haggerty, L., Carroll, R.A., McGaugh, S., Rohner, N. :

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. bioRxiv , 2023. Pubmed reference: 38014157. DOI: 10.1101/2023.11.16.567450.

2014

McGaugh, S.E., Gross, J.B., Aken, B., Blin, M., Borowsky, R., Chalopin, D., Hinaux, H., Jeffery, W.R., Keene, A., Ma, L., Minx, P., Murphy, D., O'Quin, K.E., Rétaux, S., Rohner, N., Searle, S.M., Stahl, B.A., Tabin, C., Volff, J.N., Yoshizawa, M., Warren, W.C. :

The cavefish genome reveals candidate genes for eye loss. Nat Commun 5:5307, 2014. Pubmed reference: 25329095. DOI: 10.1038/ncomms6307.

2002

Borowsky, R., Wilkens, H. :

Mapping a cave fish genome: polygenic systems and regressive evolution. J Hered 93:19-21, 2002. Pubmed reference: 12011170.

Ateles fusciceps (brown-headed spider monkey) :

2024

Pozo, G., Albuja-Quintana, M., Larreátegui, L., Gutiérrez, B., Fuentes, N., Alfonso-Cortés, F., de Lourdes Torres, M. :

Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies. G3 (Bethesda) :jkae014, 2024. Pubmed reference: 38244218. DOI: 10.1093/g3journal/jkae014.

Aythya baeri (Baer's pochard) :

2023

Zhang, L., Gao, X., Xia, T., Yang, X., Sun, G., Zhao, C., Liu, G., Zhang, H. :

Chromosome-level genome assembly of the critically endangered Baer's pochard (Aythya baeri). Sci Data 10:176, 2023. Pubmed reference: 36991020. DOI: 10.1038/s41597-023-02063-9.

Aythya fuligula (tufted duck) :

2021

Mueller, R.C., Ellström, P., Howe, K., Uliano-Silva, M., Kuo, R.I., Miedzinska, K., Warr, A., Fedrigo, O., Haase, B., Mountcastle, J., Chow, W., Torrance, J., Wood, J.M.D., Järhult, J.D., Naguib, M.M., Olsen, B., Jarvis, E.D., Smith, J., Eöry, L., Kraus, R.H.S. :

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). Gigascience 10:giab081, 2021. Pubmed reference: 34927191. DOI: 10.1093/gigascience/giab081.

Aythya marila (greater scaup) :

2023

Zhou, S., Xia, T., Gao, X., Lyu, T., Wang, L., Wang, X., Shi, L., Dong, Y., Zhang, H. :

A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila). Sci Data 10:254, 2023. Pubmed reference: 37142629. DOI: 10.1038/s41597-023-02142-x.

Bahaba taipingensis (Chinese bahaba) :

2024

Cui, R., Wu, J., Yan, K., Luo, S., Hu, Y., Feng, W., Lu, B., Wang, J. :

Phased genome assemblies reveal haplotype-specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae). Mol Ecol :e17250, 2024. Pubmed reference: 38179694. DOI: 10.1111/mec.17250.

Balaenoptera musculus (Blue whale) :

2024

Bukhman, Y.V., Morin, P.A., Meyer, S., Chu, L.F., Jacobsen, J.K., Antosiewicz-Bourget, J., Mamott, D., Gonzales, M., Argus, C., Bolin, J., Berres, M.E., Fedrigo, O., Steill, J., Swanson, S.A., Jiang, P., Rhie, A., Formenti, G., Phillippy, A.M., Harris, R.S., Wood, J.M.D., Howe, K., Kirilenko, B.M., Munegowda, C., Hiller, M., Jain, A., Kihara, D., Johnston, J.S., Ionkov, A., Raja, K., Toh, H., Lang, A., Wolf, M., Jarvis, E.D., Thomson, J.A., Chaisson, M.J.P., Stewart, R. :

A high-quality blue whale genome, segmental duplications, and historical demography. Mol Biol Evol :msae036, 2024. Pubmed reference: 38376487. DOI: 10.1093/molbev/msae036.

Bathydraco marri (deepwater dragon) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Bison bison (American bison) :

2024

Stroupe, S., Derr, J.N. :

Development and evaluation of a novel single nucleotide polymorphism panel for North American bison. Evol Appl 17:e13658, 2024. Pubmed reference: 38390379. DOI: 10.1111/eva.13658.

2023

Stroupe, S., Martone, C., McCann, B., Juras, R., Kjöllerström, H.J., Raudsepp, T., Beard, D., Davis, B.W., Derr, J.N. :

Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation. G3 (Bethesda) , 2023. Pubmed reference: 37481261. DOI: 10.1093/g3journal/jkad156.

2021

Dobson, L.K., Zimin, A., Bayles, D., Fritz-Waters, E., Alt, D., Olsen, S., Blanchong, J., Reecy, J., Smith, T.P.L., Derr, J.N. :

De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification. Anim Genet , 2021. Pubmed reference: 33780561. DOI: 10.1111/age.13060.

Oppenheimer, J., Rosen, B.D., Heaton, M.P., Vander Ley, B.L., Shafer, W.R., Schuetze, F.T., Stroud, B., Kuehn, L.A., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Bickhart, D.M., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Smith, T.P.L. :

A reference genome assembly of American bison, Bison bison bison. J Hered 112:174-183, 2021. Pubmed reference: 33595645. DOI: 10.1093/jhered/esab003.

Bison bonasus (European bison) :

2024

Wehrenberg, G., Tokarska, M., Cocchiararo, B., Nowak, C. :

A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison. Sci Rep 14:1875, 2024. Pubmed reference: 38253649. DOI: 10.1038/s41598-024-51495-9.

Boaedon fuliginosus (brown house snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Boleophthalmus pectinirostris (great blue-spotted mudskipper) :

2023

Bian, C., Huang, Y., Li, R., Xu, P., You, X., Lv, Y., Ruan, Z., Chen, J., Xu, J., Shi, Q. :

Genomics comparisons of three chromosome-level mudskipper genome assemblies reveal molecular clues for water-to-land evolution and adaptation. J Adv Res , 2023. Pubmed reference: 37220853. DOI: 10.1016/j.jare.2023.05.005.

Bombyx mori (domestic silkworm) :

2023

Waizumi, R., Tsubota, T., Jouraku, A., Kuwazaki, S., Yokoi, K., Iizuka, T., Yamamoto, K., Sezutsu, H. :

Highly accurate genome assembly of an improved high-yielding silkworm strain, Nichi01. G3 (Bethesda) , 2023. Pubmed reference: 36814357. DOI: 10.1093/g3journal/jkad044.

Bos gaurus (gaur) :

2022

Low, W.Y., Rosen, B.D., Ren, Y., Bickhart, D.M., To, T.H., Martin, F.J., Billis, K., Sonstegard, T.S., Sullivan, S.T., Hiendleder, S., Williams, J.L., Heaton, M.P., Smith, T.P.L. :

Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. BMC Genomics 23:344, 2022. Pubmed reference: 35508966. DOI: 10.1186/s12864-022-08561-1.

Bos grunniens (domestic yak) :

2024

Peng, W., Fu, C., Shu, S., Wang, G., Wang, H., Yue, B., Zhang, M., Liu, X., Liu, Y., Zhang, J., Zhong, J., Wang, J. :

Whole-genome resequencing of major populations revealed domestication-related genes in yaks. BMC Genomics 25:69, 2024. Pubmed reference: 38233755. DOI: 10.1186/s12864-024-09993-7.

Jiang, H., Chai, Z.X., Chen, X.Y., Zhang, C.F., Zhu, Y., Ji, Q.M., Xin, J.W. :

Yak genome database: a multi-omics analysis platform. BMC Genomics 25:346, 2024. Pubmed reference: 38580907. DOI: 10.1186/s12864-024-10274-6.

2023

Duhan, N., Kaur, S., Kaundal, R. :

Liu, X., Liu, W., Lenstra, J.A., Zheng, Z., Wu, X., Yang, J., Li, B., Yang, Y., Qiu, Q., Liu, H., Li, K., Liang, C., Guo, X., Ma, X., Abbott, R.J., Kang, M., Yan, P., Liu, J. :

Evolutionary origin of genomic structural variations in domestic yaks. Nat Commun 14:5617, 2023. Pubmed reference: 37726270. DOI: 10.1038/s41467-023-41220-x.

Li, B., Yang, J., Liu, Y., Jiang, M. :

Genome variation map of domestic Qinghai-Tibet plateau yaks by SLAF-Seq reveals genetic footprint during artificial selection. Animals (Basel) 13, 2023. Pubmed reference: 37760363. DOI: 10.3390/ani13182963.

Bos indicus (indicine cattle (zebu)) :

2024

Muthusamy, P.V., Vakayil Mani, R., Kumari, S., Kaur, M., Bhaskar, B., Raghavan Pillai, R., Sajeev Kumar, T., Anilkumar, T.V., Singh, N.S. :

Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle - elucidating genetic variation. Front Genet 15:1338224, 2024. Pubmed reference: 38510276. DOI: 10.3389/fgene.2024.1338224.

2023

Rahman, J.U., Kumar, D., Singh, S.P., Shahi, B.N., Ghosh, A.K., Verma, M.K., Pathak, A., Dar, A.H., Kumar, A., Sharma, R.K. :

Genome-wide identification and annotation of SNPs and their mapping in candidate genes related to milk production and fertility traits in Badri cattle. Trop Anim Health Prod 55:117, 2023. Pubmed reference: 36928332. DOI: 10.1007/s11250-023-03535-1.

Braga, L.G., Chud, T.C.S., Watanabe, R.N., Savegnago, R.P., Sena, T.M., do Carmo, A.S., Machado, M.A., Panetto, J.C.D.C., da Silva, M.V.G.B., Munari, D.P. :

Identification of copy number variations in the genome of Dairy Gir cattle. PLoS One 18:e0284085, 2023. Pubmed reference: 37036840. DOI: 10.1371/journal.pone.0284085.

Raja, T.V., Alex, R., Singh, U., Kumar, S., Das, A.K., Sengar, G., Singh, A.K. :

Genome wide mining of SNPs and INDELs through ddRAD sequencing in Sahiwal cattle. Anim Biotechnol :1-15, 2023. Pubmed reference: 37093232. DOI: 10.1080/10495398.2023.2200517.

Powell, J., Talenti, A., Fisch, A., Hemmink, J.D., Paxton, E., Toye, P., Santos, I., Ferreira, B.R., Connelley, T.K., Morrison, L.J., Prendergast, J.G.D. :

Profiling the immune epigenome across global cattle breeds. Genome Biol 24:127, 2023. Pubmed reference: 37218021. DOI: 10.1186/s13059-023-02964-3.

Chakraborty, A., Bisht, M.S., Saxena, R., Mahajan, S., Pulikkan, J., Sharma, V.K. :

Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds. Genes Genomics , 2023. Pubmed reference: 37231295. DOI: 10.1007/s13258-023-01401-w.

Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., Wen, J., Yang, Q., Deng, W., Nanaei, H.A., Wang, Y., Wang, F., Zhang, Z., Rosen, B.D., Heller, R., Jiang, Y. :

A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species. Genome Res , 2023. Pubmed reference: 37714713. DOI: 10.1101/gr.277481.122.

Bos indicus x Bos taurus (hybrid cattle) :

2024

Wei, Z., Zhang, L., Gao, L., Chen, J., Peng, L., Yang, L. :

Chromosome-level genome assembly and annotation of the Yunling cattle with PacBio and Hi-C sequencing data. Sci Data 11:233, 2024. Pubmed reference: 38395911. DOI: 10.1038/s41597-024-03066-w.

Bos taurus (taurine cattle) :

2024

Dorji, J., Reverter, A., Alexandre, P.A., Chamberlain, A.J., Vander-Jagt, C.J., Kijas, J., Porto-Neto, L.R. :

Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test. Genet Sel Evol 56:11, 2024. Pubmed reference: 38321371. DOI: 10.1186/s12711-024-00879-6.

Leonard, A.S., Mapel, X.M., Pausch, H. :

Pangenome genotyped structural variation improves molecular phenotype mapping in cattle. Genome Res :gr.278267.123, 2024. Pubmed reference: 38355307. DOI: 10.1101/gr.278267.123.

Beiki, H., Murdoch, B.M., Park, C.A., Kern, C., Kontechy, D., Becker, G., Rincon, G., Jiang, H., Zhou, H., Thorne, J., Koltes, J.E., Michal, J.J., Davenport, K., Rijnkels, M., Ross, P.J., Hu, R., Corum, S., McKay, S., Smith, T.P.L., Liu, W., Ma, W., Zhang, X., Xu, X., Han, X., Jiang, Z., Hu, Z.L., Reecy, J.M. :

Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology. Gigascience 13:giae019, 2024. Pubmed reference: 38626724. DOI: 10.1093/gigascience/giae019.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. Nucleic Acids Res 51:D1388-D1396, 2023. Pubmed reference: 36062570. DOI: 10.1093/nar/gkac750.

Sasaki, S., Haga, Y., Wakaguri, H., Abe, K., Suzuki, Y. :

De novo genome assembly of Japanese Black cattle as model of an economically relevant animal. Methods Mol Biol 2632:41-55, 2023. Pubmed reference: 36781720. DOI: 10.1007/978-1-0716-2996-3_4.

Liu, Y., Mu, Y., Wang, W., Ahmed, Z., Wei, X., Lei, C., Ma, Z. :

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle. Front Vet Sci 10:1148070, 2023. Pubmed reference: 37065216. DOI: 10.3389/fvets.2023.1148070.

Lee, Y.L., Bosse, M., Takeda, H., Moreira, G.C.M., Karim, L., Druet, T., Oget-Ebrad, C., Coppieters, W., Veerkamp, R.F., Groenen, M.A.M., Georges, M., Bouwman, A.C., Charlier, C. :

High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data. BMC Genomics 24:225, 2023. Pubmed reference: 37127590. DOI: 10.1186/s12864-023-09259-8.

Cai, W., Zhang, Y., Chang, T., Wang, Z., Zhu, B., Chen, Y., Gao, X., Xu, L., Zhang, L., Gao, H., Song, J., Li, J. :

The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle. J Anim Sci Biotechnol 14:78, 2023. Pubmed reference: 37165455. DOI: 10.1186/s40104-023-00876-7.

Leonard, A.S., Crysnanto, D., Mapel, X.M., Bhati, M., Pausch, H. :

Graph construction method impacts variation representation and analyses in a bovine super-pangenome. Genome Biol 24:124, 2023. Pubmed reference: 37217946. DOI: 10.1186/s13059-023-02969-y.

Powell, J., Talenti, A., Fisch, A., Hemmink, J.D., Paxton, E., Toye, P., Santos, I., Ferreira, B.R., Connelley, T.K., Morrison, L.J., Prendergast, J.G.D. :

Profiling the immune epigenome across global cattle breeds. Genome Biol 24:127, 2023. Pubmed reference: 37218021. DOI: 10.1186/s13059-023-02964-3.

Salavati, M., Clark, R., Becker, D., Kühn, C., Plastow, G., Dupont, S., Moreira, G.C.M., Charlier, C., Clark, E.L. :

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing. G3 (Bethesda) , 2023. Pubmed reference: 37216666. DOI: 10.1093/g3journal/jkad108.

Eché, C., Iampietro, C., Birbes, C., Dréau, A., Kuchly, C., Di Franco, A., Klopp, C., Faraut, T., Djebali, S., Castinel, A., Zytnicki, M., Denis, E., Boussaha, M., Grohs, C., Boichard, D., Gaspin, C., Milan, D., Donnadieu, C. :

A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling. Sci Data 10:369, 2023. Pubmed reference: 37291142. DOI: 10.1038/s41597-023-02249-1.

Melzer, N., Qanbari, S., Ding, X., Wittenburg, D. :

CLARITY: a Shiny app for interactive visualisation of the bovine physical-genetic map. Front Genet 14:1082782, 2023. Pubmed reference: 37323679. DOI: 10.3389/fgene.2023.1082782.

Smith, T.P.L., Bickhart, D.M., Boichard, D., Chamberlain, A.J., Djikeng, A., Jiang, Y., Low, W.Y., Pausch, H., Demyda-Peyrás, S., Prendergast, J., Schnabel, R.D., Rosen, B.D. :

The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biol 24:139, 2023. Pubmed reference: 37337218. DOI: 10.1186/s13059-023-02975-0.

Triant, D.A., Walsh, A.T., Hartley, G.A., Petry, B., Stegemiller, M.R., Nelson, B.M., McKendrick, M.M., Fuller, E.P., Cockett, N.E., Koltes, J.E., McKay, S.D., Green, J.A., Murdoch, B.M., Hagen, D.E., Elsik, C.G. :

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome , 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Jang, J., Jung, J., Lee, Y.H., Lee, S., Baik, M., Kim, H. :

Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies. Sci Data 10:560, 2023. Pubmed reference: 37612339. DOI: 10.1038/s41597-023-02453-z.

Yuan, C., Tang, L., Lopdell, T., Petrov, V.A., Oget-Ebrad, C., Moreira, G.C.M., Gualdrón Duarte, J.L., Sartelet, A., Cheng, Z., Salavati, M., Wathes, C.D., Crowe, M.A. :

An organism-wide ATAC-seq peak catalogue for the bovine and its use to identify regulatory variants. Genome Res , 2023. Pubmed reference: 37751945. DOI: 10.1101/gr.277947.123.

Li, T.T., Xia, T., Wu, J.Q., Hong, H., Sun, Z.L., Wang, M., Ding, F.R., Wang, J., Jiang, S., Li, J., Pan, J., Yang, G., Feng, J.N., Dai, Y.P., Zhang, X.M., Zhou, T., Li, T. :

De novo genome assembly depicts the immune genomic characteristics of cattle. Nat Commun 14:6601, 2023. Pubmed reference: 37857610. DOI: 10.1038/s41467-023-42161-1.

2022

Yang, L., Gao, Y., Li, M., Park, K.E., Liu, S., Kang, X., Liu, M., Oswalt, A., Fang, L., Telugu, B.P., Sattler, C.G., Li, C.J., Cole, J.B., Seroussi, E., Xu, L., Yang, L., Zhou, Y., Li, L., Zhang, H., Rosen, B.D., Van Tassell, C.P., Ma, L., Liu, G.E. :

Genome-wide recombination map construction from single sperm sequencing in cattle. BMC Genomics 23:181, 2022. Pubmed reference: 35247961. DOI: 10.1186/s12864-022-08415-w.

Raz, R., Roth, Z., Gershoni, M. :

ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples. Sci Data 9:469, 2022. Pubmed reference: 35918364. DOI: 10.1038/s41597-022-01597-8.

2021

Heaton, M.P., Smith, T.P.L., Bickhart, D.M., Vander Ley, B.L., Kuehn, L.A., Oppenheimer, J., Shafer, W.R., Schuetze, F.T., Stroud, B., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Rosen, B.D. :

A reference genome assembly of Simmental cattle, Bos taurus taurus. J Hered 112:184-91, 2021. Pubmed reference: 33438035. DOI: 10.1093/jhered/esab002.

Erratum to: A reference genome assembly of Simmental cattle, Bos taurus taurus. J Hered , 2021. Pubmed reference: 34436588. DOI: 10.1093/jhered/esab039.

MacPhillamy, C., Pitchford, W.S., Alinejad-Rokny, H., Low, W.Y. :

Opportunity to improve livestock traits using 3D genomics. Anim Genet , 2021. Pubmed reference: 34494283. DOI: 10.1111/age.13135.

Neumann, G.B., Korkuć, P., Arends, D., Wolf, M.J., May, K., Reißmann, M., Elzaki, S., König, S., Brockmann, G.A. :

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN). BMC Genomics 22:905, 2021. Pubmed reference: 34922441. DOI: 10.1186/s12864-021-08237-2.

2020

De Lorenzi, L., Parma, P. :

Identification of Some Errors in the Genome Assembly of Bovidae by FISH. Cytogenet Genome Res , 2020. Pubmed reference: 32235117. DOI: 10.1159/000506221.

Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M., Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. :

De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience 9, 2020. Pubmed reference: 32191811. DOI: 10.1093/gigascience/giaa021.

Triant, D.A., Le Tourneau, J.J., Diesh, C.M., Unni, D.R., Shamimuzzaman, M., Walsh, A.T., Gardiner, J., Goldkamp, A.K., Li, Y., Nguyen, H.N., Roberts, C., Zhao, Z., Alexander, L.J., Decker, J.E., Schnabel, R.D., Schroeder, S.G., Sonstegard, T.S., Taylor, J.F., Rivera, R.M., Hagen, D.E., Elsik, C.G. :

Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. Anim Genet , 2020. Pubmed reference: 32537769. DOI: 10.1111/age.12962.

2019

Sasaki, S., Muraki, E., Inoue, Y., Suezawa, R., Nikadori, H., Yoshida, Y., Nariai, S., Hideshima, R., Moriwaki, S., Nakashima, R., Uchiyama, K., Yoshinari, K., Takeda, M., Kojima, T. :

Genotypes and allele frequencies of buried SNPs in a bovine single-nucleotide polymorphism array in Japanese Black cattle. Anim Sci J 90:1503-1509, 2019. Pubmed reference: 31599477. DOI: 10.1111/asj.13293.

Womack, J.E.J. :

Mapping Genes Is Good for You. Annu Rev Anim Biosci 7:1-16, 2019. Pubmed reference: 30296836. DOI: 10.1146/annurev-animal-020518-114902.

2015

Ma, L., O'Connell, J.R., VanRaden, P.M., Shen, B., Padhi, A., Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G.E., Da, Y., Wiggans, G.R. :

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis. PLoS Genet 11:e1005387, 2015. Pubmed reference: 26540184. DOI: 10.1371/journal.pgen.1005387.

2013

Kõks, S., Lilleoja, R., Reimann, E., Salumets, A., Reemann, P., Jaakma, Ü. :

Sequencing and annotated analysis of the Holstein cow genome. Mamm Genome 24:309-21, 2013. Pubmed reference: 23893136. DOI: 10.1007/s00335-013-9464-0.

2012

Boichard, D., Chung, H., Dassonneville, R., David, X., Eggen, A., Fritz, S., Gietzen, K.J., Hayes, B.J., Lawley, C.T., Sonstegard, T.S., Van Tassell, C.P., VanRaden, P.M., Viaud-Martinez, K.A., Wiggans, G.R. :

Design of a bovine low-density SNP array optimized for imputation. PLoS One 7:e34130, 2012. Pubmed reference: 22470530. DOI: 10.1371/journal.pone.0034130.

2011

Stothard, P., Choi, J.W., Basu, U., Sumner-Thomson, J.M., Meng, Y., Liao, X., Moore, S.S. :

Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12:559, 2011. Pubmed reference: 22085807. DOI: 10.1186/1471-2164-12-559.

Rincon, G., Weber, K.L., Eenennaam, A.L., Golden, B.L., Medrano, J.F. :

Hot topic: performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J Dairy Sci 94:6116-21, 2011. Pubmed reference: 22118099. DOI: 10.3168/jds.2011-4764.

2009

Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J.A., Salzberg, S.L. :

A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 10:R42, 2009. Pubmed reference: 19393038. DOI: 10.1186/gb-2009-10-4-r42.

Liu, Y., Qin, X., Song, X.Z., Jiang, H., Shen, Y., Durbin, K.J., Lien, S., Kent, M.P., Sodeland, M., Ren, Y., Zhang, L., Sodergren, E., Havlak, P., Worley, K.C., Weinstock, G.M., Gibbs, R.A. :

Bos taurus genome assembly. BMC Genomics 10:180, 2009. Pubmed reference: 19393050. DOI: 10.1186/1471-2164-10-180.

Bovine Genome Sequencing and Analysis Consortium :

The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522-8, 2009. Pubmed reference: 19390049. DOI: 10.1126/science.1169588.

Eck, S.H., Benet-Pagès, A., Flisikowski, K., Meitinger, T., Fries, R., Strom, T.M. :

Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol 10:R82, 2009. Pubmed reference: 19660108. DOI: 10.1186/gb-2009-10-8-r82.

Bovine HapMap Consortium et al. :

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528-32, 2009. Pubmed reference: 19390050. DOI: 10.1126/science.1167936.

Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P. :

Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4:e5350, 2009. Pubmed reference: 19390634. DOI: 10.1371/journal.pone.0005350.

2008

Charlier, C., Coppieters, W., Rollin, F., Desmecht, D., Agerholm, JS., Cambisano, N., Carta, E., Dardano, S., Dive, M., Fasquelle, C., Frennet, JC., Hanset, R., Hubin, X., Jorgensen, C., Karim, L., Kent, M., Harvey, K., Pearce, BR., Simon, P., Tama, N., Nie, H., Vandeputte, S., Lien, S., Longeri, M., Fredholm, M., Harvey, RJ., Georges, M. :

Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat Genet 40:449-54, 2008. Pubmed reference: 18344998. DOI: 10.1038/ng.96.

Van Tassell, C.P., Smith, T.P., Matukumalli, L.K., Taylor, J.F., Schnabel, R.D., Lawley, C.T., Haudenschild, C.D., Moore, S.S., Warren, W.C., Sonstegard, T.S. :

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247-52, 2008. Pubmed reference: 18297082. DOI: 10.1038/nmeth.1185.

2007

Snelling, W.M., Chiu, R., Schein, J.E., Hobbs, M., Abbey, C.A., Adelson, D.L., Aerts, J., Bennett, G.L., Bosdet, I.E., Boussaha, M., Brauning, R., Caetano, A.R., Costa, M.M., Crawford, A.M., Dalrymple, B.P., Eggen, A., Everts-van der Wind, A., Floriot, S., Gautier, M., Gill, C.A., Green, R.D., Holt, R., Jann, O., Jones, S.J., Kappes, S.M., Keele, J.W., de Jong, P.J., Larkin, D.M., Lewin, H.A., McEwan, J.C., McKay, S., Marra, M.A., Mathewson, C.A., Matukumalli, L.K., Moore, S.S., Murdoch, B., Nicholas, F.W., Osoegawa, K., Roy, A., Salih, H., Schibler, L., Schnabel, R.D., Silveri, L., Skow, L.C., Smith, T.P., Sonstegard, T.S., Taylor, J.F., Tellam, R., Van Tassell, C.P., Williams, J.L., Womack, J.E., Wye, N.H., Yang, G., Zhao, S. :

A physical map of the bovine genome. Genome Biol 8:R165, 2007. Pubmed reference: 17697342. DOI: 10.1186/gb-2007-8-8-r165.

2006

Womack, J.E. :

The bovine genome. Genome Dyn 2:69-78, 2006. Pubmed reference: 18753770. DOI: 10.1159/000095095.

Jann, O.C., Aerts, J., Jones, M., Hastings, N., Law, A., McKay, S., Marques, E., Prasad, A., Yu, J., Moore, S.S., Floriot, S., Mahé, M.F., Eggen, A., Silveri, L., Negrini, R., Milanesi, E., Ajmone-Marsan, P., Valentini, A., Marchitelli, C., Savarese, M.C., Janitz, M., Herwig, R., Hennig, S., Gorni, C., Connor, E.E., Sonstegard, T.S., Smith, T., Drögemüller, C., Williams, J.L. :

A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics 7:283, 2006. Pubmed reference: 17087818. DOI: 10.1186/1471-2164-7-283.

Weikard, R., Goldammer, T., Laurent, P., Womack, J.E., Kuehn, C. :

A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits. BMC Genomics 7:53, 2006. Pubmed reference: 16542434. DOI: 10.1186/1471-2164-7-53.

2003

Larkin, D.M., Everts-van, der, Wind, A., Rebeiz, M., Schweitzer, P.A., Bachman, S., Green, C., Wright, C.L., Campos, E.J., Benson, L.D., Edwards, J., Liu, L., Osoegawa, K., Womack, J.E., de, Jong, P.J., Lewin, H.A. :

A cattle-human comparative map built with cattle BAC-ends and human genome sequence Genome Research 13:1966-72, 2003. Pubmed reference: 12902387. DOI: 10.1101/gr.1560203.

2002

Weikard, R., Kuhn, C., Goldammer, T., Laurent, P., Womack, J.E., Schwerin, M. :

Targeted construction of a high-resolution, integrated, comprehensive, and comparative map for a region specific to bovine chromosome 6 based on radiation hybrid mapping Genomics 79:768-776, 2002. Pubmed reference: 12036290. DOI: 10.1006/geno.2002.6778.

Gautier, M., Hayes, H., Eggen, A. :

An extensive and comprehensive radiation hybrid map of bovine Chromosome 15: comparison with human Chromosome 11 Mammalian Genome 13:316-319, 2002. Pubmed reference: 12115035. DOI: 10.1007/s00335-001-3069-8.

Schlapfer, J., Stahlberger-Saitbekova, N., Comincini, S., Gaillard, C., Hills, D., Meyer, R.K., Williams, J.L., Womack, J., Zurbriggen, A., Dolf, G. :

A higher resolution radiation hybrid map of bovine chromosome 13 Genetics Selection Evolution 34:255-267, 2002.

Drogemuller, C., Bader, A., Wohlke, A., Kuiper, H., Leeb, T., Distl, O. :

A high-resolution comparative RH map of the proximal part of bovine chromosome 1 Animal Genetics 33:271-279, 2002. Pubmed reference: 12139506.

Williams, J.L., Eggen, A., Ferretti, L., Farr, C.J., Gautier, M., Amati, G., Ball, G., Caramorr, T., Critcher, R., Costa, S., Hextall, P., Hills, D., Jeulin, A., Kiguwa, S.L., Ross, O., Smith, A.L., Saunier, K., Urquhart, B., Waddington, D. :

A bovine whole-genome radiation hybrid panel and outline map Mammalian Genome 13:469-474, 2002. Pubmed reference: 12226714. DOI: 10.1007/s00335-002-3001-x.

Jiang, Z.H., Melville, J.S., Cao, H.H., Kumar, S., Filipski, A., Gibbins, A.M.V. :

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome Genome 45:769-776, 2002. Pubmed reference: 12175081.

Reed, K.M., Ihara, N., Mariani, P., Mendoza, K.M., Jensen, L.E., Bellavia, R., de, Leon, F.A.P., Bennett, G.L., Sugimoto, Y., Beattie, C.W. :

High-resolution genetic map of bovine chromosome 29 through focused marker development Cytogenetic & Genome Research 96:210-216, 2002.

Antoniou, E., Gallagher, D., Taylor, J., Davis, S., Womack, J., Grosz, M. :

A comparative map of bovine chromosome 25 with human chromosomes 7 and 16 Cytogenetic & Genome Research 97:128-132, 2002.

Liu, W.S., Mariani, P., Beattie, C.W., Alexander, L.J., Ponce, De, Leon, F.A. :

A radiation hybrid map for the bovine Y Chromosome Mammalian Genome 13:320-6, 2002. Pubmed reference: 12115036. DOI: 10.1007/s00335-001-2133-8.

2001

Sonstegard, T.S., Bennett, G.L., Kalm, E., Kappes, S.M., Lewin, H.A., Olsaker, I., Schmutz, S., Thomsen, H., Vage, D.I., Van, Tassell, C.P., Xu, N. :

Consensus and comprehensive linkage maps of bovine chromosome 25 Animal Genetics 32:114-115, 2001. Pubmed reference: 11421953.

2000

Vage, D.I., Olsaker, I., Klungland, H., Gomez-Raya, L., Lien, S. :

A male genetic map designed for quantitative trait loci mapping in Norwegian cattle Acta Agriculturae Scandinavica Section A-Animal Science 50:56-63, 2000.

Ozawa, A., Band, M.R., Larson, J.H., Donovan, J., Green, C.A., Womack, J.E., Lewin, H.A. :

Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping Proceedings of the National Academy of Sciences of the United States of America 97:4150-4155, 2000. Pubmed reference: 10737760. DOI: 10.1073/pnas.050007097.

Amarante, M.R.V., Yang, Y.P., Kata, S.R., Lopes, C.R., Womack, J.E. :

RH maps of bovine chromosomes 15 and 29: conservation of human chromosomes 11 and 5 Mammalian Genome 11:364-368, 2000. Pubmed reference: 10790535.

Band, M.R., Larson, J.H., Rebeiz, M., Green, C.A., Heyen, D.W., Donovan, J., Windish, R., Steining, C., Mahyuddin, P., Womack, J.E., Lewin, H.A. :

An ordered comparative map of the cattle and human genomes Genome Research 10:1359-1368, 2000. Pubmed reference: 10984454.

1999

Rexroad, C.E., Schlapfer, J.S., Yang, Y., Harlizius, B., Womack, J.E. :

A radiation hybrid map of bovine chromosome one Animal Genetics 30:325-332, 1999. Pubmed reference: 10582277.

Rexroad, C.E., Womack, J.E. :

Parallel RH mapping of BTA1 with HSA3 and HSA21 Mammalian Genome 10:1095-1097, 1999. Pubmed reference: 10556430.

Gu, Z., Womack, J.E., Kirkpatrick, B.W. :

A radiation hybrid map of bovine chromosome 7 and comparative mapping with human chromosome 19 p arm Mammalian Genome 10:1112-1114, 1999. Pubmed reference: 10556435.

1998

Yang, Y.P., Rexroad, C.E., Schlapfer, J., Womack, J.E. :

An integrated radiation hybrid map of bovine chromosome 19 and ordered comparative mapping with human chromosome 17 Genomics 48:93-99, 1998. Pubmed reference: 9503021. DOI: 10.1006/geno.1997.5143.

Yang, Y.P., Womack, J.E. :

Parallel radiation hybrid mapping - a powerful tool for high-resolution genomic comparison Genome Research 8:731-736, 1998. Pubmed reference: 9685320.

Band, M., Larson, J.H., Womack, J.E., Lewin, H.A. :

A radiation hybrid map of BTA23 - identification of a chromosomal rearrangement leading to separation of the cattle mhc class ii subregions Genomics 53:269-275, 1998. Pubmed reference: 9799592. DOI: 10.1006/geno.1998.5507.

1997

Barendse, W., Vaiman, D., Kemp, S.J., Sugimoto, Y., Armitage, S.M., Williams, J.L., Sun, H.S., Eggen, A., Agaba, M., Aleyasin, S.A., Band, M., Bishop, M.D., Buitkamp, J., Byrne, K., Collins, F., Cooper, L., Coppettiers, W., Denys, B., Drinkwater, R.D., Easterday, K., Elduque, C., Ennis, S., Erhardt, G., Ferretti, L., Flavin, N., et al. :

A medium-density genetic linkage map of the bovine genome Mammalian Genome 8:21-28, 1997. Pubmed reference: 9021143.

Ferretti, L., Urquhart, B.G.D., Eggen, A., Olsaker, I., Harlizius, B., Castiglioni, B., Mezzelani, A., Toldo, S.S., Thieven, U., Zhang, Y., Morgan, A.L.G., Teres, V.M., Schwerin, M., Martinburriel, I., Chowdhary, B.P., Erhardt, G., Nijman, I.J., Cribiu, E.P., Barendse, W., Leveziel, H., Fries, R., Williams, J.L. :

Cosmid-derived markers anchoring the bovine genetic map to the physical map Mammalian Genome 8:29-36, 1997. Pubmed reference: 9021144.

Sonstegard, T.S., Lopezcorrales, N.L., Kappes, S.M., Stone, R.T., Ambady, S., Deleon, F.A.P., Beattie, C.W. :

An integrated genetic and physical map of the bovine x chromosome Mammalian Genome 8:16-20, 1997. Pubmed reference: 9021142.

Kappes, S.M., Keele, J.W., Stone, R.T., Sonstegard, T.S., Smith, T.P.L., Mcgraw, R.A., Lopezcorrales, N.L., Beattie, C.W. :

A second-generation linkage map of the bovine genome Genome Research 7:235-249, 1997. Pubmed reference: 9074927.

Kalm, E. :

Genome mapping by cattle [German] Archiv fur Tierzucht-Archives of Animal Breeding 40:74-79, 1997.

Smith, T.P.L., Lopezcorrales, N., Grosz, M.D., Beattie, C.W., Kappes, S.M. :

Anchoring of bovine chromosomes 4, 6, 7, 10, and 14 linkage group telomeric ends via fish analysis of lambda clones Mammalian Genome 8:333-336, 1997. Pubmed reference: 9107677.

Beever, J.E., Fisher, S.R., Guerin, G., Lewin, H.A. :

Mapping of eight human chromosome 1 orthologs to cattle chromosomes 3 and 16 Mammalian Genome 8:533-536, 1997. Pubmed reference: 9196004.

Agaba, M.K., Kemp, S.J., Barendse, W., Teale, A. :

Comparative mapping in cattle of genes located on human chromosome 18 Mammalian Genome 8:530-532, 1997. Pubmed reference: 9196003.

Barendse, W. :

A medium density genetic linkage map of the bovine genome (vol 8, pg 21, 1997) Mammalian Genome 8:798, 1997.

Womack, J.E., Johnson, J.S., Owens, E.K., Rexroad, C.E., Schlapfer, J., Yang, Y.P. :

A whole-genome radiation hybrid panel for bovine gene mapping Mammalian Genome 8:854-856, 1997. Pubmed reference: 9337401.

1996

Chowdhary, B.P., Fronicke, L., Gustavsson, I., Scherthan, H. :

Comparative analysis of the cattle and human genomes - detection of zoo-FISH and gene mapping-based chromosomal homologies Mammalian Genome 7:297-302, 1996. Pubmed reference: 8661702.

Beever, J.E., Lewin, H.A., Barendse, W., Andersson, L., Armitage, S.M., Beattie, C.W., Burns, B.M., Davis, S.K., Kappes, S.M., Kirkpatrick, B.W., Ma, R.Z., Mcgraw, R.A., Stone, R.T., Taylor, J.F. :

Report of the first workshop on the genetic map of bovine chromosome 23 Animal Genetics 27:69-75, 1996. Pubmed reference: 8856895.

Ma, R.Z., Beever, J.E., Da, Y., Green, C.A., Russ, I., Park, C., Heyen, D.W., Everts, R.E., Fisher, S.R., Overton, K.M., Teale, A.J., Kemp, S.J., Hines, H.C., Guerin, G., Lewin, H.A. :

A male linkage map of the cattle (bos taurus) genome Journal of Heredity 87:261-271, 1996. Pubmed reference: 8776874.

Andersson, L., Archibald, A., Ashburner, M., Audun, S., Barendse, W., Bitgood, J., Bottema, C., Broad, T., Brown, S., Burt, D., Charlier, C., Copeland, N., Davis, S., Davisson, M., Edwards, J., Eggen, A., Elgar, G., Eppig, J.T., Franklin, I., Grewe, P., Gill, T., Graves, J.A.M., Hawken, R., Hetzel, J., Hillyard, A., Jacob, H., Jaswinska, L., Jenkins, N., Kunz, H., Levan, G., Lie, O., Lyons, L., Maccarone, P., Mellersh, C., Montgomery, G., Moore, S., Moran, C., Morizot, D., Neff, M., Nicholas, F.W., O'Brien, S.J., Parsons, Y., Peters, J., Postlethwait, J., Raymond, M., Rothschild, M., Schook, L., Sugimoto, Y., Szpirer, C., Tate, M., Taylor, J., Vandeberg, J., Wakefield, M., Wienberg, J., Womack, J. :

Comparative genome organization of vertebrates Mammalian Genome 7:717-734, 1996. Pubmed reference: 8854859.

1995

Hawkins, G.A., Toldo, S.S., Bishop, M.D., Kappes, S.M., Fries, R., Beattie, C.W. :

Physical and linkage mapping of the bovine genome with cosmids Mammalian Genome 6:249-254, 1995. Pubmed reference: 7613028.

Eggen, A., Fries, R. :

An integrated cytogenetic and meiotic map of the bovine genome Animal Genetics 26:215-236, 1995. Pubmed reference: 7661394.

Georges, M., Nielsen, D., Mackinnon, M., Mishra, A., Okimoto, R., Pasquino, A.T., Sargeant, L.S., Sorensen, A., Steele, M.R., Zhao, X. :

Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics 139:907-20, 1995. Pubmed reference: 7713441.

1994

Bishop, M.D., Kappes, S.M., Keele, J.W., Stone, R.T., Sunden, S.L.F., Hawkins, G.A., Toldo, S.S., Fries, R., Grosz, M.D., Yoo, J.Y., Beattie, C.W. :

A Genetic Linkage Map for Cattle Genetics 136:619-639, 1994. Pubmed reference: 7908653.

Barendse, W., Armitage, S.M., Kossarek, L.M., Shalom, A., Kirkpatrick, B.W., Ryan, A.M., Clayton, D., Li, L., Neibergs, H.L., Zhang, N., Grosse, W.M., Weiss, J., Creighton, P., Mccarthy, F., Ron, M., Teale, A.J., Fries, R., Mcgraw, R.A., Moore, S.S., Georges, M., Soller, M., Womack, J.E., Hetzel, D.J.S. :

A Genetic Linkage Map of the Bovine Genome Nature Genetics 6:227-235, 1994. Pubmed reference: 8012383. DOI: 10.1038/ng0394-227.

Echard, G., Broad, T.E., Hill, D., Pearce, P. :

Present Status of the Ovine Gene Map (Ovis aries) - Comparison with the Bovine Map (Bos taurus) Mammalian Genome 5:324-332, 1994. Pubmed reference: 8043945.

Beattie, C.W. :

Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.

1993

Vaiman, D., Bahridarwich, I., Mercier, D., Yerle, M., Eggen, A., Leveziel, H., Guerin, G., Gellin, J., Cribiu, E.P. :

Mapping of New Bovine Microsatellites on Cattle Chromosome-15 with Somatic Cell Hybrids, Linkage Analysis, and Fluorescence Insitu Hybridization Mammalian Genome 4:676-679, 1993. Pubmed reference: 8281017.

Fries, R., Eggen, A., Womack, J.E. :

The Bovine Genome Map (Vol 4, Pg 405, 1993) Mammalian Genome 4:731, 1993.

Toldo, S.S., Fries, R., Steffen, P., Neibergs, H.L., Barendse, W., Womack, J.E., Hetzel, D.J.S., Stranzinger, G. :

Physically Mapped, Cosmid-Derived Microsatellite Markers as Anchor Loci on Bovine Chromosomes Mammalian Genome 4:720-727, 1993. Pubmed reference: 8111120.

Barendse, W., Armitage, S.M., Kirkpatrick, B.W., Moore, S.S., Georges, M., Womack, J.E., Hetzel, J. :

A Genetic Map of Index DNA Loci on Bovine Chromosome 21 Genomics 18:598-601, 1993. Pubmed reference: 8307569.

Fries, R., Eggen, A., Womack, J.E. :

The bovine gene map Mammalian Genome 4:405-428, 1993. Pubmed reference: 8104056.

1989

Fries, R., Beckmann, J.S., Georges, M., Soller, M., Womack, J. :

The bovine gene map. Anim Genet 20:3-29, 1989. Pubmed reference: 2567135. DOI: 10.1111/j.1365-2052.1989.tb00838.x.

Bovichtus diacanthus :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Bovichtus variegatus (thornfish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Brachyistius frenatus (kelp perch) :

2023

Toy, J.A., Bernardi, G. :

A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage. J Hered , 2023. Pubmed reference: 36790952. DOI: 10.1093/jhered/esad009.

Bradypodion pumilum :

2023

Taft, J.M., Tolley, K.A., Alexander, G.J., Geneva, A.J. :

De novo-whole genome assemblies for two Southern African dwarf chameleons (Bradypodion, Chamaeleonidae). Genome Biol Evol , 2023. Pubmed reference: 37847614. DOI: 10.1093/gbe/evad182.

Bradypodion ventrale (Southern dwarf chameleon) :

2023

Taft, J.M., Tolley, K.A., Alexander, G.J., Geneva, A.J. :

De novo-whole genome assemblies for two Southern African dwarf chameleons (Bradypodion, Chamaeleonidae). Genome Biol Evol , 2023. Pubmed reference: 37847614. DOI: 10.1093/gbe/evad182.

Bubalus bubalis (water buffalo) :

2023

Si, J., Dai, D., Li, K., Fang, L., Zhang, Y. :

A multi-tissue gene expression atlas of water buffalo (Bubalus bubalis) reveals transcriptome conservation between buffalo and cattle. Genes (Basel) 14:890, 2023. Pubmed reference: 37107649. DOI: 10.3390/genes14040890.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome , 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Ahmad, S.F., Chandrababu Shailaja, C., Vaishnav, S., Kumar, A., Gaur, G.K., Janga, S.C., Ahmad, S.M., Malla, W.A., Dutt, T. :

Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds. BMC Genomics 24:616, 2023. Pubmed reference: 37845620. DOI: 10.1186/s12864-023-09720-8.

2022

Khan, A., Singh, K., Jaiswal, S., Raza, M., Jasrotia, R.S., Kumar, A., Gurjar, A.K.S., Kumari, J., Nayan, V., Iquebal, M.A., Angadi, U.B., Rai, A., Datta, T.K., Kumar, D. :

Whole-genome-based web genomic resource for water buffalo (Bubalus bubalis). Front Genet 13:809741, 2022. Pubmed reference: 35480326. DOI: 10.3389/fgene.2022.809741.

Wang, X., Li, Z., Feng, T., Luo, X., Xue, L., Mao, C., Cui, K., Li, H., Huang, J., Huang, K., Rehman, S.U., Shi, D., Wu, D., Ruan, J., Liu, Q. :

Chromosome-level genome and recombination map of the male buffalo. Gigascience 12, 2022. Pubmed reference: 37589307. DOI: 10.1093/gigascience/giad063.

2021

Nascimento, A.V., Romero, A.R.S., Nawaz, M.Y., Cardoso, D.F., Santos, D.J.A., Gondro, C., Tonhati, H. :

An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly. Anim Genet 52:505-8, 2021. Pubmed reference: 34106478. DOI: 10.1111/age.13103.

2020

El-Khishin, D.A., Ageez, A., Saad, M.E., Ibrahim, A., Shokrof, M., Hassan, L.R., Abouelhoda, M.I. :

Sequencing and assembly of the Egyptian buffalo genome. PLoS One 15:e0237087, 2020. Pubmed reference: 32813723. DOI: 10.1371/journal.pone.0237087.

2019

Low, W.Y., Tearle, R., Bickhart, D.M., Rosen, B.D., Kingan, S.B., Swale, T., Thibaud-Nissen, F., Murphy, T.D., Young, R., Lefevre, L., Hume, D.A., Collins, A., Ajmone-Marsan, P., Smith, T.P.L., Williams, J.L. :

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nat Commun 10:260, 2019. Pubmed reference: 30651564. DOI: 10.1038/s41467-018-08260-0.

2017

Iamartino, D., Nicolazzi, E.L., Van Tassell, C.P., Reecy, J.M., Fritz-Waters, E.R., Koltes, J.E., Biffani, S., Sonstegard, T.S., Schroeder, S.G., Ajmone-Marsan, P., Negrini, R., Pasquariello, R., Ramelli, P., Coletta, A., Garcia, J.F., Ali, A., Ramunno, L., Cosenza, G., de Oliveira, D.A.A., Drummond, M.G., Bastianetto, E., Davassi, A., Pirani, A., Brew, F., Williams, J.L. :

Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis). PLoS One 12:e0185220, 2017. Pubmed reference: 28981529. DOI: 10.1371/journal.pone.0185220.

Williams, J.L., Iamartino, D., Pruitt, K.D., Sonstegard, T., Smith, T.P.L., Low, W.Y., Biagini, T., Bomba, L., Capomaccio, S., Castiglioni, B., Coletta, A., Corrado, F., Ferré, F., Iannuzzi, L., Lawley, C., Macciotta, N., McClure, M., Mancini, G., Matassino, D., Mazza, R., Milanesi, M., Moioli, B., Morandi, N., Ramunno, L., Peretti, V., Pilla, F., Ramelli, P., Schroeder, S., Strozzi, F., Thibaud-Nissen, F., Zicarelli, L., Ajmone-Marsan, P., Valentini, A., Chillemi, G., Zimin, A. :

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50). Gigascience 6:1-6, 2017. Pubmed reference: 29048578. DOI: 10.1093/gigascience/gix088.

1998

Iannuzzi, L. :

A genetic physical map in river buffalo (Bubalus bubalis, 2n=50) Caryologia 51:311-318, 1998.

1997

Dehondt, H.A., Gallagher, D., Oraby, H., Othman, O.E., Bosma, A.A., Womack, J.E., Elnahas, S.M. :

Gene mapping in the river buffalo (Bubalus bubalis l) - five syntenic groups Journal of Animal Breeding & Genetics-Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 114:79-85, 1997.

Bungarus multicinctus (many-banded krait) :

2023

Liu, B., Cui, L., Deng, Z., Ma, Y., Yang, D., Gong, Y., Xu, Y., Lan, T., Yang, S., Huang, S. :

The genome assembly and annotation of the many-banded krait, Bungarus multicinctus. GigaByte 2023:gigabyte82, 2023. Pubmed reference: 37404266. DOI: 10.46471/gigabyte.82.

Cairina moschata (Muscovy duck) :

2021

Jiang, F., Jiang, Y., Wang, W., Xiao, C., Lin, R., Xie, T., Sung, W.K., Li, S., Jakovlić, I., Chen, J., Du, X. :

A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses. BMC Genomics 22:581, 2021. Pubmed reference: 34330207. DOI: 10.1186/s12864-021-07897-4.

Callipepla californica (California quail) :

2023

Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., Bowie, R.C.K. :

A highly contiguous genome assembly for the California quail (Callipepla californica). J Hered , 2023. Pubmed reference: 36763048. DOI: 10.1093/jhered/esad008.

Callithrix jacchus (white-tufted-ear marmoset) :

2023

Harris, R.A., Raveendran, M., Warren, W., LaDeana, H.W., Tomlinson, C., Graves-Lindsay, T., Green, R.E., Schmidt, J.K., Colwell, J.C., Makulec, A.T., Cole, S.A., Cheeseman, I.H., Ross, C.N., Capuano, S., Eichler, E.E., Levine, J.E., Rogers, J. :

Whole genome analysis of SNV and Indel polymorphism in common marmosets (Callithrix jacchus). Genes (Basel) 14:2185, 2023. Pubmed reference: 38137007. DOI: 10.3390/genes14122185.

2021

Yang, C., Zhou, Y., Marcus, S., Formenti, G., Bergeron, L.A., Song, Z., Bi, X., Bergman, J., Rousselle, M.M.C., Zhou, C., Zhou, L., Deng, Y., Fang, M., Xie, D., Zhu, Y., Tan, S., Mountcastle, J., Haase, B., Balacco, J., Wood, J., Chow, W., Rhie, A., Pippel, M., Fabiszak, M.M., Koren, S., Fedrigo, O., Freiwald, W.A., Howe, K., Yang, H., Phillippy, A.M., Schierup, M.H., Jarvis, E.D., Zhang, G. :

Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature 594(7862):227-233, 2021. Pubmed reference: 33910227. DOI: 10.1038/s41586-021-03535-x.

2020

Jayakumar, V., Ishii, H., Seki, M., Kumita, W., Inoue, T., Hase, S., Sato, K., Okano, H., Sasaki, E., Sakakibara, Y. :

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data. BMC Genomics 21:243, 2020. Pubmed reference: 32241258. DOI: 10.1186/s12864-020-6657-2.

Calotes versicolor (garden lizard) :

2023

Wang, Q., He, F., Huang, R.Y., Yang, X., Yang, D., Ngatia, J.N., Gong, Y., Xu, Y., Huang, S., Liu, H. :

Draft genome of the oriental garden lizard (Calotes versicolor). Front Genet 14:1091544, 2023. Pubmed reference: 36891152. DOI: 10.3389/fgene.2023.1091544.

Calotriton arnoldi (Montseny brook newt) :

2024

Talavera, A., Palmada-Flores, M., Burriel-Carranza, B., Valbuena-Ureña, E., Mochales-Riaño, G., Adams, D.C., Tejero-Cicuéndez, H., Soler-Membrives, A., Amat, F., Guinart, D., Carbonell, F., Obon, E., Marquès-Bonet, T., Carranza, S. :

Genomic insights into the Montseny brook newt (Calotriton arnoldi), a critically endangered glacial relict. iScience 27:108665, 2024. Pubmed reference: 38226169. DOI: 10.1016/j.isci.2023.108665.

Calotriton asper (Pyrenean brook newt) :

2024

Calypte anna (Anna's hummingbird) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Camelus bactrianus (Bactrian camel) :

2023

Bei, L., He, C., Liu, J., Han, C., Zhou, H. :

Genome-wide identification and characterization of microsatellite markers in Bactrian Camel. Genomics :110726, 2023. Pubmed reference: 37832857. DOI: 10.1016/j.ygeno.2023.110726.

2019

Futas, J., Oppelt, J., Jelinek, A., Elbers, J.P., Wijacki, J., Knoll, A., Burger, P.A., Horin, P. :

Natural killer cell receptor genes in camels: Another mammalian model. Front Genet 10:620, 2019. Pubmed reference: 31312212. DOI: 10.3389/fgene.2019.00620.

Camelus dromedarius (Arabian camel) :

2020

Sabahat, S., Brauning, R., Clarke, S.M., Nadeem, A., Thomson, P.C., Khatkar, M.S. :

SNP discovery and population structure analysis in Lassi and Marecha camel breeds using a genotyping by sequencing method. Anim Genet 51:620-623, 2020. Pubmed reference: 32421863. DOI: 10.1111/age.12953.

2019

Ruvinskiy, D., Larkin, D.M., Farré, M. :

A near chromosome assembly of the dromedary camel genome. Front Genet 10:32, 2019. Pubmed reference: 30804979. DOI: 10.3389/fgene.2019.00032.

Futas, J., Oppelt, J., Jelinek, A., Elbers, J.P., Wijacki, J., Knoll, A., Burger, P.A., Horin, P. :

Natural killer cell receptor genes in camels: Another mammalian model. Front Genet 10:620, 2019. Pubmed reference: 31312212. DOI: 10.3389/fgene.2019.00620.

Campylomormyrus compressirostris :

2023

Cheng, F., Dennis, A.B., Osuoha, J.I., Canitz, J., Kirschbaum, F., Tiedemann, R. :

A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha. BMC Genomics 24:129, 2023. Pubmed reference: 36941548. DOI: 10.1186/s12864-023-09196-6.

Canis aureus (golden jackal) :

2023

Sosale, M.S., Songsasen, N., İbiş, O., Edwards, C.W., Figueiró, H.V., Koepfli, K.P. :

The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica). Gene 866:147303, 2023. Pubmed reference: 36854348. DOI: 10.1016/j.gene.2023.147303.

Canis latrans (coyote) :

2024

Bredemeyer, K.R., vonHoldt, B.M., Foley, N.M., Childers, I., Brzeski, K.E., Murphy, W.J. :

The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies. J Hered :esae013, 2024. Pubmed reference: 38416051. DOI: 10.1093/jhered/esae013.

Canis lupus (gray wolf) :

2024

Smeds, L., Huson, L.S.A., Ellegren, H. :

Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 17:e13652, 2024. Pubmed reference: 38333557. DOI: 10.1111/eva.13652.

Bredemeyer, K.R., vonHoldt, B.M., Foley, N.M., Childers, I., Brzeski, K.E., Murphy, W.J. :

2019

Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., Zhai, S., Xiao, J., Zhang, Z., Bao, Y., Zhang, Y.P., Wang, G.D., Zhao, W. :

iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Res 47:D793-D800, 2019. Pubmed reference: 30371881. DOI: 10.1093/nar/gky1041.

Canis lupus dingo (dingo) :

2023

Ballard, J.W.O., Field, M.A., Edwards, R.J., Wilson, L.A.B., Koungoulos, L.G., Rosen, B.D., Chernoff, B., Dudchenko, O., Omer, A., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Chan, E., Zammit, R., Hayes, V., Aiden, E.L. :

The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 12, 2023. Pubmed reference: 36994871. DOI: 10.1093/gigascience/giad018.

Canis lupus familiaris (dog) :

2023

Hsu, W.T., Williamson, P., Khatkar, M.S. :

Identification of genomic signatures in Bullmastiff dogs using composite selection signals analysis of 23 purebred clades. Animals (Basel) 13:1149, 2023. Pubmed reference: 37048405. DOI: 10.3390/ani13071149.

Kowal, K., Tkaczyk-Wlizło, A., Jusiak, M., Grzybowska-Szatkowska, L., Ślaska, B. :

Canis MitoSNP database: a functional tool useful for comparative analyses of human and canine mitochondrial genomes. J Appl Genet , 2023. Pubmed reference: 37351774. DOI: 10.1007/s13353-023-00764-w.

Son, K.H., Aldonza, M.B.D., Nam, A.R., Lee, K.H., Lee, J.W., Shin, K.J., Kang, K., Cho, J.Y. :

Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies. Sci Adv 9:eade3399, 2023. Pubmed reference: 37406108. DOI: 10.1126/sciadv.ade3399.

Duhan, N., Kaur, S., Kaundal, R. :

Meadows, J.R.S., Kidd, J.M., Wang, G.D., Parker, H.G., Schall, P.Z., Bianchi, M., Christmas, M.J., Bougiouri, K., Buckley, R.M., Hitte, C., Nguyen, A.K., Wang, C., Jagannathan, V., Niskanen, J.E., Frantz, L.A.F., Arumilli, M., Hundi, S., Lindblad-Toh, K., Ginja, C., Agustina, K.K., André, C., Boyko, A.R., Davis, B.W., Drögemüller, M., Feng, X.Y., Gkagkavouzis, K., Iliopoulos, G., Harris, A.C., Hytönen, M.K., Kalthoff, D.C., Liu, Y.H., Lymberakis, P., Poulakakis, N., Pires, A.E., Racimo, F., Ramos-Almodovar, F., Savolainen, P., Venetsani, S., Tammen, I., Triantafyllidis, A., vonHoldt, B., Wayne, R.K., Larson, G., Nicholas, F.W., Lohi, H., Leeb, T., Zhang, Y.P., Ostrander, E.A. :

Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 24:187, 2023. Pubmed reference: 37582787. DOI: 10.1186/s13059-023-03023-7.

Schall, P.Z., Winkler, P.A., Petersen-Jones, S.M., Yuzbasiyan-Gurkan, V., Kidd, J.M. :

Genome-wide methylation patterns from canine nanopore assemblies. G3 (Bethesda) , 2023. Pubmed reference: 37681359. DOI: 10.1093/g3journal/jkad203.

Du, W., Liu, X., Huang, L., Zheng, Y., Wu, W., Huang, Q., Li, T., Wei, R., Yang, Q., Deng, S., Liao, J., Liu, C., Chen, L. :

Developmental validation of a novel multiple genotyping assay with 24 canine STR loci. Vet Q :1-34, 2023. Pubmed reference: 37746714. DOI: 10.1080/01652176.2023.2262521.

Yang, I.S., Jang, I., Yang, J.O., Choi, J., Kim, M.S., Kim, K.K., Seung, B.J., Cheong, J.H., Sur, J.H., Nam, H., Lee, B., Kim, J., Kim, S. :

CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris). BMC Genomics 24:613, 2023. Pubmed reference: 37828501. DOI: 10.1186/s12864-023-09655-0.

2021

Wang, C., Wallerman, O., Arendt, M.L., Sundström, E., Karlsson, Å., Nordin, J., Mäkeläinen, S., Pielberg, G.R., Hanson, J., Ohlsson, Å., Saellström, S., Rönnberg, H., Ljungvall, I., Häggström, J., Bergström, T.F., Hedhammar, Å., Meadows, J.R.S., Lindblad-Toh, K. :

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Commun Biol 4:185, 2021. Pubmed reference: 33568770. DOI: 10.1038/s42003-021-01698-x.

Edwards, R.J., Field, M.A., Ferguson, J.M., Dudchenko, O., Keilwagen, J., Rosen, B.D., Johnson, G.S., Rice, E.S., Hillier, D., Hammond, J.M., Towarnicki, S.G., Omer, A., Khan, R., Skvortsova, K., Bogdanovic, O., Zammit, R.A., Aiden, E.L., Warren, W.C., Ballard, J.W.O. :

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 22:188, 2021. Pubmed reference: 33726677. DOI: 10.1186/s12864-021-07493-6.

Jagannathan, V., Hitte, C., Kidd, J.M., Masterson, P., Murphy, T.D., Emery, S., Davis, B., Buckley, R.M., Liu, Y.H., Zhang, X.Q., Leeb, T., Zhang, Y.P., Ostrander, E.A., Wang, G.D. :

Dog10K_Boxer_Tasha_1.0: A long-read assembly of the dog reference genome. Genes (Basel) 12:847, 2021. Pubmed reference: 34070911. DOI: 10.3390/genes12060847.

Serres-Armero, A., Davis, B.W., Povolotskaya, I.S., Morcillo-Suarez, C., Plassais, J., Juan, D., Ostrander, E.A., Marques-Bonet, T. :

Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 31:762-774, 2021. Pubmed reference: 33863806. DOI: 10.1101/gr.266049.120.

2020

Field, M.A., Rosen, B.D., Dudchenko, O., Chan, E.K.F., Minoche, A.E., Edwards, R.J., Barton, K., Lyons, R.J., Tuipulotu, D.E., Hayes, V.M., D Omer, A., Colaric, Z., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Smith, M.A., Aiden, E.L., Smith, T.P.L., Zammit, R.A., Ballard, J.W.O. :

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Gigascience 9, 2020. Pubmed reference: 32236524. DOI: 10.1093/gigascience/giaa027.

2019

Hayward, J.J., White, M.E., Boyle, M., Shannon, L.M., Casal, M.L., Castelhano, M.G., Center, S.A., Meyers-Wallen, V.N., Simpson, K.W., Sutter, N.B., Todhunter, R.J., Boyko, A.R. :

Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genet 15:e1008003, 2019. Pubmed reference: 31525180. DOI: 10.1371/journal.pgen.1008003.

Ostrander, E.A., Wang, G.D., Larson, G., vonHoldt, B.M., Davis, B.W., Jagannathan, V., Hitte, C., Wayne, R.K., Zhang, Y.P. :

Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. Natl Sci Rev 6:810-824, 2019. Pubmed reference: 31598383. DOI: 10.1093/nsr/nwz049.

Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., Zhai, S., Xiao, J., Zhang, Z., Bao, Y., Zhang, Y.P., Wang, G.D., Zhao, W. :

iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Res 47:D793-D800, 2019. Pubmed reference: 30371881. DOI: 10.1093/nar/gky1041.

2018

Holden, L.A., Arumilli, M., Hytönen, M.K., Hundi, S., Salojärvi, J., Brown, K.H., Lohi, H. :

Assembly and analysis of unmapped genome sequence reads reveal novel sequence and variation in dogs. Sci Rep 8:10862, 2018. Pubmed reference: 30022108. DOI: 10.1038/s41598-018-29190-3.

2014

Hoeppner, M.P., Lundquist, A., Pirun, M., Meadows, J.R., Zamani, N., Johnson, J., Sundström, G., Cook, A., Fitzgerald, M.G., Swofford, R., Mauceli, E., Moghadam, B.T., Greka, A., Alföldi, J., Abouelleil, A., Aftuck, L., Bessette, D., Berlin, A., Brown, A., Gearin, G., Lui, A., Macdonald, J.P., Priest, M., Shea, T., Turner-Maier, J., Zimmer, A., Lander, E.S., di Palma, F., Lindblad-Toh, K., Grabherr, M.G. :

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS One 9:e91172, 2014. Pubmed reference: 24625832. DOI: 10.1371/journal.pone.0091172.

2010

Wong, A.K., Ruhe, A.L., Dumont, B.L., Robertson, K.R., Guerrero, G., Shull, S.M., Ziegle, J.S., Millon, L.V., Broman, K.W., Payseur, B.A., Neff, M.W. :

A comprehensive linkage map of the dog genome. Genetics 184:595-605, 2010. Pubmed reference: 19966068. DOI: 10.1534/genetics.109.106831.

2008

Thomas, R., Duke, S.E., Karlsson, E.K., Evans, A., Ellis, P., Lindblad-Toh, K., Langford, C.F., Breen, M. :

A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis. Cytogenet Genome Res 122:110-21, 2008. Pubmed reference: 19096206. DOI: 10.1159/000163088.

2007

Thomas, R., Duke, S.E., Bloom, S.K., Breen, T.E., Young, A.C., Feiste, E., Seiser, E.L., Tsai, P.C., Langford, C.F., Ellis, P., Karlsson, E.K., Lindblad-Toh, K., Breen, M. :

A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog. J Hered 98:474-84, 2007. Pubmed reference: 17702974. DOI: 10.1093/jhered/esm053.

Sargan, D.R., Aguirre-Hernandez, J., Galibert, F., Ostrander, E.A. :

An extended microsatellite set for linkage mapping in the domestic dog. J Hered 98:221-31, 2007. Pubmed reference: 17406025. DOI: 10.1093/jhered/esm006.

2005

Lindblad-Toh, K., Wade, C.M., Mikkelsen, T.S., Karlsson, E.K., Jaffe, D.B., Kamal, M., Clamp, M., Chang, J.L., Kulbokas, E.J., Zody, M.C., Mauceli, E., Xie, X., Breen, M., Wayne, R.K., Ostrander, E.A., Ponting, C.P., Galibert, F., Smith, D.R., DeJong, P.J., Kirkness, E., Alvarez, P., Biagi, T., Brockman, W., Butler, J., Chin, C.W., Cook, A., Cuff, J., Daly, M.J., DeCaprio, D., Gnerre, S., Grabherr, M., Kellis, M., Kleber, M., Bardeleben, C., Goodstadt, L., Heger, A., Hitte, C., Kim, L., Koepfli, K.P., Parker, H.G., Pollinger, J.P., Searle, S.M., Sutter, N.B., Thomas, R., Webber, C., Baldwin, J., Abebe, A., Abouelleil, A., Aftuck, L., Ait-Zahra, M., Aldredge, T., Allen, N., An, P., Anderson, S., Antoine, C., Arachchi, H., Aslam, A., Ayotte, L., Bachantsang, P., Barry, A., Bayul, T., Benamara, M., Berlin, A., Bessette, D., Blitshteyn, B., Bloom, T., Blye, J., Boguslavskiy, L., Bonnet, C., Boukhgalter, B., Brown, A., Cahill, P., Calixte, N., Camarata, J., Cheshatsang, Y., Chu, J., Citroen, M., Collymore, A., Cooke, P., Dawoe, T., Daza, R., Decktor, K., DeGray, S., Dhargay, N., Dooley, K., Dooley, K., Dorje, P., Dorjee, K., Dorris, L., Duffey, N., Dupes, A., Egbiremolen, O., Elong, R., Falk, J., Farina, A., Faro, S., Ferguson, D., Ferreira, P., Fisher, S., FitzGerald, M., Foley, K., Foley, C., Franke, A., Friedrich, D., Gage, D., Garber, M., Gearin, G., Giannoukos, G., Goode, T., Goyette, A., Graham, J., Grandbois, E., Gyaltsen, K., Hafez, N., Hagopian, D., Hagos, B., Hall, J., Healy, C., Hegarty, R., Honan, T., Horn, A., Houde, N., Hughes, L., Hunnicutt, L., Husby, M., Jester, B., Jones, C., Kamat, A., Kanga, B., Kells, C., Khazanovich, D., Kieu, A.C., Kisner, P., Kumar, M., Lance, K., Landers, T., Lara, M., Lee, W., Leger, J.P., Lennon, N., Leuper, L., LeVine, S., Liu, J., Liu, X., Lokyitsang, Y., Lokyitsang, T., Lui, A., Macdonald, J., Major, J., Marabella, R., Maru, K., Matthews, C., McDonough, S., Mehta, T., Meldrim, J., Melnikov, A., Meneus, L., Mihalev, A., Mihova, T., Miller, K., Mittelman, R., Mlenga, V., Mulrain, L., Munson, G., Navidi, A., Naylor, J., Nguyen, T., Nguyen, N., Nguyen, C., Nguyen, T., Nicol, R., Norbu, N., Norbu, C., Novod, N., Nyima, T., Olandt, P., O'Neill, B., O'Neill, K., Osman, S., Oyono, L., Patti, C., Perrin, D., Phunkhang, P., Pierre, F., Priest, M., Rachupka, A., Raghuraman, S., Rameau, R., Ray, V., Raymond, C., Rege, F., Rise, C., Rogers, J., Rogov, P., Sahalie, J., Settipalli, S., Sharpe, T., Shea, T., Sheehan, M., Sherpa, N., Shi, J., Shih, D., Sloan, J., Smith, C., Sparrow, T., Stalker, J., Stange-Thomann, N., Stavropoulos, S., Stone, C., Stone, S., Sykes, S., Tchuinga, P., Tenzing, P., Tesfaye, S., Thoulutsang, D., Thoulutsang, Y., Topham, K., Topping, I., Tsamla, T., Vassiliev, H., Venkataraman, V., Vo, A., Wangchuk, T., Wangdi, T., Weiand, M., Wilkinson, J., Wilson, A., Yadav, S., Yang, S., Yang, X., Young, G., Yu, Q., Zainoun, J., Zembek, L., Zimmer, A., Lander, E.S. :

Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-19, 2005. Pubmed reference: 16341006. DOI: 10.1038/nature04338.

2004

Switonski, M., Szczerbal, I., Nowacka, J. :

The dog genome map and its use in mammalian comparative genomics. J Appl Genet 45:195-214, 2004. Pubmed reference: 15131351.

2003

Guyon, R., Lorentzen, T.D., Hitte, C., Kim, L., Cadieu, E., Parker, H.G., Quignon, P., Lowe, J.K., Renier, C., Gelfenbeyn, B., Vignaux, F., DeFrance, H.B., Gloux, S., Mahairas, G.G., Andre, C., Galibert, F., Ostrander, E.A. :

A 1-Mb resolution radiation hybrid map of the canine genome Proceedings of the National Academy of Sciences of the United States of America 100:5296-301, 2003. Pubmed reference: 12700351. DOI: 10.1073/pnas.0831002100.

Spriggs, H.F., Holmes, N.G., Breen, M.G., Deloukas, P.G., Langford, C.F., Ross, M.T., Carter, N.P., Davis, M.E., Knights, C.E., Smith, A.E., Farr, C.J., McCarthy, L.C., Binns, M.M. :

Construction and integration of radiation-hybrid and cytogenetic maps of dog Chromosome X Mammalian Genome 14:214-21, 2003. Pubmed reference: 12647244. DOI: 10.1007/s00335-002-3051-0.

Roberts, M.C., Hitte, C.C., Hendrickson, J.A., Hoffmann, D.E., Flickinger, G.H., Rutherford, M.S., Guyon, R.S., Galibert, F.S., Mickelson, J.R. :

Characterization and radiation hybrid mapping of expressed sequence tags from the canine brain Mammalian Genome 14:203-13, 2003. Pubmed reference: 12647243. DOI: 10.1007/s00335-002-2207-2.

2002

Dukes-McEwan, J., Jackson, I.J. :

The promises and problems of linkage analysis by using the current canine genome map Mammalian Genome 13:667-672, 2002. Pubmed reference: 12461654. DOI: 10.1007/s00335-002-4004-3.

2001

Breen, M., Jouquand, S., Renier, C., Mellersh, C.S., Hitte, C., Holmes, N.G., Cheron, A., Suter, N., Vignaux, F., Bristow, A.E., Priat, C., McCann, E., Andre, C., Boundy, S., Gitsham, P., Thomas, R., Bridge, W.L., Spriggs, H.F., Ryder, E.J., Curson, A., Sampson, J., Ostrander, E.A., Binns, M.M., Galibert, F. :

Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes Genome Research 11:1784-1795, 2001. Pubmed reference: 11591656. DOI: 10.1101/gr.189401.

2000

Mellersh, C.S., Hitte, C., Richman, M., Vignaux, F., Priat, C., Jouquand, S., Werner, P., Andre, C., DeRose, S., Patterson, D.F., Ostrander, E.A., Galibert, F. :

An integrated linkage-radiation hybrid map of the canine genome Mammalian Genome 11:120-130, 2000. Pubmed reference: 10656926.

1999

Vignaux, F., Priat, C., Jouquand, S., Hitte, C., Jiang, Z., Cheron, A., Renier, C., Andre, C., Galibert, F. :

Toward a dog radiation hybrid map Journal of Heredity 90:62-67, 1999. Pubmed reference: 9987906.

Langston, A.A., Mellersh, C.S., Wiegand, N.A., Acland, G.M., Ray, K., Aguirre, G.D., Ostrander, E.A. :

Toward a framework linkage map of the canine genome Journal of Heredity 90:7-14, 1999. Pubmed reference: 9987896.

Dolf, G., Batt, R., Baumle, E., Binns, M., Brenig, B., Bull, B., Dunner, S., Fredholm, M., Gaillard, C., Gerlach, J., Giger, U., Goldspink, G., Graphodatsky, A.S., Holmes, N., Judd, S., Juneja, K., Kelly, E.P., Kent, M.G., King, W.A., Lingaas, F., Long, S.E., Lubas, G., Mariat, D., Marki, U., Matthews, M., et al. :

DogMap: An international collaboration toward a low-resolution canine genetic marker map Journal of Heredity 90:3-6, 1999. Pubmed reference: 9987895.

Neff, M.W., Broman, K.W., Mellersh, C.S., Ray, K., Acland, G.M., Aguirre, G.D., Ziegle, J.S., Ostrander, E.A., Rine, J. :

A second-generation genetic linkage map of the domestic dog, Canis familiaris Genetics 151:803-820, 1999. Pubmed reference: 9927471.

Vignaux, F., Hitte, C., Priat, C., Chuat, J.C., Andre, C., Galibert, F. :

Construction and optimization of a dog whole-genome radiation hybrid panel Mammalian Genome 10:888-894, 1999. Pubmed reference: 10441740.

Werner, P., Mellersh, C.S., Raducha, M.G., DeRose, S., Acland, G.M., Prociuk, U., Wiegand, N., Aguirre, G.D., Henthorn, P.S., Patterson, D.F., Ostrander, E.A. :

Anchoring of canine linkage groups with chromosome-specific markers Mammalian Genome 10:814-823, 1999. Pubmed reference: 10430668.

Priat, C., Jiang, Z.H.H., Renier, C., Andre, C., Gailbert, F. :

Characterization of 463 Type I markers suitable for dog genome mapping Mammalian Genome 10:803-813, 1999. Pubmed reference: 10430667.

Yang, F., O'Brien, P.C.M., Milne, B.S., Graphodatsky, A.S., Solanky, N., Trifonov, V., Rens, W., Sargan, D., Ferguson-Smith, M.A. :

A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps Genomics 62:189-202, 1999. Pubmed reference: 10610712. DOI: 10.1006/geno.1999.5989.

Lyons, L.A., Kehler, J.S., O'Brien, S.J. :

Development of comparative anchor tagged sequences (CATS) for canine genome mapping. J Hered 90:15-26, 1999. Pubmed reference: 9987897.

1998

Anon. :

Canine genetic linkage map just six months away Veterinary Record 142:383, 1998.

Anon. :

Cornell team helps put dog on the map Canine Practice 23:1 ff., 1998.

Priat, C., Hitte, C., Vignaux, F., Renier, C., Jiang, Z.H., Jouquand, S., Cheron, A., Andre, C., Galibert, F. :

A whole-genome radiation hybrid map of the dog genome Genomics 54:361-378, 1998. Pubmed reference: 9878239. DOI: 10.1006/geno.1998.5602.

1997

Lingaas, F., Sorensen, A., Juneja, R.K., Johansson, S., Fredholm, M., Wintero, A.K., Sampson, J., Mellersh, C., Curzon, A., Holmes, N.G., Binns, M.M., Dickens, H.F., Ryder, E.J., Gerlach, J., Baumle, E., Dolf, G. :

Towards construction of a canine linkage map - establishment of 16 linkage groups Mammalian Genome 8:218-221, 1997. Pubmed reference: 9069125.

Leveque, N.W. :

Canine genome mapping a dogged pursuit American Journal of Veterinary Research 58:936-937, 1997.

Mellersh, C.S., Langston, A.A., Acland, G.M., Fleming, M.A., Ray, K., Wiegand, N.A., Francisco, L.V., Gibbs, M., Aguirre, G.D., Ostrander, E.A. :

A linkage map of the canine genome Genomics 46:326-336, 1997. Pubmed reference: 9441735. DOI: 10.1006/geno.1997.5098.

1996

Anon. :

Canine genome project offers hope for the future Veterinary Record 138:406, 1996.

1993

Miller, S.K. :

Search for Genes That Make Mans Best Friend New Scientist 138:5, 1993.

Caperea marginata (pygmy right whale) :

2023

Wolf, M., Zapf, K., Gupta, D.K., Hiller, M., Árnason, Ú., Janke, A. :

The genome of the pygmy right whale illuminates the evolution of rorquals. BMC Biol 21:79, 2023. Pubmed reference: 37041515. DOI: 10.1186/s12915-023-01579-1.

Capra aegagrus (wild goat) :

2015

Dong, Y., Zhang, X., Xie, M., Arefnezhad, B., Wang, Z., Wang, W., Feng, S., Huang, G., Guan, R., Shen, W., Bunch, R., McCulloch, R., Li, Q., Li, B., Zhang, G., Xu, X., Kijas, J.W., Salekdeh, G.H., Wang, W., Jiang, Y. :

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genomics 16:431, 2015. Pubmed reference: 26044654. DOI: 10.1186/s12864-015-1606-1.

Capra hircus (goat) :

2024

Belay, S., Belay, G., Nigussie, H., Jian-Lin, H., Tijjani, A., Ahbara, A.M., Tarekegn, G.M., Woldekiros, H.S., Mor, S., Dobney, K., Lebrasseur, O., Hanotte, O., Mwacharo, J.M. :

Whole-genome resource sequences of 57 indigenous Ethiopian goats. Sci Data 11:139, 2024. Pubmed reference: 38287052. DOI: 10.1038/s41597-024-02973-2.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Zhang, H., Liang, Y., Chen, S., Xuan, Z., Jiang, Y., Li, R., Cao, Y. :

Full-length transcriptome sequencing reveals extreme incomplete annotation of the goat genome. Anim Genet , 2023. Pubmed reference: 36849788. DOI: 10.1111/age.13311.

Arslan, M. :

Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus). Mamm Genome , 2023. Pubmed reference: 37004528. DOI: 10.1007/s00335-023-09990-3.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome , 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

2021

Bhat, B., Ganai, N.A., Singh, A., Mir, R., Ahmad, S.M., Majeed Zargar, S., Malik, F. :

Changthangi Pashmina goat genome: Sequencing, assembly, and annotation. Front Genet 12:695178, 2021. Pubmed reference: 34354739. DOI: 10.3389/fgene.2021.695178.

2019

Wang, F.H., Zhang, L., Li, X.K., Fan, Y.X., Qiao, X., Gong, G., Yan, X.C., Zhang, L.T., Wang, Z.Y., Wang, R.J., Liu, Z.H., Wang, Z.X., He, L., Zhang, Y., Li, J.Q., Zhao, Y.H., Su, R. :

[Progress in goat genome studies]. Yi Chuan 41:928-938, 2019. Pubmed reference: 31624055. DOI: 10.16288/j.yczz.19-147.

Li, R., Fu, W., Su, R., Tian, X., Du, D., Zhao, Y., Zheng, Z., Chen, Q., Gao, S., Cai, Y., Wang, X., Li, J., Jiang, Y. :

Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome. Front Genet 10:1169, 2019. Pubmed reference: 31803240. DOI: 10.3389/fgene.2019.01169.

2017

Bickhart, D.M., Rosen, B.D., Koren, S., Sayre, B.L., Hastie, A.R., Chan, S., Lee, J., Lam, E.T., Liachko, I., Sullivan, S.T., Burton, J.N., Huson, H.J., Nystrom, J.C., Kelley, C.M., Hutchison, J.L., Zhou, Y., Sun, J., Crisà, A., Ponce de León, F.A., Schwartz, J.C., Hammond, J.A., Waldbieser, G.C., Schroeder, S.G., Liu, G.E., Dunham, M.J., Shendure, J., Sonstegard, T.S., Phillippy, A.M., Van Tassell, C.P., Smith, T.P. :

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat Genet 49:643-650, 2017. Pubmed reference: 28263316. DOI: 10.1038/ng.3802.

Worley, K.C. :

A golden goat genome. Nat Genet 49:485-486, 2017. Pubmed reference: 28358125. DOI: 10.1038/ng.3824.

2014

Du, X., Servin, B., Womack, J.E., Cao, J., Yu, M., Dong, Y., Wang, W., Zhao, S. :

An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae. BMC Genomics 15:625, 2014. Pubmed reference: 25052253. DOI: 10.1186/1471-2164-15-625.

2013

Dong, Y., Xie, M., Jiang, Y., Xiao, N., Du, X., Zhang, W., Tosser-Klopp, G., Wang, J., Yang, S., Liang, J., Chen, W., Chen, J., Zeng, P., Hou, Y., Bian, C., Pan, S., Li, Y., Liu, X., Wang, W., Servin, B., Sayre, B., Zhu, B., Sweeney, D., Moore, R., Nie, W., Shen, Y., Zhao, R., Zhang, G., Li, J., Faraut, T., Womack, J., Zhang, Y., Kijas, J., Cockett, N., Xu, X., Zhao, S., Wang, J., Wang, W. :

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 31:135-41, 2013. Pubmed reference: 23263233. DOI: 10.1038/nbt.2478.

1998

Schibler, L., Vaiman, D., Oustry, A., Girauddelville, C., Cribiu, E.P. :

Comparative gene mapping - a fine-scale survey of chromosome rearrangements between ruminants and humans Genome Research 8:901-915, 1998. Pubmed reference: 9750190.

1996

Vaiman, D., Schibler, L., Bourgeois, F., Oustry, A., Amigues, Y., Cribiu, E.P. :

A genetic linkage map of the male goat genome Genetics 144:279-305, 1996. Pubmed reference: 8878693.

Caranx ignobilis (giant trevally) :

2022

Pickett, B.D., Glass, J.R., Johnson, T.P., Ridge, P.G., Kauwe, J.S.K. :

The genome of a giant (trevally): Caranx ignobilis. GigaByte 2022:gigabyte67, 2022. Pubmed reference: 36824527. DOI: 10.46471/gigabyte.67.

Carassius auratus (goldfish) :

2021

Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :

Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish. Nat Genet 53:1493-1503, 2021. Pubmed reference: 34594040. DOI: 10.1038/s41588-021-00933-9.

2019

Omori, Y., Kon, T. :

Goldfish: an old and new model system to study vertebrate development, evolution and human disease. J Biochem 165:209-218, 2019. Pubmed reference: 30219851. DOI: 10.1093/jb/mvy076.

Caretta caretta (Loggerhead turtle) :

2023

Chang, G., Jones, S., Leelakumari, S., Ashkani, J., Culibrk, L., O'Neill, K., Tse, K., Cheng, D., Chuah, E., McDonald, H., Kirk, H., Pandoh, P., Pari, S., Angelini, V., Kyle, C., Bertorelle, G., Zhao, Y., Mungall, A., Moore, R., Vilaça, S., Jones, S. :

The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758. F1000Res 12:336, 2023. Pubmed reference: 37455852. DOI: 10.12688/f1000research.131283.2.

Carettochelys insculpta (pitted-shelled turtle) :

2024

Li, Y., Liu, Y., Zheng, J., Wu, B., Cui, X., Xu, W., Zhu, C., Qiu, Q., Wang, K. :

A chromosome-level genome assembly of the pig-nosed turtle (Carettochelys insculpta). Sci Data 11:311, 2024. Pubmed reference: 38521795. DOI: 10.1038/s41597-024-03157-8.

Cavia porcellus (domestic guinea pig) :

2023

Borja Lozano, M.V., Vigil Santillán, B., More Montoya, M.J., Morón Barraza, J.A., García-Serquén, A.L., Gutiérrez Reynoso, G., Yalta-Macedo, C.E. :

Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes. Anim Genet , 2023. Pubmed reference: 37796666. DOI: 10.1111/age.13367.

Romanenko, S.A., Kliver, S.F., Serdyukova, N.A., Perelman, P.L., Trifonov, V.A., Seluanov, A., Gorbunova, V., Azpurua, J., Pereira, J.C., Ferguson-Smith, M.A., Graphodatsky, A.S. :

Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human. Sci Rep 13:21055, 2023. Pubmed reference: 38030702. DOI: 10.1038/s41598-023-46595-x.

Centropyge bicolor (bicolor angelfish) :

2023

Zhang, S., Song, Y., Liu, M., Yuan, Z., Zhang, M., Zhang, H., Seim, I., Fan, G., Liu, S., Liu, X. :

Chromosome-level genome of butterflyfish unveils genomic features of unique color patterns and morphological traits. DNA Res , 2023. Pubmed reference: 37590994. DOI: 10.1093/dnares/dsad018.

Centruroides vittatus :

2023

Yamashita, T., Rhoads, D.D., Pummill, J. :

A robust genome and assembly with transcriptomic data from the striped scorpion, Centruroides vittatus. bioRxiv , 2023. Pubmed reference: 37609349. DOI: 10.1101/2023.08.04.551372.

Cervidae (deer) :

2023

Proskuryakova, A.A., Ivanova, E.S., Makunin, A.I., Larkin, D.M., Ferguson-Smith, M.A., Yang, F., Uphyrkina, O.V., Perelman, P.L., Graphodatsky, A.S. :

Comparative studies of X chromosomes in Cervidae family. Sci Rep 13:11992, 2023. Pubmed reference: 37491593. DOI: 10.1038/s41598-023-39088-4.

2002

Slate, J., Van Stijn, T.C., Anderson, R.M., McEwan, K.M., Maqbool, N.J., Mathias, H.C., Bixley, M.J., Stevens, D.R., Molenaar, A.J., Beever, J.E., Galloway, S.M., Tate, M.L. :

A deer (subfamily cervinae) genetic linkage map and the evolution of ruminant Genomes Genetics 160:1587-1597, 2002. Pubmed reference: 11973312.

1995

Tate, M.L., Mathias, H.C., Fennessy, P.F., Dodds, K.G., Penty, J.M., Hill, D.F. :

A new gene mapping resource: Interspecies hybrids between Pere David's deer (Elaphurus davidianus) and red deer (Cervus elaphus) Genetics 139:1383-1391, 1995. Pubmed reference: 7768446.

Cervus elaphus (red deer) :

2021

Vozdova, M., Kubickova, S., Cernohorska, H., Fröhlich, J., Rubes, J. :

Anchoring the CerEla1.0 genome assembly to red deer (Cervus elaphus) and cattle (Bos taurus) chromosomes and specification of evolutionary chromosome rearrangements in cervidae. Animals (Basel) 11, 2021. Pubmed reference: 34573579. DOI: 10.3390/ani11092614.

2018

Bana, N.Á., Nyiri, A., Nagy, J., Frank, K., Nagy, T., Stéger, V., Schiller, M., Lakatos, P., Sugár, L., Horn, P., Barta, E., Orosz, L. :

The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes. Mol Genet Genomics 293:665-684, 2018. Pubmed reference: 29294181. DOI: 10.1007/s00438-017-1412-3.

2017

Johnston, S.E., Huisman, J., Ellis, P.A., Pemberton, J.M. :

A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer (Cervus elaphus). G3 (Bethesda) 7:2859-2870, 2017. Pubmed reference: 28667018. DOI: 10.1534/g3.117.044198.

Cetoscarus ocellatus (spotted parrotfish) :

2024

Tea, Y.K., Zhou, Y., Ewart, K.M., Cheng, G., Kawasaki, K., DiBattista, J.D., Ho, S.Y.W., Lo, N., Fan, S. :

The spotted parrotfish genome provides insights into the evolution of a coral reef dietary specialist (Teleostei: Labridae: Scarini: Cetoscarus ocellatus). Ecol Evol 14:e11148, 2024. Pubmed reference: 38476702. DOI: 10.1002/ece3.11148.

Chaenocephalus aceratus (blackfin icefish) :

2024

Lee, S.J., Kim, J., Choi, E.K., Jo, E., Cho, M., Kim, J.H., Park, H. :

Author Correction: A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus. Sci Data 11:47, 2024. Pubmed reference: 38191547. DOI: 10.1038/s41597-023-02861-1.

2023

Lee, S.J., Kim, J., Choi, E.K., Jo, E., Cho, M., Kim, J.H., Park, H. :

A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus. Sci Data 10:657, 2023. Pubmed reference: 37752129. DOI: 10.1038/s41597-023-02561-w.

Chaenodraco wilsoni (spiny icefish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Chaetodon auriga (threadfin butterflyfish) :

2023

Zhang, S., Song, Y., Liu, M., Yuan, Z., Zhang, M., Zhang, H., Seim, I., Fan, G., Liu, S., Liu, X. :

Chromosome-level genome of butterflyfish unveils genomic features of unique color patterns and morphological traits. DNA Res , 2023. Pubmed reference: 37590994. DOI: 10.1093/dnares/dsad018.

Chaetodon trifasciatus (melon butterflyfish) :

2023

Zhang, S., Song, Y., Liu, M., Yuan, Z., Zhang, M., Zhang, H., Seim, I., Fan, G., Liu, S., Liu, X. :

Chromosome-level genome of butterflyfish unveils genomic features of unique color patterns and morphological traits. DNA Res , 2023. Pubmed reference: 37590994. DOI: 10.1093/dnares/dsad018.

Champsocephalus esox (pike icefish) :

2023

Rivera-Colón, A.G., Rayamajhi, N., Fazal Minhas, B., Madrigal, G., Bilyk, K.T., Yoon, V., Hüne, M., Gregory, S., Cheng, C.C., Catchen, J.M. :

Genomics of secondarily temperate adaptation in the only non-antarctic icefish. Mol Biol Evol , 2023. Pubmed reference: 36806940. DOI: 10.1093/molbev/msad029.

Champsocephalus gunnari (mackerel icefish) :

2023

Rivera-Colón, A.G., Rayamajhi, N., Fazal Minhas, B., Madrigal, G., Bilyk, K.T., Yoon, V., Hüne, M., Gregory, S., Cheng, C.C., Catchen, J.M. :

Genomics of secondarily temperate adaptation in the only non-antarctic icefish. Mol Biol Evol , 2023. Pubmed reference: 36806940. DOI: 10.1093/molbev/msad029.

Channa argus (northern snakehead) :

2017

Xu, J., Bian, C., Chen, K., Liu, G., Jiang, Y., Luo, Q., You, X., Peng, W., Li, J., Huang, Y., Yi, Y., Dong, C., Deng, H., Zhang, S., Zhang, H., Shi, Q., Xu, P. :

Draft genome of the Northern snakehead, Channa argus. Gigascience 6:1-5, 2017. Pubmed reference: 28327946. DOI: 10.1093/gigascience/gix011.

Charina bottae :

2022

Grismer, J.L., Escalona, M., Miller, C., Beraut, E., Fairbairn, C.W., Marimuthu, M.P.A., Nguyen, O., Toffelmier, E., Wang, I.J., Shaffer, H.B. :

Reference genome of the Rubber Boa, Charina bottae (Serpentes: Boidae). J Hered , 2022. Pubmed reference: 36056886. DOI: 10.1093/jhered/esac048.

Chelidonichthys spinosus (red gurnard) :

2023

Wang, Y., Zhang, H., Xian, W., Iwasaki, W. :

Chromosome genome assembly and annotation of the spiny red gurnard (Chelidonichthys spinosus). Sci Data 10:443, 2023. Pubmed reference: 37438353. DOI: 10.1038/s41597-023-02357-y.

Chelmon rostratus (copperband butterflyfish) :

2023

Zhang, S., Song, Y., Liu, M., Yuan, Z., Zhang, M., Zhang, H., Seim, I., Fan, G., Liu, S., Liu, X. :

Chromosome-level genome of butterflyfish unveils genomic features of unique color patterns and morphological traits. DNA Res , 2023. Pubmed reference: 37590994. DOI: 10.1093/dnares/dsad018.

Chelonia mydas (green sea turtle) :

2023

Dolfo, V., Boissin, E., Tatarata, M., Planes, S. :

Characterization of 25 new microsatellite markers for the green turtle (Chelonia mydas) and cross-species amplification in other marine turtle species. Mol Biol Rep , 2023. Pubmed reference: 36877349. DOI: 10.1007/s11033-023-08341-4.

Chiloscyllium griseum (grey bambooshark) :

2024

Harshan, P., Sukumaran, S., Gopalakrishnan, A. :

De novo transcriptome for Chiloscyllium griseum, a long-tail carpet shark of the Indian waters. Sci Data 11:285, 2024. Pubmed reference: 38461175. DOI: 10.1038/s41597-024-03093-7.

Chionobathyscus dewitti :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Chlorocebus sabaeus (green monkey) :

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Chrysolophus amherstiae (Lady Amherst's pheasant) :

2024

Garg, K.M., Dovih, P., Chattopadhyay, B. :

Hybrid de novo genome assembly of the sexually dimorphic Lady Amherst's pheasant. DNA Res :dsae001, 2024. Pubmed reference: 38168719. DOI: 10.1093/dnares/dsae001.

Clarias batrachus (walking catfish) :

2023

Liu, K., Xie, N., Wang, Y., Liu, X. :

The utilization of reference-guided assembly and in silico libraries improves the draft genome of Clarias batrachus and Culter alburnus. Mar Biotechnol (NY) , 2023. Pubmed reference: 37661218. DOI: 10.1007/s10126-023-10248-x.

Clarias fuscus (whitespotted clarias) :

2023

Tian, C.X., Lin, X.H., Zhou, D.Y., Chen, Y., Shen, Y.J., Ye, M.H., Duan, C.Y., Zhang, Y.L., Yang, B.L., Deng, S.P., Zhu, C.H., Li, G.L. :

A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region. BMC Genomics 24:291, 2023. Pubmed reference: 37254055. DOI: 10.1186/s12864-023-09394-2.

Clinocottus analis (woolly sculpin) :

2023

Wright, D.B., Escalona, M., Marimuthu, M.P.A., Sahasrabudhe, R., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Miller, C., Shaffer, H.B., Bernardi, G. :

Reference genome of the Woolly Sculpin, Clinocottus analis. J Hered 114:60-67, 2023. Pubmed reference: 36107748. DOI: 10.1093/jhered/esac055.

Clupea harengus (Atlantic herring) :

2019

Pettersson, M.E., Rochus, C.M., Han, F., Chen, J., Hill, J., Wallerman, O., Fan, G., Hong, X., Xu, Q., Zhang, H., Liu, S., Liu, X., Haggerty, L., Hunt, T., Martin, F.J., Flicek, P., Bunikis, I., Folkvord, A., Andersson, L. :

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection. Genome Res 29:1919-1928, 2019. Pubmed reference: 31649060. DOI: 10.1101/gr.253435.119.

2016

Martinez Barrio, A., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M., Zhang, H., Dainat, J., Ekman, D., Höppner, M., Jern, P., Martin, M., Nystedt, B., Liu, X., Chen, W., Liang, X., Shi, C., Fu, Y., Ma, K., Zhan, X., Feng, C., Gustafson, U., Rubin, C.J., Sällman Almén, M., Blass, M., Casini, M., Folkvord, A., Laikre, L., Ryman, N., Ming-Yuen Lee, S., Xu, X., Andersson, L. :

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. Elife 5, 2016. Pubmed reference: 27138043. DOI: 10.7554/eLife.12081.

Cociella crocodila (crocodile flathead) :

2021

Zhao, R., Lu, Z., Cai, S., Gao, T., Xu, S. :

Whole genome survey and genetic markers development of crocodile flathead Cociella crocodilus. Anim Genet 52:891-895, 2021. Pubmed reference: 34486145. DOI: 10.1111/age.13136.

Coelodonta antiquitatis (woolly rhinoceros) :

2023

Seeber, P.A., Palmer, Z., Schmidt, A., Chagas, A., Kitagawa, K., Marinova-Wolff, E., Tafelmaier, Y., Epp, L.S. :

The first European woolly rhinoceros mitogenomes, retrieved from cave hyena coprolites, suggest long-term phylogeographic differentiation. Biol Lett 19:20230343, 2023. Pubmed reference: 37909055. DOI: 10.1098/rsbl.2023.0343.

Coilia nasus (Japanese grenadier anchovy) :

2023

Ma, F., Wang, Y., Su, B., Zhao, C., Yin, D., Chen, C., Yang, Y., Wang, C., Luo, B., Wang, H., Deng, Y., Xu, P., Yin, G., Jian, J., Liu, K. :

Gap-free genome assembly of anadromous Coilia nasus. Sci Data 10:360, 2023. Pubmed reference: 37280262. DOI: 10.1038/s41597-023-02278-w.

Cololabis saira (Pacific saury) :

2024

Sato, M., Fukuda, K., Kadota, M., Makino-Itou, H., Tatsumi, K., Yamauchi, S., Kuraku, S. :

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology. DNA Res 31:dsae004, 2024. Pubmed reference: 38451834. DOI: 10.1093/dnares/dsae004.

Nakamura, Y., Yasuike, M., Fuji, T., Suyama, S., Mekuchi, M. :

Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira). DNA Res :dsae010, 2024. Pubmed reference: 38566577. DOI: 10.1093/dnares/dsae010.

Colossoma macropomum (tambaqui) :

2021

Varela, E.S., Bekaert, M., Ganeco-Kirschnik, L.N., Torati, L.S., Shiotsuki, L., de Almeida, F.L., Villela, L.C.V., Rezende, F.P., da Silva Barroso, A., de Freitas, L.E.L., Taggart, J.B., Migaud, H. :

A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum. BMC Genomics 22:709, 2021. Pubmed reference: 34598670. DOI: 10.1186/s12864-021-08037-8.

Columba guinea (speckled pigeon) :

2023

Maclary, E.T., Holt, C., Concepcion, G.T., Sović, I., Vickrey, A.I., Yandell, M., Kronenberg, Z., Shapiro, M.D. :

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid. bioRxiv , 2023. Pubmed reference: 37873124. DOI: 10.1101/2023.10.11.561892.

Maclary, E.T., Holt, C., Concepcion, G.T., Sović, I., Vickrey, A.I., Yandell, M., Kronenberg, Z., Shapiro, M.D. :

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid. G3 (Bethesda) :jkad280, 2023. Pubmed reference: 38066578. DOI: 10.1093/g3journal/jkad280.

Columba livia (rock pigeon) :

2023

Wang, Y., Wang, X., Luo, Y., Zhang, J., Lin, Y., Wu, J., Zeng, B., Liu, L., Yan, P., Liang, J., Guo, H., Jin, L., Tang, Q., Long, K., Li, M. :

Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating' pigeon. PLoS Genet 19:e1010746, 2023. Pubmed reference: 37289658. DOI: 10.1371/journal.pgen.1010746.

Maclary, E.T., Holt, C., Concepcion, G.T., Sović, I., Vickrey, A.I., Yandell, M., Kronenberg, Z., Shapiro, M.D. :

Conuropsis carolinensis (Carolina parakeet) :

2020

Evolutionary history, genomic adaptation to toxic diet, and extinction of the Carolina parakeet. Curr Biol 30:108-114.e5, 2020. Pubmed reference: 31839456. DOI: 10.1016/j.cub.2019.10.066.

Corynorhinus townsendii (Townsend's big-eared bat) :

2023

Capel, S.L.R., Hamilton, N.M., Fraser, D., Escalona, M., Nguyen, O., Sacco, S., Sahasrabudhe, R., Seligmann, W., Vazquez, J.M., Sudmant, P.H., Morrison, M.L., Wayne, R.K., Buchalski, M.R. :

Reference genome of Townsend's big-eared bat, Corynorhinus townsendii. J Hered :esad078, 2023. Pubmed reference: 38092381. DOI: 10.1093/jhered/esad078.

Cottoperca gobio :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Cottoperca trigloides (channel bull blenny) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Coturnix japonica (Japanese quail) :

2020

Morris, K.M., Hindle, M.M., Boitard, S., Burt, D.W., Danner, A.F., Eory, L., Forrest, H.L., Gourichon, D., Gros, J., Hillier, L.W., Jaffredo, T., Khoury, H., Lansford, R., Leterrier, C., Loudon, A., Mason, A.S., Meddle, S.L., Minvielle, F., Minx, P., Pitel, F., Seiler, J.P., Shimmura, T., Tomlinson, C., Vignal, A., Webster, R.G., Yoshimura, T., Warren, W.C., Smith, J. :

The quail genome: insights into social behaviour, seasonal biology and infectious disease response. BMC Biol 18:14, 2020. Pubmed reference: 32050986. DOI: 10.1186/s12915-020-0743-4.

Cranoglanis bouderius :

2022

Xu, Y., Shao, F., Chen, W., Ni, L., Peng, Z. :

A chromosome-level genome of the helmet catfish (Cranoglanis bouderius). Front Genet 13:962406, 2022. Pubmed reference: 36035162. DOI: 10.3389/fgene.2022.962406.

Crocodylus porosus (Australian saltwater crocodile) :

2020

Ghosh, A., Johnson, M.G., Osmanski, A.B., Louha, S., Bayona-Vásquez, N.J., Glenn, T.C., Gongora, J., Green, R.E., Isberg, S., Stevens, R.D., Ray, D.A. :

A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in crocodylidae. Genome Biol Evol 12:3635-3646, 2020. Pubmed reference: 31821505. DOI: 10.1093/gbe/evz269.

2014

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449, 2014. Pubmed reference: 25504731. DOI: 10.1126/science.1254449.

Crocuta crocuta (spotted hyena) :

2023

Seeber, P.A., Palmer, Z., Schmidt, A., Chagas, A., Kitagawa, K., Marinova-Wolff, E., Tafelmaier, Y., Epp, L.S. :

Cromileptes altivelis (humpback grouper) :

2024

Liu, J., Sun, H., Tang, L., Wang, Y., Wang, Z., Mao, Y., Huang, H., Zhang, Q. :

Chromosome-level genome assembly of humpback grouper using PacBio HiFi reads and Hi-C technologies. Sci Data 11:51, 2024. Pubmed reference: 38195804. DOI: 10.1038/s41597-023-02907-4.

Crossoptilon crossoptilon (white-eared pheasant) :

2024

Wu, S., Wang, K., Dou, T., Yuan, S., Wu, D.D., Ge, C., Jia, J., Su, Z. :

High-quality genome assembly of a C. crossoptilon and related functional and genetics data resources. Sci Data 11:247, 2024. Pubmed reference: 38413610. DOI: 10.1038/s41597-024-03087-5.

Crotalus oreganus :

2023

Westeen, E.P., Escalona, M., Holding, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Perri, R., Fisher, R.N., Toffelmier, E., Shaffer, H.B., Wang, I.J. :

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex. J Hered , 2023. Pubmed reference: 37493092. DOI: 10.1093/jhered/esad045.

Cryodraco antarcticus :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Culter alburnus (topmouth culter) :

2023

Liu, K., Xie, N., Wang, Y., Liu, X. :

Cyanistes caeruleus (Blue tit) :

2010

Hansson, B., Ljungqvist, M., Dawson, DA., Mueller, JC., Olano-Marin, J., Ellegren, H., Nilsson, JA. :

Avian genome evolution: insights from a linkage map of the blue tit (Cyanistes caeruleus). Heredity 104:67-78, 2010. Pubmed reference: 19707235. DOI: 10.1038/hdy.2009.107.

Cyanocitta stelleri (Steller's jay) :

2023

Benham, P.M., Cicero, C., DeRaad, D.A., McCormack, J.E., Wayne, R.K., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., Bowie, R.C.K. :

A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri). J Hered , 2023. Pubmed reference: 37395718. DOI: 10.1093/jhered/esad042.

Cygnus atratus (black swan) :

2023

Chong, Y., Tu, X., Lu, Y., Gao, Z., He, X., Hong, J., Wu, J., Wu, D., Xi, D., Deng, W. :

Two high-quality Cygnus genome assemblies reveal genomic variations associated with plumage color. Int J Mol Sci 24:16953, 2023. Pubmed reference: 38069278. DOI: 10.3390/ijms242316953.

Cygnus olor (mute swan) :

2023

Chong, Y., Tu, X., Lu, Y., Gao, Z., He, X., Hong, J., Wu, J., Wu, D., Xi, D., Deng, W. :

Two high-quality Cygnus genome assemblies reveal genomic variations associated with plumage color. Int J Mol Sci 24:16953, 2023. Pubmed reference: 38069278. DOI: 10.3390/ijms242316953.

Cylindrophis ruffus (red cylinder snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Cynomys gunnisoni (Gunnison's prairie dog) :

2020

Tsuchiya, M.T.N., Dikow, R.B., Cassin-Sackett, L. :

First genome sequence of the Gunnison's prairie dog (Cynomys gunnisoni), a keystone species and player in the transmission of sylvatic plague. Genome Biol Evol 12:618-625, 2020. Pubmed reference: 32277812. DOI: 10.1093/gbe/evaa069.

Cyprinus carpio (common carp) :

2021

Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :

2014

Xu, P., Zhang, X., Wang, X., Li, J., Liu, G., Kuang, Y., Xu, J., Zheng, X., Ren, L., Wang, G., Zhang, Y., Huo, L., Zhao, Z., Cao, D., Lu, C., Li, C., Zhou, Y., Liu, Z., Fan, Z., Shan, G., Li, X., Wu, S., Song, L., Hou, G., Jiang, Y., Jeney, Z., Yu, D., Wang, L., Shao, C., Song, L., Sun, J., Ji, P., Wang, J., Li, Q., Xu, L., Sun, F., Feng, J., Wang, C., Wang, S., Wang, B., Li, Y., Zhu, Y., Xue, W., Zhao, L., Wang, J., Gu, Y., Lv, W., Wu, K., Xiao, J., Wu, J., Zhang, Z., Yu, J., Sun, X. :

Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet 46:1212-9, 2014. Pubmed reference: 25240282. DOI: 10.1038/ng.3098.

2013

Zhao, L., Zhang, Y., Ji, P., Zhang, X., Zhao, Z., Hou, G., Huo, L., Liu, G., Li, C., Xu, P., Sun, X. :

A dense genetic linkage map for common carp and its integration with a BAC-based physical map. PLoS One 8:e63928, 2013. Pubmed reference: 23704958. DOI: 10.1371/journal.pone.0063928.

Danio rerio (zebrafish) :

1999

Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., Talbot, W.S. :

A genetic linkage map for zebrafish: Comparative analysis and localization of genes and expressed sequences Genome Research 9:334-347, 1999. Pubmed reference: 10207156.

1998

Knapik, E.W., Goodman, A., Ekker, M., Chevrette, M., Delgado, J., Neuhauss, S., Shimoda, N., Driever, W., Fishman, M.C., Jacob, H.J. :

A microsatellite genetic linkage map for zebrafish (danio rerio) Nature Genetics 18:338-343, 1998. Pubmed reference: 9537415. DOI: 10.1038/ng0498-338.

Postlethwait, J.H., Yan, Y.L., Gates, M.A., Horne, S., Amores, A., Brownlie, A., Donovan, A., Egan, E.S., Force, A., Gong, Z.Y., Goutel, C., Fritz, A., Kelsh, R., Knapik, E., Liao, E., Paw, B., Ransom, D., Singer, A., Thomson, M., Abduljabbar, T.S., Yelick, P., Beier, D., Joly, J.S., Larhammar, D., Rosa, F., et al. :

Vertebrate genome evolution and the zebrafish gene map Nature Genetics 18:345-349, 1998. Pubmed reference: 9537416. DOI: 10.1038/ng0498-345.

1996

Johnson, S.L., Gates, M.A., Johnson, M., Talbot, W.S., Horne, S., Baik, K., Rude, S., Wong, J.R., Postlethwait, J.H. :

Centromere-linkage analysis and consolidation of the zebrafish genetic map Genetics 142:1277-1288, 1996. Pubmed reference: 8846904.

Dascyllus trimaculatus (three spot damselfish) :

2023

Roberts, M.B., Schultz, D.T., Gatins, R., Escalona, M., Bernardi, G. :

Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus. G3 (Bethesda) , 2023. Pubmed reference: 36905099. DOI: 10.1093/g3journal/jkac339.

Decapterus maruadsi (Japanese scad) :

2024

Chen, L., Zhou, Z., Zhou, Z., Yang, J., Deng, Y., Bai, Y., Pu, F., Zhou, T., Xu, P. :

Chromosome-level assembly and gene annotation of Decapterus maruadsi genome using Nanopore and Hi-C technologies. Sci Data 11:69, 2024. Pubmed reference: 38218740. DOI: 10.1038/s41597-024-02912-1.

Deinagkistrodon acutus (Chinese moccasin) :

2023

Wang, X., Liu, L., Zhu, W., Wang, S., Shi, M., Yang, S., Lu, H., Cao, J. :

Genome assembly and annotation of the sharp-nosed pit viper Deinagkistrodon acutus based on next-generation sequencing data. GigaByte 2023:gigabyte88, 2023. Pubmed reference: 37711277. DOI: 10.46471/gigabyte.88.

Delichon dasypus (Asian house martin) :

2024

Chan, Y.F., Lu, C.W., Kuo, H.C., Hung, C.M. :

A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait. G3 (Bethesda) :jkae077, 2024. Pubmed reference: 38607414. DOI: 10.1093/g3journal/jkae077.

Delphinus delphis (saddleback dolphin) :

None

[No authors listed] :

, None. Pubmed reference: 38627659.

Diadophis punctatus (Ringneck snake) :

2023

Westeen, E.P., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Fisher, R.N., Toffelmier, E., Shaffer, H.B., Wang, I.J. :

A reference genome assembly for the continentally-distributed ring-necked snake, Diadophis punctatus. J Hered , 2023. Pubmed reference: 37688363. DOI: 10.1093/jhered/esad051.

Diceros bicornis (black rhinoceros) :

2024

Kraaijeveld, K., Bossers, K., Petrusevski, N., Pieterman, S., Bruins-van Sonsbeek, L.G.R., Wittink, F. :

ONT read assembly of the black rhino genome. BMC Genom Data 25:27, 2024. Pubmed reference: 38443836. DOI: 10.1186/s12863-024-01214-0.

Dissostichus eleginoides (Patagonian toothfish) :

2024

Ryder, D., Stone, D., Minardi, D., Riley, A., Avant, J., Cross, L., Soeffker, M., Davidson, D., Newman, A., Thomson, P., Darby, C., van Aerle, R. :

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome. BMC Genomics 25:233, 2024. Pubmed reference: 38438840. DOI: 10.1186/s12864-024-10141-4.

Distichodus sexfasciatus (sixbar distichodus) :

2023

Yang, X., Song, Y., Zhang, R., Yu, M., Guo, X., Guo, H., Du, X., Sun, S., Li, C., Mao, X., Fan, G., Liu, X. :

Dolloidraco longedorsalis :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Dugong dugon (dugong) :

2024

Baker, D.N., Abueg, L., Escalona, M., Farquharson, K.A., Lanyon, J.M., Le Duc, D., Schöneberg, T., Absolon, D., Sims, Y., Fedrigo, O., Jarvis, E.D., Belov, K., Hogg, C.J., Shapiro, B. :

A chromosome-level genome assembly for the dugong (Dugong dugon). J Hered :esae003, 2024. Pubmed reference: 38245832. DOI: 10.1093/jhered/esae003.

Dysomma anguillare (shortbelly eel) :

2023

Yang, T.Y., Zhu, Z.Y., Liu, Y.P., Wang, S.G. :

The first genome-wide survey of shortbelly eel (Dysomma anguillare Barnard, 1923) to provide genomic characteristics, microsatellite markers and complete mitogenome information. Biochem Genet , 2023. Pubmed reference: 37906301. DOI: 10.1007/s10528-023-10543-1.

Elaphe carinata :

2023

Fan, J., Huang, R., Yang, D., Gong, Y., Cui, Z., Wang, X., Su, Z., Yu, J., Zhang, Y., Zhang, T., Jiang, Z., Lan, T., Wang, H., Huang, S. :

Genome assembly and annotation of the king ratsnake, Elaphe carinata. GigaByte 2023:gigabyte101, 2023. Pubmed reference: 38098688. DOI: 10.46471/gigabyte.101.

Elephantidae (elephants) :

2003

Yang, F., Alkalaeva, E.Z., Perelman, P.L., Pardini, A.T., Harrison, W.R., O'Brien, P.C., Fu, B., Graphodatsky, A.S., Ferguson-Smith, M.A., Robinson, T.J. :

Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype. Proc Natl Acad Sci U S A 100:1062-6, 2003. Pubmed reference: 12552116. DOI: 10.1073/pnas.0335540100.

Frönicke, L., Wienberg, J., Stone, G., Adams, L., Stanyon, R. :

Towards the delineation of the ancestral eutherian genome organization: comparative genome maps of human and the African elephant (Loxodonta africana) generated by chromosome painting. Proc Biol Sci 270:1331-40, 2003. Pubmed reference: 12965023. DOI: 10.1098/rspb.2003.2383.

Elephas maximus (Asiatic elephant) :

2024

Shi, M., Chen, F., Sahu, S.K., Wang, Q., Yang, S., Wang, Z., Chen, J., Liu, H., Hou, Z., Fang, S.G., Lan, T. :

Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants. Sci Data 11:63, 2024. Pubmed reference: 38212399. DOI: 10.1038/s41597-023-02729-4.

2023

Cernohorska, H., Kubickova, S., Musilova, P., Vozdova, M., Vodicka, R., Rubes, J. :

Supernumerary Marker Chromosome Identified in Asian Elephant (Elephas maximus). Animals (Basel) 13, 2023. Pubmed reference: 36830488. DOI: 10.3390/ani13040701.

Prado, N.A., Armstrong, E.E., Brown, J.L., Goldenberg, S.Z., Leimgruber, P., Pearson, V.R., Maldonado, J.E., Campana, M.G. :

Genomic resources for Asian (Elephas maximus) and African Savannah elephant (Loxodonta africana) conservation and health research. J Hered , 2023. Pubmed reference: 37246890. DOI: 10.1093/jhered/esad034.

Li, X., Wang, P., Pan, Q., Liu, G., Liu, W., Omotoso, O., Du, J., Li, Z., Yu, Y., Huang, Y., Zhu, P., Li, M., Zhou, X. :

Chromosome-level Asian elephant genome assembly and comparative genomics of long-lived mammals reveal the common substitutions for cancer resistance. Aging Cell :e13917, 2023. Pubmed reference: 37395176. DOI: 10.1111/acel.13917.

Embiotoca jacksoni (black perch) :

2022

Bernardi, G., Toy, J.A., Escalona, M., Marimuthu, M.P.A., Sahasrabudhe, R., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Miller, C., Shaffer, H.B. :

Reference genome of the black surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California kelp forest fish that lacks a pelagic larval stage. J Hered 113:657-664, 2022. Pubmed reference: 35809222. DOI: 10.1093/jhered/esac034.

Enhydra lutris (sea otter) :

2019

Beichman, A.C., Koepfli, K.P., Li, G., Murphy, W., Dobrynin, P., Kliver, S., Tinker, M.T., Murray, M.J., Johnson, J., Lindblad-Toh, K., Karlsson, E.K., Lohmueller, K.E., Wayne, R.K. :

Aquatic adaptation and depleted diversity: A deep dive into the genomes of the sea otter and giant otter. Mol Biol Evol 36:2631-2655, 2019. Pubmed reference: 31212313. DOI: 10.1093/molbev/msz101.

2017

Jones, S.J., Haulena, M., Taylor, G.A., Chan, S., Bilobram, S., Warren, R.L., Hammond, S.A., Mungall, K.L., Choo, C., Kirk, H., Pandoh, P., Ally, A., Dhalla, N., Tam, A.K.Y., Troussard, A., Paulino, D., Coope, R.J.N., Mungall, A.J., Moore, R., Zhao, Y., Birol, I., Ma, Y., Marra, M., Jones, S.J.M. :

The genome of the Northern sea otter (Enhydra lutris kenyoni). Genes (Basel) 8, 2017. Pubmed reference: 29232880. DOI: 10.3390/genes8120379.

Entelurus aequoreus (snake pipefish) :

None

[No authors listed] :

, None. Pubmed reference: 38239770.

Epinephelus awoara (yellow grouper) :

2024

Zhang, W., Yang, Y., Hua, S., Ruan, Q., Li, D., Wang, L., Wang, X., Wen, X., Liu, X., Meng, Z. :

Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara. Sci Data 11:151, 2024. Pubmed reference: 38296995. DOI: 10.1038/s41597-024-02989-8.

Eptesicus nilssonii (northern bat) :

2023

Laine, V.N., Pulliainen, A.T., Lilley, T.M. :

Reference genome for the Northern bat (Eptesicus nilssonii), a most northern bat species. J Hered , 2023. Pubmed reference: 37791665. DOI: 10.1093/jhered/esad056.

Equus asinus (ass (donkey)) :

2023

Duhan, N., Kaur, S., Kaundal, R. :

Jevit, M.J., Castaneda, C., Paria, N., Das, P.J., Miller, D., Antczak, D.F., Kalbfleisch, T.S., Davis, B.W., Raudsepp, T. :

Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep 13:20180, 2023. Pubmed reference: 37978222. DOI: 10.1038/s41598-023-47583-x.

2022

Miao, X., Yu, Y., Zhao, Z., Wang, Y., Qian, X., Wang, Y., Li, S., Wang, C. :

Chromosome-level haplotype assembly for Equus asinu. Front Genet 13:738105, 2022. Pubmed reference: 35692816. DOI: 10.3389/fgene.2022.738105.

2020

Wang, C., Li, H., Guo, Y., Huang, J., Sun, Y., Min, J., Wang, J., Fang, X., Zhao, Z., Wang, S., Zhang, Y., Liu, Q., Jiang, Q., Wang, X., Guo, Y., Yang, C., Wang, Y., Tian, F., Zhuang, G., Fan, Y., Gao, Q., Li, Y., Ju, Z., Li, J., Li, R., Hou, M., Yang, G., Liu, G., Liu, W., Guo, J., Pan, S., Fan, G., Zhang, W., Zhang, R., Yu, J., Zhang, X., Yin, Q., Ji, C., Jin, Y., Yue, G., Liu, M., Xu, J., Liu, S., Jordana, J., Noce, A., Amills, M., Wu, D.D., Li, S., Zhou, X., Zhong, J. :

Donkey genomes provide new insights into domestication and selection for coat color. Nat Commun 11:6014, 2020. Pubmed reference: 33293529. DOI: 10.1038/s41467-020-19813-7.

Equus caballus (horse) :

2023

Peng, S., Dahlgren, A.R., Donnelly, C.G., Hales, E.N., Petersen, J.L., Bellone, R.R., Kalbfleisch, T., Finno, C.J. :

Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genet 19:e1010468, 2023. Pubmed reference: 36862752. DOI: 10.1371/journal.pgen.1010468.

Tozaki, T., Ohnuma, A., Kikuchi, M., Ishige, T., Kakoi, H., Hirota, K.I., Takahashi, Y., Nagata, S.I. :

Short insertion and deletion discoveries via whole-genome sequencing of 101 Thoroughbred racehorses. Genes (Basel) 14:638, 2023. Pubmed reference: 36980910. DOI: 10.3390/genes14030638.

Gu, J., Li, S., Zhu, B., Liang, Q., Chen, B., Tang, X., Chen, C., Wu, D.D., Li, Y. :

Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing. Mol Ecol Resour , 2023. Pubmed reference: 37259205. DOI: 10.1111/1755-0998.13818.

Tozaki, T., Ohnuma, A., Kikuchi, M., Ishige, T., Kakoi, H., Hirora, K.I., Nagata, S.I. :

Use of whole-genome variants and their frequency data to estimate haplotype structure in the Thoroughbred genome. Anim Genet , 2023. Pubmed reference: 37336519. DOI: 10.1111/age.13338.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome , 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Vasoya, D., Tzelos, T., Benedictus, L., Karagianni, A.E., Pirie, S., Marr, C., Oddsdóttir, C., Fintl, C., Connelley, T. :

High-resolution genotyping of expressed equine MHC reveals a highly complex MHC structure. Genes (Basel) 14, 2023. Pubmed reference: 37510326. DOI: 10.3390/genes14071422.

Duhan, N., Kaur, S., Kaundal, R. :

Cappelletti, E., Piras, F.M., Sola, L., Santagostino, M., Petersen, J.L., Bellone, R.R., Finno, C.J., Peng, S., Kalbfleisch, T.S., Bailey, E., Nergadze, S.G., Giulotto, E. :

The localization of centromere protein A is conserved among tissues. Commun Biol 6:963, 2023. Pubmed reference: 37735603. DOI: 10.1038/s42003-023-05335-7.

Jevit, M.J., Castaneda, C., Paria, N., Das, P.J., Miller, D., Antczak, D.F., Kalbfleisch, T.S., Davis, B.W., Raudsepp, T. :

Tang, X., Zhu, B., Ren, R., Chen, B., Li, S., Gu, J. :

Genome-wide copy number variation detection in a large cohort of diverse horse breeds by whole-genome sequencing. Front Vet Sci 10:1296213, 2023. Pubmed reference: 38076560. DOI: 10.3389/fvets.2023.1296213.

2021

Peng, S., Petersen, J.L., Bellone, R.R., Kalbfleisch, T., Kingsley, N.B., Barber, A.M., Cappelletti, E., Giulotto, E., Finno, C.J. :

Decoding the equine genome: Lessons from ENCODE. Genes (Basel) 12:1707, 2021. Pubmed reference: 34828313. DOI: 10.3390/genes12111707.

Durward-Akhurst, S.A., Schaefer, R.J., Grantham, B., Carey, W.K., Mickelson, J.R., McCue, M.E. :

Genetic variation and the distribution of variant types in the horse. Front Genet 12:758366, 2021. Pubmed reference: 34925451. DOI: 10.3389/fgene.2021.758366.

2020

Beeson, S.K., Mickelson, J.R., McCue, M.E. :

Equine recombination map updated to EquCab3.0. Anim Genet 51:341-2, 2020. Pubmed reference: 31887785. DOI: 10.1111/age.12898.

Schaefer, R.J., McCue, M.E. :

Equine genotyping arrays. Vet Clin North Am Equine Pract 36:183-93, 2020. Pubmed reference: 32534852. DOI: 10.1016/j.cveq.2020.03.001.

2018

Janečka, J.E., Davis, B.W., Ghosh, S., Paria, N., Das, P.J., Orlando, L., Schubert, M., Nielsen, M.K., Stout, T.A.E., Brashear, W., Li, G., Johnson, C.D., Metz, R.P., Zadjali, A.M.A., Love, C.C., Varner, D.D., Bellott, D.W., Murphy, W.J., Chowdhary, B.P., Raudsepp, T. :

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nat Commun 9:2945, 2018. Pubmed reference: 30054462. DOI: 10.1038/s41467-018-05290-6.

Kalbfleisch, T.S., Rice, E.S., DePriest, M.S., Walenz, B.P., Hestand, M.S., Vermeesch, J.R., O Connell, B.L., Fiddes, I.T., Vershinina, A.O., Saremi, N.F., Petersen, J.L., Finno, C.J., Bellone, R.R., McCue, M.E., Brooks, S.A., Bailey, E., Orlando, L., Green, R.E., Miller, D.C., Antczak, D.F., MacLeod, J.N. :

Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol 1:197, 2018. Pubmed reference: 30456315. DOI: 10.1038/s42003-018-0199-z.

2017

Schaefer, R.J., Schubert, M., Bailey, E., Bannasch, D.L., Barrey, E., Bar-Gal, G.K., Brem, G., Brooks, S.A., Distl, O., Fries, R., Finno, C.J., Gerber, V., Haase, B., Jagannathan, V., Kalbfleisch, T., Leeb, T., Lindgren, G., Lopes, M.S., Mach, N., da Câmara Machado, A., MacLeod, J.N., McCoy, A., Metzger, J., Penedo, C., Polani, S., Rieder, S., Tammen, I., Tetens, J., Thaller, G., Verini-Supplizi, A., Wade, C.M., Wallner, B., Orlando, L., Mickelson, J.R., McCue, M.E. :

Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 18:565, 2017. Pubmed reference: 28750625. DOI: 10.1186/s12864-017-3943-8.

2012

McCue, M.E., Bannasch, D.L., Petersen, J.L., Gurr, J., Bailey, E., Binns, M.M., Distl, O., Guérin, G., Hasegawa, T., Hill, E.W., Leeb, T., Lindgren, G., Penedo, M.C., Røed, K.H., Ryder, O.A., Swinburne, J.E., Tozaki, T., Valberg, S.J., Vaudin, M., Lindblad-Toh, K., Wade, C.M., Mickelson, J.R. :

A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet 8:e1002451, 2012. Pubmed reference: 22253606. DOI: 10.1371/journal.pgen.1002451.

2010

Mittmann, E.H., Wrede, J., Pook, J., Distl, O. :

Identification of 21 781 equine microsatellites on the horse genome assembly 2.0. Anim Genet 41:222, 2010. Pubmed reference: 19793266. DOI: 10.1111/j.1365-2052.2009.01970.x.

2009

Wade, C.M., Giulotto, E., Sigurdsson, S., Zoli, M., Gnerre, S., Imsland, F., Lear, T.L., Adelson, D.L., Bailey, E., Bellone, R.R., Blöcker, H., Distl, O., Edgar, R.C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J.N., Penedo, M.C., Raison, J.M., Sharpe, T., Vogel, J., Andersson, L., Antczak, D.F., Biagi, T., Binns, M.M., Chowdhary, B.P., Coleman, S.J., Della Valle, G., Fryc, S., Guérin, G., Hasegawa, T., Hill, E.W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J.R., Murray, J., Nergadze, S.G., Onofrio, R., Pedroni, S., Piras, M.F., Raudsepp, T., Rocchi, M., Røed, K.H., Ryder, O.A., Searle, S., Skow, L., Swinburne, J.E., Syvänen, A.C., Tozaki, T., Valberg, S.J., Vaudin, M., White, J.R., Zody, M.C. :

Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326:865-7, 2009. Pubmed reference: 19892987. DOI: 10.1126/science.1178158.

2008

Raudsepp, T., Gustafson-Seabury, A., Durkin, K., Wagner, M.L., Goh, G., Seabury, C.M., Brinkmeyer-Langford, C., Lee, E.J., Agarwala, R., Stallknecht-Rice, E., Schäffer, A.A., Skow, L.C., Tozaki, T., Yasue, H., Penedo, M.C., Lyons, L.A., Khazanehdari, K.A., Binns, M.M., MacLeod, J.N., Distl, O., Guérin, G., Leeb, T., Mickelson, J.R., Chowdhary, B.P. :

A 4,103 marker integrated physical and comparative map of the horse genome. Cytogenet Genome Res 122:28-36, 2008. Pubmed reference: 18931483. DOI: 10.1159/000151313.

Chowdhary, B.P., Raudsepp, T. :

The horse genome derby: racing from map to whole genome sequence. Chromosome Res 16:109-27, 2008. Pubmed reference: 18274866. DOI: 10.1007/s10577-008-1204-z.

Brinkmeyer-Langford, C., Raudsepp, T., Gustafson-Seabury, A., Chowdhary, B.P. :

A BAC contig map over the proximal approximately 3.3 Mb region of horse chromosome 21. Cytogenet Genome Res 120:164-72, 2008. Pubmed reference: 18467843. DOI: 10.1159/000118758.

2007

Tozaki, T., Swinburne, J., Hirota, K., Hasegawa, T., Ishida, N., Tobe, T. :

Improved resolution of the comparative horse-human map: investigating markers with in silico and linkage mapping approaches. Gene 392:181-6, 2007. Pubmed reference: 17306472. DOI: 10.1016/j.gene.2006.12.018.

Goh, G., Raudsepp, T., Durkin, K., Wagner, M.L., Schäffer, A.A., Agarwala, R., Tozaki, T., Mickelson, J.R., Chowdhary, B.P. :

High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals. Genomics 89:89-112, 2007. Pubmed reference: 16916595. DOI: 10.1016/j.ygeno.2006.06.012.

2006

Dierks, C., Mömke, S., Drögemüller, C., Leeb, T., Chowdhary, B.P., Distl, O. :

A high-resolution comparative radiation hybrid map of equine chromosome 4q12-q22. Anim Genet 37:513-7, 2006. Pubmed reference: 16978184. DOI: 10.1111/j.1365-2052.2006.01510.x.

Chowdhary, B.P., Raudsepp, T. :

The horse genome. Genome Dyn 2:97-110, 2006. Pubmed reference: 18753773. DOI: 10.1159/000095098.

Leeb, T., Vogl, C., Zhu, B., de Jong, P.J., Binns, M.M., Chowdhary, B.P., Scharfe, M., Jarek, M., Nordsiek, G., Schrader, F., Blöcker, H. :

A human-horse comparative map based on equine BAC end sequences. Genomics 87:772-6, 2006. Pubmed reference: 16603334. DOI: 10.1016/j.ygeno.2006.03.002.

Perrocheau, M., Boutreux, V., Chadi, S., Mata, X., Decaunes, P., Raudsepp, T., Durkin, K., Incarnato, D., Iannuzzi, L., Lear, T.L., Hirota, K., Hasegawa, T., Zhu, B., de Jong, P., Cribiu, E.P., Chowdhary, B.P., Guérin, G. :

Construction of a medium-density horse gene map. Anim Genet 37:145-55, 2006. Pubmed reference: 16573529. DOI: 10.1111/j.1365-2052.2005.01401.x.

Wagner, M.L., Raudsepp, T., Goh, G., Agarwala, R., Schaffer, A.A., Dranchak, P.K., Brinkmeyer-Langford, C., Skow, L.C., Chowdhary, B.P., Mickelson, J.R. :

A 1.3-Mb interval map of equine homologs of HSA2. Cytogenet Genome Res 112:227-34, 2006. Pubmed reference: 16484777. DOI: 10.1159/000089875.

Swinburne, J.E., Boursnell, M., Hill, G., Pettitt, L., Allen, T., Chowdhary, B., Hasegawa, T., Kurosawa, M., Leeb, T., Mashima, S., Mickelson, J.R., Raudsepp, T., Tozaki, T., Binns, M. :

Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families. Genomics 87:1-29, 2006. Pubmed reference: 16314071. DOI: 10.1016/j.ygeno.2005.09.001.

2005

Brinkmeyer-Langford, C., Raudsepp, T., Lee, E.J., Goh, G., Schäffer, A.A., Agarwala, R., Wagner, M.L., Tozaki, T., Skow, L.C., Womack, J.E., Mickelson, J.R., Chowdhary, B.P. :

A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals. Mamm Genome 16:631-49, 2005. Pubmed reference: 16180145. DOI: 10.1007/s00335-005-0023-1.

Penedo, M.C., Millon, L.V., Bernoco, D., Bailey, E., Binns, M., Cholewinski, G., Ellis, N., Flynn, J., Gralak, B., Guthrie, A., Hasegawa, T., Lindgren, G., Lyons, L.A., Røed, K.H., Swinburne, J.E., Tozaki, T. :

International Equine Gene Mapping Workshop Report: a comprehensive linkage map constructed with data from new markers and by merging four mapping resources. Cytogenet Genome Res 111:5-15, 2005. Pubmed reference: 16093715. DOI: 10.1159/000085664.

Gustafson-Seabury, A., Raudsepp, T., Goh, G., Kata, S.R., Wagner, M.L., Tozaki, T., Mickelson, J.R., Womack, J.E., Skow, L.C., Chowdhary, B.P. :

High-resolution RH map of horse chromosome 22 reveals a putative ancestral vertebrate chromosome. Genomics 85:188-200, 2005. Pubmed reference: 15676277. DOI: 10.1016/j.ygeno.2004.10.012.

2004

Wagner, M.L., Goh, G., Wu, J.T., Morrison, L.Y., Alexander, L.J., Raudsepp, T., Skow, L.C., Chowdhary, B.P., Mickelson, J.R. :

Sixty-seven new equine microsatellite loci assigned to the equine radiation hybrid map. Anim Genet 35:484-6, 2004. Pubmed reference: 15566483. DOI: 10.1111/j.1365-2052.2004.01205.x.

Mickelson, J.R., Wagner, M.L., Goh, G., Wu, J.T., Morrison, L.Y., Alexander, L.J., Raudsepp, T., Skow, L.C., Chowdhary, B.P., Swinburne, J.E., Binns, M.M. :

Thirty-five new equine microsatellite loci assigned to genetic linkage and radiation hybrid maps. Anim Genet 35:481-4, 2004. Pubmed reference: 15566482. DOI: 10.1111/j.1365-2052.2004.01206.x.

Raudsepp, T., Santani, A., Wallner, B., Kata, S.R., Ren, C., Zhang, H.B., Womack, J.E., Skow, L.C., Chowdhary, B.P. :

A detailed physical map of the horse Y chromosome. Proc Natl Acad Sci U S A 101:9321-6, 2004. Pubmed reference: 15197257. DOI: 10.1073/pnas.0403011101.

Yang, F., Fu, B., O'Brien, P.C., Nie, W., Ryder, O.A., Ferguson-Smith, M.A. :

Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules. Chromosome Res 12:65-76, 2004. Pubmed reference: 14984103.

Lee, E.J., Raudsepp, T., Kata, S.R., Adelson, D., Womack, J.E., Skow, L.C., Chowdhary, B.P. :

A 1.4-Mb interval RH map of horse chromosome 17 provides detailed comparison with human and mouse homologues. Genomics 83:203-15, 2004. Pubmed reference: 14706449.

2003

Guérin, G., Bailey, E., Bernoco, D., Anderson, I., Antczak, D.F., Bell, K., Biros, I., Bjørnstad, G., Bowling, A.T., Brandon, R., Caetano, A.R., Cholewinski, G., Colling, D., Eggleston, M., Ellis, N., Flynn, J., Gralak, B., Hasegawa, T., Ketchum, M., Lindgren, G., Lyons, L.A., Millon, L.V., Mariat, D., Murray, J., Neau, A., Røed, K., Sandberg, K., Skow, L.C., Tammen, I., Tozaki, T., Van Dyk, E., Weiss, B., Young, A., Ziegle, J. :

The second generation of the International Equine Gene Mapping Workshop half-sibling linkage map. Anim Genet 34:161-8, 2003. Pubmed reference: 12755815.

Chowdhary, B.P., Raudsepp, T., Kata, S.R., Goh, G., Millon, L.V., Allan, V., Piumi, F., Guérin, G., Swinburne, J., Binns, M., Lear, T.L., Mickelson, J., Murray, J., Antczak, D.F., Womack, J.E., Skow, L.C. :

The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res 13:742-51, 2003. Pubmed reference: 12671008. DOI: 10.1101/gr.917503.

Swinburne, J.E., Turner, A., Alexander, L.J., Mickleson, J.R., Binns, M.M. :

Characterization and linkage map assignments for 61 new horse microsatellite loci (AHT49-109). Anim Genet 34:65-8, 2003. Pubmed reference: 12580791.

2002

O'Rourke, K. :

And coming around the track, looking promising ... the horse genome map. J Am Vet Med Assoc 221:15, 20, 2002. Pubmed reference: 12420810.

Chowdhary, B.P., Raudsepp, T., Honeycutt, D., Owens, E.K., Piumi, F., Guérin, G., Matise, T.C., Kata, S.R., Womack, J.E., Skow, L.C. :

Construction of a 5000(rad) whole-genome radiation hybrid panel in the horse and generation of a comprehensive and comparative map for ECA11. Mamm Genome 13:89-94, 2002. Pubmed reference: 11889556. DOI: 10.1007/s00335-001-2089-8.

2001

Lear, T.L., Brandon, R., Piumi, F., Terry, R.R., Guérin, G., Thomas, S., Bailey, E. :

Mapping of 31 horse genes in BACs by FISH. Chromosome Res 9:261-2, 2001. Pubmed reference: 11330401.

2000

Kiguwa, S.L., Hextall, P., Smith, A.L., Critcher, R., Swinburne, J., Millon, L., Binns, M.M., Goodfellow, P.N., McCarthy, L.C., Farr, C.J., Oakenfull, E.A. :

A horse whole-genome-radiation hybrid panel: chromosome 1 and 10 preliminary maps. Mamm Genome 11:803-5, 2000. Pubmed reference: 10967144.

Swinburne, J., Gerstenberg, C., Breen, M., Aldridge, V., Lockhart, L., Marti, E., Antczak, D., Eggleston-Stott, M., Bailey, E., Mickelson, J., Røed, K., Lindgren, G., von Haeringen, W., Guérin, G., Bjarnason, J., Allen, T., Binns, M. :

First comprehensive low-density horse linkage map based on two 3-generation, full-sibling, cross-bred horse reference families. Genomics 66:123-34, 2000. Pubmed reference: 10860657. DOI: 10.1006/geno.2000.6207.

1999

Caetano, A.R., Shiue, Y.L., Lyons, L.A., O'Brien, S.J., Laughlin, T.F., Bowling, A.T., Murray, J.D. :

A comparative gene map of the horse (Equus caballus). Genome Res 9:1239-49, 1999. Pubmed reference: 10613847.

Guérin, G., Bailey, E., Bernoco, D., Anderson, I., Antczak, D.F., Bell, K., Binns, M.M., Bowling, A.T., Brandon, R., Cholewinski, G., Cothran, E.G., Ellegren, H., Förster, M., Godard, S., Horin, P., Ketchum, M., Lindgren, G., McPartlan, H., Mériaux, J.C., Mickelson, J.R., Millon, L.V., Murray, J., Neau, A., Røed, K., Ziegle, J. :

Report of the International Equine Gene Mapping Workshop: male linkage map. Anim Genet 30:341-54, 1999. Pubmed reference: 10582279.

Shiue, Y.L., Bickel, L.A., Caetano, A.R., Millon, L.V., Clark, R.S., Eggleston, M.L., Michelmore, R., Bailey, E., Guérin, G., Godard, S., Mickelson, J.R., Valberg, S.J., Murray, J.D., Bowling, A.T. :

A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers. Anim Genet 30:1-9, 1999. Pubmed reference: 10050277.

1998

Bailey, E., Binns, M.M. :

The Horse Gene Map. ILAR J 39:171-176, 1998. Pubmed reference: 11528075.

Lindgren, G., Sandberg, K., Persson, H., Marklund, S., Breen, M., Sandgren, B., Carlstén, J., Ellegren, H. :

A primary male autosomal linkage map of the horse genome. Genome Res 8:951-66, 1998. Pubmed reference: 9750194.

Equus kiang (kiang) :

2023

Zhou, C., Zheng, X., Peng, K., Feng, K., Yue, B., Wu, Y. :

Chromosome-level genome assembly of the kiang (Equus kiang) illuminates genomic basis for its high-altitude adaptation. Integr Zool , 2023. Pubmed reference: 38151756. DOI: 10.1111/1749-4877.12795.

Equus przewalskii (Przewalski's horse) :

2024

Flack, N., Hughes, L., Cassens, J., Enriquez, M., Gebeyehu, S., Alshagawi, M., Hatfield, J., Kauffman, A., Brown, B., Klaeui, C., Mabrouk, I.F., Walls, C., Yeater, T., Rivas, A., Faulk, C. :

The genome of Przewalski's horse (Equus ferus przewalskii). bioRxiv :2024.02.20.581252, 2024. Pubmed reference: 38464182. DOI: 10.1101/2024.02.20.581252.

2023

Tang, X., Zhu, B., Ren, R., Chen, B., Li, S., Gu, J. :

Eremias argus :

2023

Li, W., Du, J., Yang, L., Liang, Q., Yang, M., Zhou, X., Du, W. :

Chromosome-level genome assembly and population genomics of Mongolian racerunner (Eremias argus) provide insights into high-altitude adaptation in lizards. BMC Biol 21:40, 2023. Pubmed reference: 36803146. DOI: 10.1186/s12915-023-01535-z.

Eretmochelys imbricata (hawksbill sea turtle) :

2023

Guo, Y., Tang, J., Zhuo, Z., Huang, J., Fu, Z., Song, J., Liu, M., Dong, Z., Wang, Z. :

The first high-quality chromosome-level genome of Eretmochelys imbricata using HiFi and Hi-C data. Sci Data 10:604, 2023. Pubmed reference: 37689728. DOI: 10.1038/s41597-023-02522-3.

Erythrura gouldiae (Gouldian finch) :

2018

Toomey, M.B., Marques, C.I., Andrade, P., Araújo, P.M., Sabatino, S., Gazda, M.A., Afonso, S., Lopes, R.J., Corbo, J.C., Carneiro, M. :

A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch. Proc Biol Sci 285:20181788, 2018. Pubmed reference: 30282656. DOI: 10.1098/rspb.2018.1788.

Eryx tataricus :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Eublepharis macularius (Leopard gecko) :

2023

Pinto, B.J., Gamble, T., Smith, C.H., Keating, S.E., Havird, J.C., Chiari, Y. :

The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly. J Hered , 2023. Pubmed reference: 36869788. DOI: 10.1093/jhered/esad016.

Eumicrotremus spinosus (Atlantic spiny lumpsucker) :

2023

Pinninti, L.R., Maurstad, M.F., Hoff, S.N.K., Kristensen, T., Noble, L.R., Jentoft, S., Fernandes, J.M.O. :

The complete mitochondrial genome of the Atlantic spiny lumpsucker Eumicrotremus spinosus (Fabricius, 1776). Mitochondrial DNA B Resour 8:364-367, 2023. Pubmed reference: 36926640. DOI: 10.1080/23802359.2023.2184649.

Eupleurogrammus muticus (smallhead hairtail) :

2024

Han, F.Y., Wu, R.X., Miao, B.B., Niu, S.F., Wang, Q.H., Liang, Z.B. :

Whole-genome sequencing analyses reveal the whip-like tail formation, innate immune evolution, and DNA repair mechanisms of Eupleurogrammus muticus. Animals (Basel) 14:434, 2024. Pubmed reference: 38338077. DOI: 10.3390/ani14030434.

Euprepiophis perlacea (Szechwan rat snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Felis catus (domestic cat) :

2023

Duhan, N., Kaur, S., Kaundal, R. :

Patterson, E.C., Lall, G.M., Neumann, R., Ottolini, B., Sacchini, F., Foster, A.P., Jobling, M.A., Wetton, J.H. :

Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing. Forensic Sci Int Genet 67:102944, 2023. Pubmed reference: 37820546. DOI: 10.1016/j.fsigen.2023.102944.

2021

de Groot, M., Anderson, H., Bauer, H., Bauguil, C., Bellone, R.R., Brugidou, R., Buckley, R.M., Dovč, P., Forman, O., Grahn, R.A., Kock, L., Longeri, M., Mouysset-Geniez, S., Qiu, J., Sofronidis, G., van der Goor, L.H.P., Lyons, L.A. :

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus). Anim Genet , 2021. Pubmed reference: 34143521. DOI: 10.1111/age.13100.

2020

Zhang, W., Schoenebeck, J.J. :

The ninth life of the cat reference genome, Felis_catus. PLoS Genet 16:e1009045, 2020. Pubmed reference: 33091014. DOI: 10.1371/journal.pgen.1009045.

Buckley, R.M., Davis, B.W., Brashear, W.A., Farias, F.H.G., Kuroki, K., Graves, T., Hillier, L.W., Kremitzki, M., Li, G., Middleton, R.P., Minx, P., Tomlinson, C., Lyons, L.A., Murphy, W.J., Warren, W.C. :

A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 16:e1008926, 2020. Pubmed reference: 33090996. DOI: 10.1371/journal.pgen.1008926.

Bredemeyer, K.R., Harris, A.J., Li, G., Zhao, L., Foley, N.M., Roelke-Parker, M., O'Brien, S.J., Lyons, L.A., Warren, W.C., Murphy, W.J. :

Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis). J Hered 112:165-73, 2020. Pubmed reference: 33305796. DOI: 10.1093/jhered/esaa057.

2019

Gandolfi, B., Alhaddad, H., Abdi, M., Bach, L.H., Creighton, E.K., Davis, B.W., Decker, J.E., Dodman, N.H., Ginns, E.I., Grahn, J.C., Grahn, R.A., Haase, B., Haggstrom, J., Hamilton, M.J., Helps, C.R., Kurushima, J.D., Lohi, H., Longeri, M., Malik, R., Meurs, K.M., Montague, M.J., Mullikin, J.C., Murphy, W.J., Nilson, S.M., Pedersen, N.C., Peterson, C.B., Rusbridge, C., Saif, R., Shelton, G.D., Warren, W.C., Wasim, M., Lyons, L.A. :

Author Correction: Applications and efficiencies of the first cat 63 K DNA array. Sci Rep 9:4664, 2019. Pubmed reference: 30858384. DOI: 10.1038/s41598-018-38073-6.

2018

Gandolfi, B., Alhaddad, H., Abdi, M., Bach, L.H., Creighton, E.K., Davis, B.W., Decker, J.E., Dodman, N.H., Grahn, J.C., Grahn, R.A., Haase, B., Haggstrom, J., Hamilton, M.J., Helps, C.R., Kurushima, J.D., Lohi, H., Longeri, M., Malik, R., Meurs, K.M., Montague, M.J., Mullikin, J.C., Murphy, W.J., Nilson, S.M., Pedersen, N.C., Peterson, C.B., Rusbridge, C., Saif, R., Shelton, D.G., Warren, W.C., Wasim, M., Lyons, L.A. :

Applications and efficiencies of the first cat 63K DNA array. Sci Rep 8:7024, 2018. Pubmed reference: 29728693. DOI: 10.1038/s41598-018-25438-0.

Author Correction: Applications and efficiencies of the first cat 63K DNA array. Sci Rep 8:8746, 2018. Pubmed reference: 29867197. DOI: 10.1038/s41598-018-26885-5.

2016

Li, G., Hillier, L.W., Grahn, R., Zimin, A.V., David, V.A., Menotti-Raymond, M., Middleton, R., Hannah, S., Hendrickson, S., Makunin, A., O'Brien, S.J., Minx, P., Wilson, R.K., Lyons, L.A., Warren, W.C., Murphy, W.J. :

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (Bethesda) , 2016. Pubmed reference: 27172201. DOI: 10.1534/g3.116.028746.

2014

Willet, C.E., Haase, B. :

An updated felCat5 SNP manifest for the Illumina Feline 63k SNP genotyping array. Anim Genet , 2014. Pubmed reference: 24804964. DOI: 10.1111/age.12169.

Tamazian, G., Simonov, S., Dobrynin, P., Makunin, A., Logachev, A., Komissarov, A., Shevchenko, A., Brukhin, V., Cherkasov, N., Svitin, A., Koepfli, K.P., Pontius, J., Driscoll, C.A., Blackistone, K., Barr, C., Goldman, D., Antunes, A., Quilez, J., Lorente-Galdos, B., Alkan, C., Marques-Bonet, T., Menotti-Raymond, M., David, V.A., Narfström, K., O'Brien, S.J. :

Annotated features of domestic cat - Felis catus genome. Gigascience 3:13, 2014. Pubmed reference: 25143822. DOI: 10.1186/2047-217X-3-13.

Montague, M.J., Li, G., Gandolfi, B., Khan, R., Aken, B.L., Searle, S.M., Minx, P., Hillier, L.W., Koboldt, D.C., Davis, B.W., Driscoll, C.A., Barr, C.S., Blackistone, K., Quilez, J., Lorente-Galdos, B., Marques-Bonet, T., Alkan, C., Thomas, G.W., Hahn, M.W., Menotti-Raymond, M., O'Brien, S.J., Wilson, R.K., Lyons, L.A., Murphy, W.J., Warren, W.C. :

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc Natl Acad Sci U S A 111:17230-5, 2014. Pubmed reference: 25385592. DOI: 10.1073/pnas.1410083111.

2012

Bach, L.H., Gandolfi, B., Grahn, J.C., Millon, L.V., Kent, M.S., Narfstrom, K., Cole, S.A., Mullikin, J.C., Grahn, R.A., Lyons, L.A. :

A high-resolution 15,000(Rad) radiation hybrid panel for the domestic cat. Cytogenet Genome Res 137:7-14, 2012. Pubmed reference: 22777158. DOI: 10.1159/000339416.

2010

Mullikin, J.C., Hansen, N.F., Shen, L., Ebling, H., Donahue, W.F., Tao, W., Saranga, D.J., Brand, A., Rubenfield, M.J., Young, A.C., Cruz, P. :

Light whole genome sequence for SNP discovery across domestic cat breeds. BMC Genomics 11:406, 2010. Pubmed reference: 20576142. DOI: 10.1186/1471-2164-11-406.

2009

Menotti-Raymond, M., David, V.A., Schäffer, A.A., Tomlin, J.F., Eizirik, E., Phillip, C., Wells, D., Pontius, J.U., Hannah, S.S., O'Brien, S.J. :

An autosomal genetic linkage map of the domestic cat, Felis silvestris catus. Genomics 93:305-13, 2009. Pubmed reference: 19059333. DOI: 10.1016/j.ygeno.2008.11.004.

2008

Borodin, P.M., Karamysheva, T.V., Rubtsov, N.B. :

[Immunofluorescent analysis of meiotic recombination and interference in the domestic cat]. Tsitologiia 50:62-6, 2008. Pubmed reference: 18409370.

O'Brien, S.J., Johnson, W., Driscoll, C., Pontius, J., Pecon-Slattery, J., Menotti-Raymond, M. :

State of cat genomics. Trends Genet 24:268-79, 2008. Pubmed reference: 18471926. DOI: 10.1016/j.tig.2008.03.004.

2007

Pontius, J.U., Mullikin, J.C., Smith, D.R., Agencourt Sequencing Team et al. :

Initial sequence and comparative analysis of the cat genome. Genome Res 17:1675-89, 2007. Pubmed reference: 17975172. DOI: 10.1101/gr.6380007.

2006

Murphy, W.J. :

The feline genome. Genome Dyn 2:60-8, 2006. Pubmed reference: 18753769. DOI: 10.1159/000095093.

2003

Menotti-Raymond, M., David, V.A., Roelke, M.E., Chen, Z.Q., Menotti, K.A., Sun, S., Schäffer, A.A., Tomlin, J.F., Agarwala, R., O'Brien, S.J., Murphy, W.J. :

Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus). J Hered 94:95-106, 2003. Pubmed reference: 12692169.

2002

O'Brien, S.J., Menotti-Raymond, M., Murphy, W.J., Yuhki, N. :

The Feline Genome Project. Annu Rev Genet 36:657-86, 2002. Pubmed reference: 12359739. DOI: 10.1146/annurev.genet.36.060602.145553.

2001

Sun, S., Murphy, W.J., Menotti-Raymond, M., O'Brien, S.J. :

Integration of the feline radiation hybrid and linkage maps. Mamm Genome 12:436-41, 2001. Pubmed reference: 11353390. DOI: 10.1007/s003350010289.

2000

Murphy, W.J., Sun, S., Chen, Z.Q., Yuhki, N., Hirschmann, D., Menotti-Raymond, M., O'Brien, S.J. :

A radiation hybrid map of the cat genome: Implications for comparative mapping Genome Research 10:691-702, 2000. Pubmed reference: 10810092.

1999

Menotti-Raymond, M., David, V.A., Lyons, L.A., Schäffer, A.A., Tomlin, J.F., Hutton, M.K., O'Brien, S.J. :

A genetic linkage map of microsatellites in the domestic cat (Felis catus). Genomics 57:9-23, 1999. Pubmed reference: 10191079. DOI: 10.1006/geno.1999.5743.

1997

Obrien, S.J., Cevario, S.J., Martenson, J.S., Thompson, M.A., Nash, W.G., Chang, E., Graves, J.A.M., Spencer, J.A., Cho, K.W., Tsujimoto, H., Lyons, L.A. :

Comparative gene mapping in the domestic cat (felis catus) Journal of Heredity 88:408-414, 1997. Pubmed reference: 9378918.

Obrien, S.J., Wienberg, J., Lyons, L.A. :

Comparative genomics - lessons from cats [Review] Trends in Genetics 13:393-399, 1997. Pubmed reference: 9351340.

1995

Rettenberger, G., Klett, C., Zechner, U., Bruch, J., Just, W., Vogel, W., Hameister, H. :

ZOO-FISH analysis - cat and human karyotypes closely resemble the putative ancestral mammalian karyotype Chromosome Research 3:479-486, 1995. Pubmed reference: 8581300.

1982

O'Brien, S.J., Nash, W.G. :

Genetic mapping in mammals: chromosome map of domestic cat. Science 216:257-65, 1982. Pubmed reference: 7063884.

Felis nigripes (black-footed cat) :

2024

Yuan, J., Kitchener, A.C., Lackey, L.B., Sun, T., Jiangzuo, Q., Tuohetahong, Y., Zhao, L., Yang, P., Wang, G., Huang, C., Wang, J., Hou, W., Liu, Y., Chen, W., Mi, D., Murphy, W.J., Li, G. :

The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids. Proc Natl Acad Sci U S A 121:e2310763120, 2024. Pubmed reference: 38165928. DOI: 10.1073/pnas.2310763120.

Ficedula :

2014

Kawakami, T., Backström, N., Burri, R., Husby, A., Olason, P., Rice, A.M., Alund, M., Qvarnström, A., Ellegren, H. :

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k SNP array. Mol Ecol Resour , 2014. Pubmed reference: 24784959. DOI: 10.1111/1755-0998.12270.

Furcifer pardalis :

2023

Xie, H., Chen, Z., Pang, S., Du, W. :

Efficient and highly continuous chromosome-level genome assembly of the first chameleon genome. Genome Biol Evol , 2023. Pubmed reference: 37481259. DOI: 10.1093/gbe/evad131.

Gadus morhua (Atlantic cod) :

2012

Ghigliotti, L., Fevolden, S.E., Cheng, C.H., Babiak, I., Dettai, A., Pisano, E. :

Karyotyping and cytogenetic mapping of Atlantic cod (Gadus morhua Linnaeus, 1758). Anim Genet 43:746-52, 2012. Pubmed reference: 22497346. DOI: 10.1111/j.1365-2052.2012.02343.x.

2009

Higgins, B., Hubert, S., Simpson, G., Stone, C., Bowman, S. :

Characterization of 155 EST-derived microsatellites from Atlantic cod (Gadus morhua) and validation for linkage mapping. Mol Ecol Resour 9:733-7, 2009. Pubmed reference: 21564732. DOI: 10.1111/j.1755-0998.2008.02475.x.

Gallus gallus (chicken) :

2024

Tan, X., Zhang, J., Dong, J., Huang, M., Li, Q., Wang, H., Bai, L., Cui, M., Zhou, Z., Yang, S., Wang, D. :

Whole-genome variants dataset of 209 local chickens from China. Sci Data 11:169, 2024. Pubmed reference: 38316816. DOI: 10.1038/s41597-024-02995-w.

Wu, S., Wang, K., Dou, T., Yuan, S., Yan, S., Xu, Z., Liu, Y., Jian, Z., Zhao, J., Zhao, R., Zi, X., Gu, D., Liu, L., Li, Q., Wu, D.D., Jia, J., Su, Z., Ge, C. :

High quality assemblies of four indigenous chicken genomes and related functional data resources. Sci Data 11:300, 2024. Pubmed reference: 38490983. DOI: 10.1038/s41597-024-03126-1.

Zhao, X., Wen, J., Zhang, X., Zhang, J., Zhu, T., Wang, H., Yang, W., Cao, G., Xiong, W., Liu, Y., Qu, C., Ning, Z., Qu, L. :

Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus). J Anim Sci Biotechnol 15:45, 2024. Pubmed reference: 38556896. DOI: 10.1186/s40104-024-01006-7.

Degalez, F., Charles, M., Foissac, S., Zhou, H., Guan, D., Fang, L., Klopp, C., Allain, C., Lagoutte, L., Lecerf, F., Acloque, H., Giuffra, E., Pitel, F., Lagarrigue, S. :

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Sci Rep 14:6588, 2024. Pubmed reference: 38504112. DOI: 10.1038/s41598-024-56705-y.

Wu, S., Wang, K., Dou, T., Yuan, S., Yan, S., Xu, Z., Liu, Y., Jian, Z., Zhao, J., Zhao, R., Zi, X., Gu, D., Liu, L., Li, Q., Wu, D.D., Jia, J., Su, Z., Ge, C. :

Author Correction: High quality assemblies of four indigenous chicken genomes and related functional data resources. Sci Data 11:354, 2024. Pubmed reference: 38589395. DOI: 10.1038/s41597-024-03203-5.

2023

Smith, J., Alfieri, J.M., Anthony, N., Arensburger, P., Athrey, G.N., Balacco, J., Balic, A., Bardou, P., Barela, P., Bigot, Y., Blackmon, H., Borodin, P.M., Carroll, R., Casono, M.C., Charles, M., Cheng, H., Chiodi, M., Cigan, L., Coghill, L.M., Crooijmans, R., Das, N., Davey, S., Davidian, A., Degalez, F., Dekkers, J.M., Derks, M., Diack, A.B., Djikeng, A., Drechsler, Y., Dyomin, A., Fedrigo, O., Fiddaman, S.R., Formenti, G., Frantz, L.A.F., Fulton, J.E., Gaginskaya, E., Galkina, S., Gallardo, R.A., Geibel, J., Gheyas, A., Godinez, C.J.P., Goodell, A., Graves, J.A.M., Griffin, D.K., Haase, B., Han, J.L., Hanotte, O., Henderson, L.J., Hou, Z.C., Howe, K., Huynh, L., Ilatsia, E., Jarvis, E., Johnson, S.M., Kaufman, J., Kelly, T., Kemp, S., Kern, C., Keroack, J.H., Klopp, C., Lagarrigue, S., Lamont, S.J., Lange, M., Lanke, A., Larkin, D.M., Larson, G., Layos, J.K.N., Lebrasseur, O., Malinovskaya, L.P., Martin, R.J., Martin Cerezo, M.L., Mason, A.S., McCarthy, F.M., McGrew, M.J., Mountcastle, J., Muhonja, C.K., Muir, W., Muret, K., Murphy, T., Ng'ang'a, I., Nishibori, M., O'Connor, R.E., Ogugo, M., Okimoto, R., Ouko, O., Patel, H.R., Perini, F., Pigozzi, M.I., Potter, K.C., Price, P.D., Reimer, C., Rice, E.S., Rocos, N., Rogers, T.F., Saelao, P., Schauer, J., Schnabel, R., Schneider, V., Simianer, H., Smith, A., Stevens, M.P., Stiers, K., Tiambo, C.K., Tixier-Boichard, M., Torgasheva, A.A., Tracey, A., Tregaskes, C.A., Vervelde, L., Wang, Y., Warren, W.C., Waters, P.D., Webb, D., Weigend, S., Wolc, A., Wright, A.E., Wright, D., Wu, Z., Yamagata, M., Yang, C., Yin, Z.T., Young, M.C., Zhang, G., Zhao, B., Zhou, H. :

Fourth report on chicken genes and chromosomes 2022. Cytogenet Genome Res , 2023. Pubmed reference: 36716736. DOI: 10.1159/000529376.

Huang, Z., Xu, Z., Bai, H., Huang, Y., Kang, N., Ding, X., Liu, J., Luo, H., Yang, C., Chen, W., Guo, Q., Xue, L., Zhang, X., Xu, L., Chen, M., Fu, H., Chen, Y., Yue, Z., Fukagawa, T., Liu, S., Chang, G., Xu, L. :

Evolutionary analysis of a complete chicken genome. Proc Natl Acad Sci U S A 120:e2216641120, 2023. Pubmed reference: 36780517. DOI: 10.1073/pnas.2216641120.

Jin, S., Jia, Y., Jiang, L., Cao, C., Ding, Y., Zhang, T., Liu, X., Li, Y., Geng, Z. :

Characteristics of the complete mitochondrial genome of Douhua chicken (Gallus gallus) and phylogenetic considerations. J Anim Sci , 2023. Pubmed reference: 36847733. DOI: 10.1093/jas/skad064.

Pan, Z., Wang, Y., Wang, M., Wang, Y., Zhu, X., Gu, S., Zhong, C., An, L., Shan, M., Damas, J., Halstead, M.M., Guan, D., Trakooljul, N., Wimmers, K., Bi, Y., Wu, S., Delany, M.E., Bai, X., Cheng, H.H., Sun, C., Yang, N., Hu, X., Lewin, H.A., Fang, L., Zhou, H. :

An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. Sci Adv 9:eade1204, 2023. Pubmed reference: 37134160. DOI: 10.1126/sciadv.ade1204.

Xiong, X., Liu, J., Rao, Y. :

Whole Genome Resequencing Helps Study Important Traits in Chickens. Genes (Basel) 14, 2023. Pubmed reference: 37372379. DOI: 10.3390/genes14061198.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome , 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Zhu, Q., Cai, Y., Xiao, C., Kong, L., Pan, X., Song, B., Song, Z. :

RNA sequencing transcriptomics and metabolomics in three poultry breeds. Sci Data 10:594, 2023. Pubmed reference: 37679362. DOI: 10.1038/s41597-023-02505-4.

Rice, E.S., Alberdi, A., Alfieri, J., Athrey, G., Balacco, J.R., Bardou, P., Blackmon, H., Charles, M., Cheng, H.H., Fedrigo, O., Fiddaman, S.R., Formenti, G., Frantz, L.A.F., Gilbert, M.T.P., Hearn, C.J., Jarvis, E.D., Klopp, C., Marcos, S., Mason, A.S., Velez-Irizarry, D., Xu, L., Warren, W.C. :

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol 21:267, 2023. Pubmed reference: 37993882. DOI: 10.1186/s12915-023-01758-0.

Zhu, F., Yin, Z.T., Zhao, Q.S., Sun, Y.X., Jie, Y.C., Smith, J., Yang, Y.Z., Burt, D.W., Hincke, M., Zhang, Z.D., Yuan, M.D., Kaufman, J., Sun, C.J., Li, J.Y., Shao, L.W., Yang, N., Hou, Z.C. :

A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Commun Biol 6:1233, 2023. Pubmed reference: 38057566. DOI: 10.1038/s42003-023-05619-y.

2019

Liu, R., Xing, S., Wang, J., Zheng, M., Cui, H., Crooijmans, R.P.M.A., Li, Q., Zhao, G., Wen, J. :

A new chicken 55K SNP genotyping array. BMC Genomics 20:410, 2019. Pubmed reference: 31117951. DOI: 10.1186/s12864-019-5736-8.

2018

Piégu, B., Arensburger, P., Guillou, F., Bigot, Y. :

But where did the centromeres go in the chicken genome models? Chromosome Res 26:297-306, 2018. Pubmed reference: 30225548. DOI: 10.1007/s10577-018-9585-0.

2014

Griffin, D., Burt, D.W. :

All chromosomes great and small: 10 years on. Chromosome Res , 2014. Pubmed reference: 24700106. DOI: 10.1007/s10577-014-9413-0.

2013

Kranis, A., Gheyas, A.A., Boschiero, C., Turner, F., Yu, L., Smith, S., Talbot, R., Pirani, A., Brew, F., Kaiser, P., Hocking, P.M., Fife, M., Salmon, N., Fulton, J., Strom, T.M., Haberer, G., Weigend, S., Preisinger, R., Gholami, M., Qanbari, S., Simianer, H., Watson, K.A., Woolliams, J.A., Burt, D.W. :

Development of a high density 600K SNP genotyping array for chicken. BMC Genomics 14:59, 2013. Pubmed reference: 23356797. DOI: 10.1186/1471-2164-14-59.

Gheyas, A.A., Burt, D.W. :

Microarray resources for genetic and genomic studies in chicken: A review. Genesis , 2013. Pubmed reference: 23468091. DOI: 10.1002/dvg.22387.

2011

Groenen, M.A., Megens, H.J., Zare, Y., Warren, W.C., Hillier, L.W., Crooijmans, R.P., Vereijken, A., Okimoto, R., Muir, W.M., Cheng, H.H. :

The development and characterization of a 60K SNP chip for chicken. BMC Genomics 12:274, 2011. Pubmed reference: 21627800. DOI: 10.1186/1471-2164-12-274.

2008

Muir, W.M., Wong, G.K., Zhang, Y., Wang, J., Groenen, M.A.M., Crooijmans, R.P.M.A., Megens, H.-J., Zhang, H.M., McKay, J.C., McLeod, S., Okimoto, R., Fulton, J.E., Settar, P., O'Sullivan, N.P., Vereijken, A., Jungerius-Rattink, A., Albers, G.A.A., Taylor Lawley, C., Delaney, M.E., Cheng, H.H. :

Review of the initial validation and characterization of a chicken 3K SNP array. Worlds Poultry Science Journal 64:219-226, 2008.

2007

Burt, D.W., White, S.J. :

Avian genomics in the 21st century. Cytogenet Genome Res 117:6-13, 2007. Pubmed reference: 17675839. DOI: 10.1159/000103159.

2006

Burt, D.W. :

The chicken genome. Genome Dyn 2:123-37, 2006. Pubmed reference: 18753775. DOI: 10.1159/000095100.

Mu, Y.S., Li, H. :

[Latest progress on the chicken genome project]. Yi Chuan 28:617-22, 2006. Pubmed reference: 16735245.

2005

Burt, D.W. :

Chicken genome: current status and future opportunities. Genome Res 15:1692-8, 2005. Pubmed reference: 16339367. DOI: 10.1101/gr.4141805.

Schmid, M., Nanda, I., Hoehn, H., Schartl, M., Haaf, T., Buerstedde, J.M., Arakawa, H., Caldwell, R.B., Weigend, S., Burt, D.W., Smith, J., Griffin, D.K., Masabanda, J.S., Groenen, M.A., Crooijmans, R.P., Vignal, A., Fillon, V., Morisson, M., Pitel, F., Vignoles, M., Garrigues, A., Gellin, J., Rodionov, A.V., Galkina, S.A., Lukina, N.A., Ben-Ari, G., Blum, S., Hillel, J., Twito, T., Lavi, U., David, L., Feldman, M.W., Delany, M.E., Conley, C.A., Fowler, V.M., Hedges, S.B., Godbout, R., Katyal, S., Smith, C., Hudson, Q., Sinclair, A., Mizuno, S. :

Second report on chicken genes and chromosomes 2005. Cytogenet Genome Res 109:415-79, 2005. Pubmed reference: 15905640. DOI: 10.1159/000084205.

2004

Wong, G.K., Liu, B., Wang, J., Zhang, Y., Yang, X., Zhang, Z., Meng, Q., Zhou, J., Li, D., Zhang, J., Ni, P., Li, S., Ran, L., Li, H., Zhang, J., Li, R., Li, S., Zheng, H., Lin, W., Li, G., Wang, X., Zhao, W., Li, J., Ye, C., Dai, M., Ruan, J., Zhou, Y., Li, Y., He, X., Zhang, Y., Wang, J., Huang, X., Tong, W., Chen, J., Ye, J., Chen, C., Wei, N., Li, G., Dong, L., Lan, F., Sun, Y., Zhang, Z., Yang, Z., Yu, Y., Huang, Y., He, D., Xi, Y., Wei, D., Qi, Q., Li, W., Shi, J., Wang, M., Xie, F., Wang, J., Zhang, X., Wang, P., Zhao, Y., Li, N., Yang, N., Dong, W., Hu, S., Zeng, C., Zheng, W., Hao, B., Hillier, L.W., Yang, S.P., Warren, W.C., Wilson, R.K., Brandström, M., Ellegren, H., Crooijmans, R.P., van der Poel, J.J., Bovenhuis, H., Groenen, M.A., Ovcharenko, I., Gordon, L., Stubbs, L., Lucas, S., Glavina, T., Aerts, A., Kaiser, P., Rothwell, L., Young, J.R., Rogers, S., Walker, B.A., van Hateren, A., Kaufman, J., Bumstead, N., Lamont, S.J., Zhou, H., Hocking, P.M., Morrice, D., de Koning, D.J., Law, A., Bartley, N., Burt, D.W., Hunt, H., Cheng, H.H., Gunnarsson, U., Wahlberg, P., Andersson, L., Kindlund, E., Tammi, M.T., Andersson, B., Webber, C., Ponting, C.P., Overton, I.M., Boardman, P.E., Tang, H., Hubbard, S.J., Wilson, S.A., Yu, J., Wang, J., Yang, H. :

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432:717-22, 2004. Pubmed reference: 15592405. DOI: 10.1038/nature03156.

Burt, D.W. :

Chicken genomics charts a path to the genome sequence. Brief Funct Genomic Proteomic 3:60-7, 2004. Pubmed reference: 15163360.

International Chicken Genome Sequencing Consortium :

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716, 2004. Pubmed reference: 15592404. DOI: 10.1038/nature03154.

Wallis, J.W., Aerts, J., Groenen, M.A., Crooijmans, R.P., Layman, D., Graves, T.A., Scheer, D.E., Kremitzki, C., Fedele, M.J., Mudd, N.K., Cardenas, M., Higginbotham, J., Carter, J., McGrane, R., Gaige, T., Mead, K., Walker, J., Albracht, D., Davito, J., Yang, S.P., Leong, S., Chinwalla, A., Sekhon, M., Wylie, K., Dodgson, J., Romanov, M.N., Cheng, H., de Jong, P.J., Osoegawa, K., Nefedov, M., Zhang, H., McPherson, J.D., Krzywinski, M., Schein, J., Hillier, L., Mardis, E.R., Wilson, R.K., Warren, W.C. :

A physical map of the chicken genome. Nature 432:761-4, 2004. Pubmed reference: 15592415. DOI: 10.1038/nature03030.

2003

Dodgson, J.B. :

Chicken genome sequence: a centennial gift to poultry genetics. Cytogenet Genome Res 102:291-6, 2003. Pubmed reference: 14970719. DOI: 75765.

2002

Smith, J., Paton, I.R., Murray, F., Crooijmans, R.P.M.A., Groenen, M.A.M., Burt, D.W. :

Comparative mapping of human Chromosome 19 with the chicken shows conserved synteny and gives an insight into chromosomal evolution Mammalian Genome 13:310-315, 2002. Pubmed reference: 12115034. DOI: 10.1007/s00335-001-3071-1.

2000

Smith, J., Paton, I.R., Bruley, C.K., Windsor, D., Burke, D., de, Leon, F.A.P., Burt, D.W. :

Integration of the genetic and physical maps of the chicken macrochromosomes Animal Genetics 31:20-27, 2000. Pubmed reference: 10690357.

Groenen, M.A.M., Cheng, H.H., Bumstead, N., Benkel, B.F., Briles, W.E., Burke, T., Burt, D.W., Crittenden, L.B., Dodgson, J., Hillel, J., Lamont, S., de, Leon, A.P., Soller, M., Takahashi, H., Vignal, A. :

A consensus linkage map of the chicken genome Genome Research 10:137-147, 2000. Pubmed reference: 10645958.

1998

Groenen, M.A.M., Crooijmans, R.P.M.A., Veenendaal, A., Cheng, H.H., Siwek, M., Vanderpoel, J.J. :

A comprehensive microsatellite linkage map of the chicken genome Genomics 49:265-274, 1998. Pubmed reference: 9598314. DOI: 10.1006/geno.1998.5225.

Burt, D.W., Cheng, H.H. :

The Chicken Gene Map. ILAR J 39:229-236, 1998. Pubmed reference: 11528082.

1997

Koi, M., Lamb, P.W., Filatov, L., Feinberg, A.P., Barrett, J.C. :

Construction of chicken x human microcell hybrids for human gene targeting Cytogenetics & Cell Genetics 76:72-76, 1997.

1996

Crooijmans, R.P.M.A., Vanoers, P.A.M., Strijk, J.A., Vanderpoel, J.J., Groenen, M.A.M. :

Preliminary linkage map of the chicken (gallus domesticus) genome based on microsatellite markers - 77 new markers mapped Poultry Science 75:746-754, 1996. Pubmed reference: 8737840.

Crittenden, L.B., Bitgood, J.J., Burt, D.W., Deleon, F.A.P., Tixierboichard, M. :

Nomenclature for naming loci, alleles, linkage groups and chromosomes to be used in poultry genome publications and databases Genetics Selection Evolution 28:289-297, 1996.

1995

Burt, D.W., Bumstead, N., Bitgood, J.J., Deleon, F.A.P., Crittenden, L.B. :

Chicken genome mapping: A new era in avian genetics Trends in Genetics 11:190-194, 1995. Pubmed reference: 7785078.

Cheng, H.H., Levin, I., Vallejo, R.L., Khatib, H., Dodgson, J.B., Crittenden, L.B., Hillel, J. :

Development of a genetic map of the chicken with markers of high utility Poultry Science 74:1855-1874, 1995. Pubmed reference: 8614694.

1994

Levin, I., Santangelo, L., Cheng, H., Crittenden, L.B., Dodgson, J.B. :

An Autosomal Genetic Linkage Map of the Chicken Journal of Heredity 85:79-85, 1994. Pubmed reference: 7910177.

Beattie, C.W. :

Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.

1992

Bumstead, N., Palyga, J. :

A Preliminary Linkage Map of the Chicken Genome Genomics 13:690-697, 1992. Pubmed reference: 1353476.

1990

Bitgood, J.J., Somes, R.G. Jr :

Linkage relationships and gene mapping. In "Poultry Breeding and Genetics" (ed. R.D. Crawford), Elsevier, Amsterdam; Chapter 21 :469-495, 1990.

1949

Warren, DC. :

Linkage relations of autosomal factors in the fowl. Genetics 34:333-50, 1949. Pubmed reference: 17247319.

1933

Hutt, F.B. :

Genetics of the fowl. II. a four-gene autosomal linkage group. Genetics 18:82-94, 1933. Pubmed reference: 17246679.

Warren, D.C. :

Nine independently inherited autosomal factors in the domestic fowl. Genetics 18:68-81, 1933. Pubmed reference: 17246678.

1928

Serebrovsky, A.S., Petrov, S.G. :

A case of close autosomal linkage in the fowl Journal of Heredity 19:305-306, 1928.

1921

Haldane, J.B.S. :

Linkage in poultry. Science 54:663 only, 1921. Pubmed reference: 17816160. DOI: 10.1126/science.54.1409.663.

Gavialis gangeticus (Gharial) :

2014

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449, 2014. Pubmed reference: 25504731. DOI: 10.1126/science.1254449.

Giraffa camelopardalis tippelskirchi :

2019

Farré, M., Li, Q., Darolti, I., Zhou, Y., Damas, J., Proskuryakova, A.A., Kulemzina, A.I., Chemnick, L.G., Kim, J., Ryder, O.A., Ma, J., Graphodatsky, A.S., Zhang, G., Larkin, D.M., Lewin, H.A. :

An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). Gigascience 8, 2019. Pubmed reference: 31367745. DOI: 10.1093/gigascience/giz090.

Globicephala macrorhynchus (short-finned pilot whale) :

2023

Kang, H., Liu, Q., Seim, I., Zhang, W., Li, H., Gao, H., Lin, W., Lin, M., Zhang, P., Zhang, Y., Gao, H., Wang, Y., Qin, Y., Liu, M., Dong, L., Yang, Z., Zhang, Y., Han, L., Fan, G., Li, S. :

A genome and single-nucleus cerebral cortex transcriptome atlas of the short-finned pilot whale Globicephala macrorhynchus. Mol Ecol Resour , 2023. Pubmed reference: 36826393. DOI: 10.1111/1755-0998.13775.

Gloydius shedaoensis (Shedao Island pitviper) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Gobionotothen gibberifrons (humped rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Gopherus evgoodei (Goodes thornscrub tortoise) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Gorsachius magnificus :

2024

Zheng, C., Chen, Q., Huang, S., Song, W., Chen, G., Lin, H., Xu, C., Qian, X., Cheng, Y., Jiang, A., Fan, Z., Liu, Y. :

Chromosome-scale genome assembly of the critically endangered white-eared night-heron (Gorsachius magnificus). Sci Data 11:73, 2024. Pubmed reference: 38228677. DOI: 10.1038/s41597-023-02894-6.

Gouania willdenowi (blunt-snouted clingfish) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Gymnodraco acuticeps :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Gymnothorax reevesii (Reeve's moray) :

2023

Zhang, K., Huang, Y., Zhang, Y., Liang, R., Li, Q., Li, R., Zhao, X., Bian, C., Chen, Y., Wu, J., Shi, Q., Lin, L. :

A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii). Sci Data 10:501, 2023. Pubmed reference: 37516767. DOI: 10.1038/s41597-023-02394-7.

Harpagifer antarcticus (Antarctic spiny plunderfish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Heloderma suspectum (Gila monster) :

2024

Webster, T.H., Vannan, A., Pinto, B.J., Denbrock, G., Morales, M., Dolby, G.A., Fiddes, I.T., DeNardo, D.F., Wilson, M.A. :

Lack of dosage balance and incomplete dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly. Genome Biol Evol :evae018, 2024. Pubmed reference: 38319079. DOI: 10.1093/gbe/evae018.

2023

Webster, T.H., Vannan, A., Pinto, B.J., Denbrock, G., Morales, M., Dolby, G.A., Fiddes, I.T., DeNardo, D.F., Wilson, M.A. :

Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly. bioRxiv , 2023. Pubmed reference: 37163099. DOI: 10.1101/2023.04.26.538436.

Hemiscyllium ocellatum (epaulette shark) :

2023

Sendell-Price, A.T., Tulenko, F.J., Pettersson, M., Kang, D., Montandon, M., Winkler, S., Kulb, K., Naylor, G.P., Phillippy, A., Fedrigo, O., Mountcastle, J., Balacco, J.R., Dutra, A., Dale, R.E., Haase, B., Jarvis, E.D., Myers, G., Burgess, S.M., Currie, P.D., Andersson, L., Schartl, M. :

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Nat Commun 14:6628, 2023. Pubmed reference: 37857613. DOI: 10.1038/s41467-023-42238-x.

Hepsetus odoe (African pike characin) :

2023

Yang, X., Song, Y., Zhang, R., Yu, M., Guo, X., Guo, H., Du, X., Sun, S., Li, C., Mao, X., Fan, G., Liu, X. :

Heterocephalus glaber (naked mole-rat) :

2023

Romanenko, S.A., Kliver, S.F., Serdyukova, N.A., Perelman, P.L., Trifonov, V.A., Seluanov, A., Gorbunova, V., Azpurua, J., Pereira, J.C., Ferguson-Smith, M.A., Graphodatsky, A.S. :

Hippoglossus hippoglossus (Atlantic halibut) :

2023

Weise, E.M., Van Wyngaarden, M., Den Heyer, C., Mills Flemming, J., Kess, T., Einfeldt, A.L., Fisher, J.A.D., Ditta, R., Pare, G., Ruzzante, D.E. :

SNP Panel and Genomic Sex Identification in Atlantic Halibut (Hippoglossus hippoglossus). Mar Biotechnol (NY) , 2023. Pubmed reference: 37351707. DOI: 10.1007/s10126-023-10227-2.

Histiodraco velifer :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Hydrophis curtus (Shaw's sea snake) :

2023

Ludington, A.J., Hammond, J.M., Breen, J., Deveson, I.W., Sanders, K.L. :

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 21:284, 2023. Pubmed reference: 38066641. DOI: 10.1186/s12915-023-01772-2.

Hydrophis major (olive-headed seasnake) :

2023

Ludington, A.J., Hammond, J.M., Breen, J., Deveson, I.W., Sanders, K.L. :

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 21:284, 2023. Pubmed reference: 38066641. DOI: 10.1186/s12915-023-01772-2.

Hydrophis ornatus (reef sea snake) :

2023

Ludington, A.J., Hammond, J.M., Breen, J., Deveson, I.W., Sanders, K.L. :

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 21:284, 2023. Pubmed reference: 38066641. DOI: 10.1186/s12915-023-01772-2.

Hylobates moloch (silvery gibbon) :

2023

Escalona, M., VanCampen, J., Maurer, N.W., Haukness, M., Okhovat, M., Harris, R.S., Watwood, A., Hartley, G.A., O'Neill, R.J., Medvedev, P., Makova, K.D., Vollmers, C., Carbone, L., Green, R.E. :

Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J Hered 114:35-43, 2023. Pubmed reference: 36146896. DOI: 10.1093/jhered/esac043.

Ictalurus furcatus (blue catfish) :

2023

Waldbieser, G.C., Liu, S., Yuan, Z., Older, C.E., Gao, D., Shi, C., Bosworth, B.G., Li, N., Bao, L., Kirby, M.A., Jin, Y., Wood, M.L., Scheffler, B., Simpson, S., Youngblood, R.C., Duke, M.V., Ballard, L., Phillippy, A., Koren, S., Liu, Z. :

Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biol 21:67, 2023. Pubmed reference: 37013528. DOI: 10.1186/s12915-023-01556-8.

Ictalurus punctatus (channel catfish) :

2023

Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biol 21:67, 2023. Pubmed reference: 37013528. DOI: 10.1186/s12915-023-01556-8.

2019

Zhang, S., Zhang, X., Chen, X., Xu, T., Wang, M., Qin, Q., Zhong, L., Jiang, H., Zhu, X., Liu, H., Shao, J., Zhu, Z., Shi, Q., Bian, W., You, X. :

Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus). Front Genet 10:251, 2019. Pubmed reference: 30984241. DOI: 10.3389/fgene.2019.00251.

Labeo rohita (rohu) :

2020

Das, P., Sahoo, L., Das, S.P., Bit, A., Joshi, C.G., Kushwaha, B., Kumar, D., Shah, T.M., Hinsu, A.T., Patel, N., Patnaik, S., Agarwal, S., Pandey, M., Srivastava, S., Meher, P.K., Jayasankar, P., Koringa, P.G., Nagpure, N.S., Kumar, R., Singh, M., Iquebal, M.A., Jaiswal, S., Kumar, N., Raza, M., Das Mahapatra, K., Jena, J. :

De novo assembly and genome-wide SNP discovery in rohu carp, Labeo rohita. Front Genet 11:386, 2020. Pubmed reference: 32373166. DOI: 10.3389/fgene.2020.00386.

Lagopus muta (rock ptarmigan) :

2023

Squires, T.E., Rödin-Mörch, P., Formenti, G., Tracey, A., Abueg, L., Brajuka, N., Jarvis, E., Halapi, E.C., Melsted, P., Höglund, J., Magnússon, K.P. :

A chromosome-level genome assembly for the rock ptarmigan (Lagopus muta). G3 (Bethesda) , 2023. Pubmed reference: 37141262. DOI: 10.1093/g3journal/jkad099.

Lamprotornis superbus (superb starling) :

2021

Rubenstein, D.R., Corvelo, A., MacManes, M.D., Maia, R., Narzisi, G., Rousaki, A., Vandenabeele, P., Shawkey, M.D., Solomon, J. :

Feather gene expression elucidates the developmental basis of plumage iridescence in African starlings. J Hered 112:417-429, 2021. Pubmed reference: 33885791. DOI: 10.1093/jhered/esab014.

Lateolabrax maculatus :

2024

Sun, Z., Li, S., Liu, Y., Li, W., Liu, K., Cao, X., Lin, J., Wang, H., Wang, Q., Shao, C. :

Telomere-to-telomere gapless genome assembly of the Chinese sea bass (Lateolabrax maculatus). Sci Data 11:175, 2024. Pubmed reference: 38326339. DOI: 10.1038/s41597-024-02988-9.

Laterallus jamaicensis :

2023

Hall, L.A., Wang, I.J., Escalona, M., Beraut, E., Sacco, S., Sahasrabudhe, R., Nguyen, O., Toffelmier, E., Shaffer, H.B., Beissinger, S.R. :

Reference genome of the black rail, Laterallus jamaicensis. J Hered , 2023. Pubmed reference: 37119047. DOI: 10.1093/jhered/esad025.

[No authors listed] :

Correction to: Reference genome of the black rail. J Hered , 2023. Pubmed reference: 37354561. DOI: 10.1093/jhered/esad038.

Lemur catta (Ring-tailed lemur) :

2022

Palmada-Flores, M., Orkin, J.D., Haase, B., Mountcastle, J., Bertelsen, M.F., Fedrigo, O., Kuderna, L.F.K., Jarvis, E.D., Marques-Bonet, T. :

A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). Gigascience 11, 2022. Pubmed reference: 35365833. DOI: 10.1093/gigascience/giac026.

Lepidonotothen larseni (painted notie) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Lepidonotothen nudifrons (yellowfin notie) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Lepidonotothen squamifrons (grey rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Lepisosteus osseus (longnose gar) :

2023

Mallik, R., Carlson, K.B., Wcisel, D.J., Fisk, M., Yoder, J.A., Dornburg, A. :

A chromosome level genome assembly of longnose gar, Lepisosteus osseus. G3 (Bethesda) , 2023. Pubmed reference: 37119803. DOI: 10.1093/g3journal/jkad095.

Leptotyphlops nigroterminus :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Leucoraja erinacea (little skate) :

2023

Marlétaz, F., de la Calle-Mustienes, E., Acemel, R.D., Paliou, C., Naranjo, S., Martínez-García, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.E., González-Rajal, Á., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldón, T., Nakamura, T., Tena, J.J., Lupiáñez, D.G., Rokhsar, D.S., Gómez-Skarmeta, J.L. :

The little skate genome and the evolutionary emergence of wing-like fins. Nature 616:495-503, 2023. Pubmed reference: 37046085. DOI: 10.1038/s41586-023-05868-1.

Litoria serrata (green-eyed treefrog) :

2023

Bertola, L.V., Hoskin, C.J., Jones, D.B., Zenger, K.R., McKnight, D.T., Higgie, M. :

The first linkage map for Australo-Papuan treefrogs (family: Pelodryadidae) reveals the sex-determination system of the green-eyed treefrog (Litoria serrata). Heredity (Edinb) , 2023. Pubmed reference: 37542195. DOI: 10.1038/s41437-023-00642-5.

Lophura swinhoii (Swinhoe's pheasant) :

2023

Xu, X., Wang, C., Xu, C., Yuan, J., Wang, G., Wu, Y., Huang, C., Jing, H., Yang, P., Xu, L., Peng, S., Shan, F., Xia, X., Jin, F., Hou, F., Wang, J., Mi, D., Ren, Y., Liu, Y., Irwin, D.M., Li, X., Chen, W., Li, G. :

Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii). Mol Ecol Resour , 2023. Pubmed reference: 37955396. DOI: 10.1111/1755-0998.13896.

Loxodonta africana (African savanna elephant) :

2024

Shi, M., Chen, F., Sahu, S.K., Wang, Q., Yang, S., Wang, Z., Chen, J., Liu, H., Hou, Z., Fang, S.G., Lan, T. :

Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants. Sci Data 11:63, 2024. Pubmed reference: 38212399. DOI: 10.1038/s41597-023-02729-4.

2023

Prado, N.A., Armstrong, E.E., Brown, J.L., Goldenberg, S.Z., Leimgruber, P., Pearson, V.R., Maldonado, J.E., Campana, M.G. :

Lynx canadensis (Canada lynx) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Lynx rufus (bobcat) :

2022

Lin, M., Escalona, M., Sahasrabudhe, R., Nguyen, O., Beraut, E., Buchalski, M.R., Wayne, R.K. :

A reference genome assembly of the bobcat, Lynx rufus. J Hered 113:615-623, 2022. Pubmed reference: 35696092. DOI: 10.1093/jhered/esac031.

Macaca cyclopis (Taiwan macaque) :

2023

Chiu, K.P., Stuart, L., Ooi, H.S., Yu, J., Smith, D.G., Pei, K.J. :

Genome sequencing and application of Taiwanese macaque Macaca cyclopis. Sci Rep 13:11545, 2023. Pubmed reference: 37460589. DOI: 10.1038/s41598-023-38402-4.

Macaca mulatta (Rhesus monkey) :

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

2022

Rogers, J. :

Genomic resources for rhesus macaques (Macaca mulatta). Mamm Genome , 2022. Pubmed reference: 34999909. DOI: 10.1007/s00335-021-09922-z.

Macropodus opercularis (paradise fish) :

2023

Fodor, E., Okendo, J., Szabó, N., Szabó, K., Czimer, D., Tarján-Rácz, A., Szeverényi, I., Low, B.W., Liew, J.H., Koren, S., Rhie, A., Orbán, L., Miklósi, Á., Varga, M., Burgess, S.M. :

The reference genome of the paradise fish (Macropodus opercularis). bioRxiv , 2023. Pubmed reference: 37609174. DOI: 10.1101/2023.08.10.552018.

Mandrillus sphinx (mandrill) :

2020

Yin, Y., Yang, T., Liu, H., Huang, Z., Zhang, Y., Song, Y., Wang, W., Guang, X., Sahu, S.K., Kristiansen, K. :

The draft genome of mandrill (Mandrillus sphinx): An Old World monkey. Sci Rep 10:2431, 2020. Pubmed reference: 32051450. DOI: 10.1038/s41598-020-59110-3.

Manidae (pangolins) :

2023

Houck, M.L., Koepfli, K.P., Hains, T., Khan, R., Charter, S.J., Fronczek, J.A., Misuraca, A.C., Kliver, S., Perelman, P.L., Beklemisheva, V., Graphodatsky, A., Luo, S.J., O'Brien, S.J., Lim, N.T., Chin, J.S.C., Guerra, V., Tamazian, G., Omer, A., Weisz, D., Kaemmerer, K., Sturgeon, G., Gaspard, J., Hahn, A., McDonough, M., Garcia-Treviño, I., Gentry, J., Coke, R.L., Janecka, J.E., Harrigan, R.J., Tinsman, J., Smith, T.B., Aiden, E.L., Dudchenko, O. :

Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. Chromosome Res 31:13, 2023. Pubmed reference: 37043058. DOI: 10.1007/s10577-023-09722-y.

Manis gigantea (giant pangolin) :

2023

Heighton, S.P., Allio, R., Murienne, J., Salmona, J., Meng, H., Scornavacca, C., Bastos, A.D.S., Njiokou, F., Pietersen, D.W., Tilak, M.K., Luo, S.J., Delsuc, F., Gaubert, P. :

Pangolin genomes offer key insights and resources for the world's most trafficked wild mammals. Mol Biol Evol 40, 2023. Pubmed reference: 37794645. DOI: 10.1093/molbev/msad190.

Mastacembelus armatus (zig-zag eel) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Meda fulgida (spikedace) :

2023

Alexandre, N.M., Cameron, A.C., Tian, D., Chatla, K., Kolora, S.R.R., Whiteman, N.K., Turner, T.F., Reinthal, P.N. :

Chromosome-level reference genomes of two imperiled desert fishes: Spikedace (Meda fulgida) and Loach Minnow (Tiaroga cobitis). G3 (Bethesda) , 2023. Pubmed reference: 37466215. DOI: 10.1093/g3journal/jkad157.

Megalobrama amblycephala (Wuchang bream) :

2021

Liu, H., Chen, C., Lv, M., Liu, N., Hu, Y., Zhang, H., Enbody, E.D., Gao, Z., Andersson, L., Wang, W. :

A Chromosome-Level Assembly of Blunt Snout Bream (Megalobrama amblycephala) Genome Reveals an Expansion of Olfactory Receptor Genes in Freshwater Fish. Mol Biol Evol 38:4238-4251, 2021. Pubmed reference: 34003267. DOI: 10.1093/molbev/msab152.

Meleagris gallopavo (turkey) :

2022

Barros, C.P., Derks, M.F.L., Mohr, J., Wood, B.J., Crooijmans, R.P.M.A., Megens, H.J., Bink, M.C.A.M., Groenen, M.A.M. :

A new haplotype-resolved turkey genome to enable turkey genetics and genomics research. Gigascience 12, 2022. Pubmed reference: 37489751. DOI: 10.1093/gigascience/giad051.

2010

Aslam, ML., Bastiaansen, JW., Crooijmans, RP., Vereijken, A., Megens, HJ., Groenen, MA. :

A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes. BMC Genomics 11:647, 2010. Pubmed reference: 21092123. DOI: 10.1186/1471-2164-11-647.

Dalloul, R.A., Long, J.A., Zimin, A.V., Aslam, L., Beal, K., Blomberg, L.e. .A.n.n., Bouffard, P., Burt, D.W., Crasta, O., Crooijmans, R.P., Cooper, K., Coulombe, R.A., De, S., Delany, M.E., Dodgson, J.B., Dong, J.J., Evans, C., Frederickson, K.M., Flicek, P., Florea, L., Folkerts, O., Groenen, M.A., Harkins, T.T., Herrero, J., Hoffmann, S., Megens, H.J., Jiang, A., de Jong, P., Kaiser, P., Kim, H., Kim, K.W., Kim, S., Langenberger, D., Lee, M.K., Lee, T., Mane, S., Marcais, G., Marz, M., McElroy, A.P., Modise, T., Nefedov, M., Notredame, C., Paton, I.R., Payne, W.S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Ruffier, M., Salzberg, S.L., Schatz, M.C., Scheuring, C., Schmidt, C.J., Schroeder, S., Searle, S.M., Smith, E.J., Smith, J., Sonstegard, T.S., Stadler, P.F., Tafer, H., Tu, Z.J., Van Tassell, C.P., Vilella, A.J., Williams, K.P., Yorke, J.A., Zhang, L., Zhang, H.B., Zhang, X., Zhang, Y., Reed, K.M. :

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 8, 2010. Pubmed reference: 20838655. DOI: 10.1371/journal.pbio.1000475.

2007

Reed, KM., Chaves, LD., Mendoza, KM. :

An integrated and comparative genetic map of the turkey genome. Cytogenet Genome Res 119:113-26, 2007. Pubmed reference: 18160790. DOI: 10.1159/000109627.

2005

Reed, KM., Chaves, LD., Hall, MK., Knutson, TP., Harry, DE. :

A comparative genetic map of the turkey genome. Cytogenet Genome Res 111:118-27, 2005. Pubmed reference: 16103652. DOI: 10.1159/000086380.

2003

Harry, DE., Zaitlin, D., Marini, PJ., Reed, KM. :

A first-generation map of the turkey genome. Genome 46:914-24, 2003. Pubmed reference: 14608408. DOI: 10.1139/g03-042.

1999

Huang, H.B., Song, Y.Q., Hsel, M., Zahorchak, R., Chiu, J., Teuscher, C., Smith, E.J. :

Development and characterization of genetic mapping resources for the turkey (Meleagris gallopavo) Journal of Heredity 90:240-242, 1999. Pubmed reference: 9987934.

1990

Bitgood, J.J., Somes, R.G. Jr :

Linkage relationships and gene mapping. In "Poultry Breeding and Genetics" (ed. R.D. Crawford), Elsevier, Amsterdam; Chapter 21 :469-495, 1990.

Melopsittacus undulatus (budgerigar) :

2014

Ganapathy, G., Howard, J.T., Ward, J.M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D.C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J.R., Koren, S., Warren, W.C., Zhang, G., Phillippy, A.M., Jarvis, E.D. :

High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience 3:11, 2014. Pubmed reference: 25061512. DOI: 10.1186/2047-217X-3-11.

Melospiza melodia (song sparrow) :

2024

Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., King, B.L., Thomas, W.K., Kovach, A.I., Nachman, M.W., Bowie, R.C.K. :

Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery. Genome Biol Evol :evae067, 2024. Pubmed reference: 38566597. DOI: 10.1093/gbe/evae067.

Meriones unguiculatus (Mongolian gerbil) :

2023

Brekke, T.D., Papadopulos, A.S.T., Julià, E., Fornas, O., Fu, B., Yang, F., de la Fuente, R., Page, J., Baril, T., Hayward, A., Mulley, J.F. :

A new chromosome-assigned Mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome. Mol Biol Evol , 2023. Pubmed reference: 37183864. DOI: 10.1093/molbev/msad115.

Mesocricetus auratus (golden hamster) :

2022

Lee, Y.Y., Cal-Kayitmazbatir, S., Francey, L.J., Bahiru, M.S., Hayer, K.E., Wu, G., Zeller, M.J., Roberts, R., Speers, J., Koshalek, J., Berres, M.E., Bittman, E.L., Hogenesch, J.B. :

duper is a null mutation of cryptochrome 1 in Syrian hamsters. Proc Natl Acad Sci U S A 119:e2123560119, 2022. Pubmed reference: 35471909. DOI: 10.1073/pnas.2123560119.

1997

Okuizumi, H., Ohsumi, T., Sasaki, N., Imoto, H., Mizuno, Y., Hanami, T., Yamashita, H., Kamiya, M., Takada, S., Kitamura, A., Muramatsu, M., Nishimura, M., Mori, M., Matsuda, Y., Tagaya, O., Okazaki, Y., Hayashizaki, Y. :

Linkage map of syrian hamster with restriction landmark genomic scanning Mammalian Genome 8:121-128, 1997. Pubmed reference: 9060411.

Monodelphis domestica (gray short-tailed opossum) :

2007

Mikkelsen, T.S., Wakefield, M.J., Aken, B., Amemiya, C.T., Chang, J.L., Duke, S., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S.M., Sharpe, T., Baker, M.L., Batzer, M.A., Benos, P.V., Belov, K., Clamp, M., Cook, A., Cuff, J., Das, R., Davidow, L., Deakin, J.E., Fazzari, M.J., Glass, J.L., Grabherr, M., Greally, J.M., Gu, W., Hore, T.A., Huttley, G.A., Kleber, M., Jirtle, R.L., Koina, E., Lee, J.T., Mahony, S., Marra, M.A., Miller, R.D., Nicholls, R.D., Oda, M., Papenfuss, A.T., Parra, Z.E., Pollock, D.D., Ray, D.A., Schein, J.E., Speed, T.P., Thompson, K., VandeBerg, J.L., Wade, C.M., Walker, J.A., Waters, P.D., Webber, C., Weidman, J.R., Xie, X., Zody, M.C. :

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167-77, 2007. Pubmed reference: 17495919. DOI: 10.1038/nature05805.

Moschus moschiferus (Siberian musk deer) :

2020

Yi, L., Dalai, M., Su, R., Lin, W., Erdenedalai, M., Luvsantseren, B., Chimedtseren, C., Wang, Z., Hasi, S. :

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features. BMC Genomics 21:108, 2020. Pubmed reference: 32005147. DOI: 10.1186/s12864-020-6495-2.

Mugil cephalus (flathead mullet) :

2022

Shekhar, M.S., Katneni, V.K., Jangam, A.K., Krishnan, K., Prabhudas, S.K., Jani Angel, J.R., Sukumaran, K., Kailasam, M., Jena, J. :

First report of chromosome-level genome assembly for flathead grey mullet, Mugil cephalus (Linnaeus, 1758). Front Genet 13:911446, 2022. Pubmed reference: 35783261. DOI: 10.3389/fgene.2022.911446.

Muscicapa striata (spotted flycatcher) :

2023

Baudrin, G., Pons, J.M., Bed'Hom, B., Gil, L., Boyer, R., Dusabyinema, Y., Jiguet, F., Fuchs, J. :

A reference genome assembly for the Spotted Flycatcher (Muscicapa striata). Genome Biol Evol , 2023. Pubmed reference: 37506263. DOI: 10.1093/gbe/evad140.

Mustela lutreola (European mink) :

2023

Skorupski, J., Brandes, F., Seebass, C., Festl, W., Śmietana, P., Balacco, J., Jain, N., Tilley, T., Abueg, L., Wood, J., Sims, Y., Formenti, G., Fedrigo, O., Jarvis, E.D. :

Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761. Int J Mol Sci 24, 2023. Pubmed reference: 37834264. DOI: 10.3390/ijms241914816.

Mustela nigripes (black-footed ferret) :

2023

Kliver, S., Houck, M.L., Perelman, P.L., Totikov, A., Tomarovsky, A., Dudchenko, O., Omer, A.D., Colaric, Z., Weisz, D., Aiden, E.L., Chan, S., Hastie, A., Komissarov, A., Ryder, O.A., Graphodatsky, A., Johnson, W.E., Maldonado, J.E., Pukazhenthi, B.S., Marinari, P.E., Wildt, D.E., Koepfli, K.P. :

Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). J Hered , 2023. Pubmed reference: 37249392. DOI: 10.1093/jhered/esad035.

Mycteria americana (wood stork) :

2023

Flamio, R., Ramstad, K.M. :

Chromosome-level genome of the wood stork (Mycteria americana) provides insight into avian chromosome evolution. J Hered :esad077, 2023. Pubmed reference: 38079393. DOI: 10.1093/jhered/esad077.

Myotis yumanensis :

2023

Curti, J., Fraser, D., Escalona, M., Fairbairn, C.W., Sacco, S., Sahasrabudhe, R., Nguyen, O., Seligmann, W., Sudmant, P.H., Toffelmier, E., Vazquez, J.M., Wayne, R., Shaffer, H.B., Buchalski, M.R. :

A genome assembly of the Yuma myotis bat, Myotis yumanensis. J Hered , 2023. Pubmed reference: 37712349. DOI: 10.1093/jhered/esad053.

Myrmecobius fasciatus (numbat) :

2022

Peel, E., Silver, L., Brandies, P., Hayakawa, T., Belov, K., Hogg, C.J. :

Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial. GigaByte 2022:gigabyte47, 2022. Pubmed reference: 36824518. DOI: 10.46471/gigabyte.47.

Naja atra (Chinese cobra) :

2023

Wang, J., Wu, Y., Wang, S., Mu, W., Zeng, W., Chen, X., Jiang, K., Yang, L., Hu, G., He, F. :

The genome assembly and annotation of the Chinese cobra, Naja atra. GigaByte 2023:gigabyte99, 2023. Pubmed reference: 38033372. DOI: 10.46471/gigabyte.99.

Neosalanx taihuensis :

2023

Zhou, Y., Zhang, X., Jian, J., Wang, C., Fang, D., Jiang, S., Ren, L., Ge, Y., Wang, H., You, Y., Chen, C. :

Gap-free genome assembly of Salangid icefish Neosalanx taihuensis. Sci Data 10:768, 2023. Pubmed reference: 37925542. DOI: 10.1038/s41597-023-02677-z.

Neovison vison (American mink) :

2024

Davoudi, P., Do, D.N., Colombo, S., Rathgeber, B., Sargolzaei, M., Plastow, G., Wang, Z., Hu, G., Valipour, S., Miar, Y. :

Genome-wide association studies for economically important traits in mink using copy number variation. Sci Rep 14:24, 2024. Pubmed reference: 38167844. DOI: 10.1038/s41598-023-50497-3.

Davoudi, P., Do, D.N., Rathgeber, B., Colombo, S., Sargolzaei, M., Plastow, G., Wang, Z., Miar, Y. :

Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data. J Anim Breed Genet , 2024. Pubmed reference: 38389405. DOI: 10.1111/jbg.12859.

2017

Cai, Z., Petersen, B., Sahana, G., Madsen, L.B., Larsen, K., Thomsen, B., Bendixen, C., Lund, M.S., Guldbrandtsen, B., Panitz, F. :

The first draft reference genome of the American mink (Neovison vison). Sci Rep 7:14564, 2017. Pubmed reference: 29109430. DOI: 10.1038/s41598-017-15169-z.

2012

Anistoroaei, R., Nielsen, V., Markakis, M.N., Karlskov-Mortensen, P., Jørgensen, C.B., Christensen, K., Fredholm, M. :

A re-assigned American mink (Neovison vison) map optimal for genome-wide studies. Gene 511:66-72, 2012. Pubmed reference: 22982743. DOI: 10.1016/j.gene.2012.08.033.

2009

Anistoroaei, R., Ansari, S., Farid, A., Benkel, B., Karlskov-Mortensen, P., Christensen, K. :

An extended anchored linkage map and virtual mapping for the American mink genome based on homology to human and dog. Genomics 94:204-10, 2009. Pubmed reference: 19520153. DOI: 10.1016/j.ygeno.2009.05.014.

2007

Anistoroaei, R., Menzorov, A., Serov, O., Farid, A., Christensen, K. :

The first linkage map of the American mink (Mustela vison). Anim Genet 38:384-8, 2007. Pubmed reference: 17596125. DOI: 10.1111/j.1365-2052.2007.01621.x.

1987

Serov, O.L., Gradov, A.A., Rubtsov, N.B., Zhdanova, N.S., Pack, S.D., Sukoyan, M.A., Mullakandov, M.R., Zakijan, S.M. :

Genetic map of the American mink: gene conservation and organization of chromosomes. Isozymes Curr Top Biol Med Res 15:179-215, 1987. Pubmed reference: 3298154.

Nestor notabilis (Kea) :

2014

Zhang, G., Li, C., Li, Q., Li, B., Larkin, D.M., Lee, C., Storz, J.F., Antunes, A., Greenwold, M.J., Meredith, R.W., Ödeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H., Yang, W., Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Wang, J., Fan, Y., da Fonseca, R.R., Alfaro-Núñez, A., Schubert, M., Orlando, L., Mourier, T., Howard, J.T., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, M.V., Hara, E., Smith, J., Farré, M., Narayan, J., Slavov, G., Romanov, M.N., Borges, R., Machado, J.P., Khan, I., Springer, M.S., Gatesy, J., Hoffmann, F.G., Opazo, J.C., Håstad, O., Sawyer, R.H., Kim, H., Kim, K.W., Kim, H.J., Cho, S., Li, N., Huang, Y., Bruford, M.W., Zhan, X., Dixon, A., Bertelsen, M.F., Derryberry, E., Warren, W., Wilson, R.K., Li, S., Ray, D.A., Green, R.E., O'Brien, S.J., Griffin, D., Johnson, W.E., Haussler, D., Ryder, O.A., Willerslev, E., Graves, G.R., Alström, P., Fjeldså, J., Mindell, D.P., Edwards, S.V., Braun, E.L., Rahbek, C., Burt, D.W., Houde, P., Zhang, Y., Yang, H., Wang, J. :

Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311-20, 2014. Pubmed reference: 25504712. DOI: 10.1126/science.1251385.

Notiomystis cincta :

2023

Bailey, S., Guhlin, J., Senanayake, D.S., Scherer, P., Brekke, P., Ewen, J.G., Santure, A.W., Whibley, A. :

Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics. Mol Ecol Resour , 2023. Pubmed reference: 37332137. DOI: 10.1111/1755-0998.13823.

Notothenia rossii (marbled rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Numida meleagris (helmeted guineafowl) :

2019

Vignal, A., Boitard, S., Thebault, N., Dayo, G.K., Yapi-Gnaore, V., Youssao, I., Berthouly-Salazar, C., Pálinkás-Bodzsár, N., Guémené, D., Thibaud-Nissen, F., Warren, W.C., Tixier-Boichard, M., Rognon, X. :

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour , 2019. Pubmed reference: 30945415. DOI: 10.1111/1755-0998.13017.

Nyctereutes procyonoides (raccoon dog) :

2021

Chueca, L.J., Kochmann, J., Schell, T., Greve, C., Janke, A., Pfenninger, M., Klimpel, S. :

De novo genome assembly of the raccoon dog (Nyctereutes procyonoides). Front Genet 12:658256, 2021. Pubmed reference: 33995489. DOI: 10.3389/fgene.2021.658256.

Ochotona princeps (American pika) :

2021

Sjodin, B.M.F., Galbreath, K.E., Lanier, H.C., Russello, M.A. :

Chromosome-level reference genome assembly for the American pika (Ochotona princeps). J Hered 112:549-557, 2021. Pubmed reference: 34036348. DOI: 10.1093/jhered/esab031.

2016

Fontanesi, L., Di Palma, F., Flicek, P., Smith, A.T., Thulin, C.G., Alves, P.C. :

LaGomiCs-Lagomorph Genomics Consortium: An international collaborative effort for sequencing the genomes of an entire mammalian order. J Hered 107:295-308, 2016. Pubmed reference: 26921276. DOI: 10.1093/jhered/esw010.

Octopus vulgaris (common octopus) :

2023

Destanovik, D., Schultz, D.T., Styfhals, R., Cruz, F., Gómez-Garrido, J., Gut, M., Gut, I., Fiorito, G., Simakov, O., Alioto, T.S., Ponte, G., Seuntjens, E. :

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797). G3 (Bethesda) , 2023. Pubmed reference: 37850903. DOI: 10.1093/g3journal/jkad220.

Odocoileus virginianus (white-tailed deer) :

2022

London, E.W., Roca, A.L., Novakofski, J.E., Mateus-Pinilla, N.E. :

A de novo chromosome-level genome assembly of the white-tailed deer, Odocoileus virginianus. J Hered 113:479-489, 2022. Pubmed reference: 35511871. DOI: 10.1093/jhered/esac022.

Odontamblyopus rebecca :

2024

Lü, Z., Yu, Z., Luo, W., Liu, T., Wang, Y., Liu, Y., Liu, J., Liu, B., Gong, L., Liu, L., Li, Y. :

Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca). Sci Data 11:160, 2024. Pubmed reference: 38307872. DOI: 10.1038/s41597-024-02997-8.

Odontobutis potamophila :

2017

Zhang, H., Huang, L., Yin, S., Zhang, G., Ding, Y., Zang, X. :

High-density SNP-based genetic map for Odontobutis potamophila. Anim Genet 48:126-127, 2017. Pubmed reference: 27476504. DOI: 10.1111/age.12471.

Oenanthe hispanica melanoleuca :

2023

Peona, V., Palacios-Gimenez, O.M., Lutgen, D., Olsen, R.A., Alaei Kakhki, N., Andriopoulos, P., Bontzorlos, V., Schweizer, M., Suh, A., Burri, R. :

An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca). G3 (Bethesda) , 2023. Pubmed reference: 37097035. DOI: 10.1093/g3journal/jkad088.

Okapia johnstoni (okapi) :

2022

Winter, S., Coimbra, R.T.F., Helsen, P., Janke, A. :

A Chromosome-Scale Genome Assembly of the Okapi (Okapia johnstoni). J Hered 113:568-576, 2022. Pubmed reference: 35788365. DOI: 10.1093/jhered/esac033.

Oncorhynchus keta (chum salmon) :

2023

Rondeau, E.B., Christensen, K.A., Johnson, H.A., Sakhrani, D., Biagi, C.A., Wetklo, M., Despins, C.A., Leggatt, R.A., Minkley, D.R., Withler, R.E., Beacham, T.D., Koop, B.F., Devlin, R.H. :

Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function. G3 (Bethesda) , 2023. Pubmed reference: 37293843. DOI: 10.1093/g3journal/jkad127.

Oncorhynchus mykiss (rainbow trout) :

2022

Bernard, M., Dehaullon, A., Gao, G., Paul, K., Lagarde, H., Charles, M., Prchal, M., Danon, J., Jaffrelo, L., Poncet, C., Patrice, P., Haffray, P., Quillet, E., Dupont-Nivet, M., Palti, Y., Lallias, D., Phocas, F. :

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Front Genet 13:941340, 2022. Pubmed reference: 35923696. DOI: 10.3389/fgene.2022.941340.

2015

Palti, Y., Gao, G., Liu, S., Kent, M.P., Lien, S., Miller, M.R., Rexroad, C.E., Moen, T. :

The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout. Mol Ecol Resour 15:662-72, 2015. Pubmed reference: 25294387. DOI: 10.1111/1755-0998.12337.

2014

Berthelot, C., Brunet, F., Chalopin, D., Juanchich, A., Bernard, M., Noël, B., Bento, P., Da Silva, C., Labadie, K., Alberti, A., Aury, J.M., Louis, A., Dehais, P., Bardou, P., Montfort, J., Klopp, C., Cabau, C., Gaspin, C., Thorgaard, G.H., Boussaha, M., Quillet, E., Guyomard, R., Galiana, D., Bobe, J., Volff, J.N., Genêt, C., Wincker, P., Jaillon, O., Roest Crollius, H., Guiguen, Y. :

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun 5:3657, 2014. Pubmed reference: 24755649. DOI: 10.1038/ncomms4657.

2012

Guyomard, R., Boussaha, M., Krieg, F., Hervet, C., Quillet, E. :

A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts. BMC Genet 13:15, 2012. Pubmed reference: 22424132. DOI: 10.1186/1471-2156-13-15.

2011

Palti, Y., Genet, C., Luo, M.C., Charlet, A., Gao, G., Hu, Y., Castaño-Sánchez, C., Tabet-Canale, K., Krieg, F., Yao, J., Vallejo, R.L., Rexroad, C.E. :

A first generation integrated map of the rainbow trout genome. BMC Genomics 12:180, 2011. Pubmed reference: 21473775. DOI: 10.1186/1471-2164-12-180.

2009

Phillips, R.B., Keatley, K.A., Morasch, M.R., Ventura, A.B., Lubieniecki, K.P., Koop, B.F., Danzmann, R.G., Davidson, W.S. :

Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss). BMC Genet 10:46, 2009. Pubmed reference: 19689812. DOI: 10.1186/1471-2156-10-46.

2006

Guyomard, R., Mauger, S., Tabet-Canale, K., Martineau, S., Genet, C., Krieg, F., Quillet, E. :

A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 7:302, 2006. Pubmed reference: 17137492. DOI: 10.1186/1471-2164-7-302.

2000

Sakamoto, T., Danzmann, R.G., Gharbi, K., Howard, P., Ozaki, A., Khoo, S.K., Woram, R.A., Okamoto, N., Ferguson, M.M., Holm, L.E., Guyomard, R., Hoyheim, B. :

A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates Genetics 155:1331-1345, 2000. Pubmed reference: 10880492.

1998

Young, W.P., Wheeler, P.A., Coryell, V.H., Keim, P., Thorgaard, G.H. :

A detailed linkage map of rainbow trout produced using doubled haploids Genetics 148:839-850, 1998. Pubmed reference: 9504929.

Oncorhynchus nerka (sockeye salmon) :

2012

Everett, M.V., Miller, M.R., Seeb, J.E. :

Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics 13:521, 2012. Pubmed reference: 23031582. DOI: 10.1186/1471-2164-13-521.

Oplegnathus fasciatus (barred knifejaw) :

2021

Bai, Y., Gong, J., Zhou, Z., Li, B., Zhao, J., Ke, Q., Zou, X., Pu, F., Wu, L., Zheng, W., Zhou, T., Xu, P. :

Chromosome-level assembly of the Southern Rock Bream (Oplegnathus fasciatus) genome using PacBio and Hi-C technologies. Front Genet 12:811798, 2021. Pubmed reference: 34992639. DOI: 10.3389/fgene.2021.811798.

Orcinus orca (killer whale) :

2023

Foote, A.D., Alexander, A., Ballance, L.T., Constantine, R., Galletti Vernazzani Muñoz, B., Guinet, C., Robertson, K.M., Sinding, M.S., Sironi, M., Tixier, P., Totterdell, J., Towers, J.R., Wellard, R., Pitman, R.L., Morin, P.A. :

"Type D" killer whale genomes reveal long-term small population size and low genetic diversity. J Hered 114:94-109, 2023. Pubmed reference: 36971118. DOI: 10.1093/jhered/esac070.

Oreochromis mossambicus (Mozambique tilapia) :

2021

Tao, W., Cao, J., Xiao, H., Zhu, X., Dong, J., Kocher, T.D., Lu, M., Wang, D. :

A chromosome-level genome assembly of Mozambique tilapia (Oreochromis mossambicus) reveals the structure of sex determining regions. Front Genet 12:796211, 2021. Pubmed reference: 34956335. DOI: 10.3389/fgene.2021.796211.

Oreochromis mossambicus x Oreochromis niloticus :

2022

Etherington, G.J., Nash, W., Ciezarek, A., Mehta, T.K., Barria, A., Peñaloza, C., Khan, M.G.Q., Durrant, A., Forrester, N., Fraser, F., Irish, N., Kaithakottil, G.G., Lipscombe, J., Trong, T., Watkins, C., Swarbreck, D., Angiolini, E., Cnaani, A., Gharbi, K., Houston, R.D., Benzie, J.A.H., Haerty, W. :

Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus. BMC Genomics 23:832, 2022. Pubmed reference: 36522771. DOI: 10.1186/s12864-022-09065-8.

Oreochromis niloticus (Nile tilapia) :

2011

Lee, B.Y., Coutanceau, J.P., Ozouf-Costaz, C., D'Cotta, H., Baroiller, J.F., Kocher, T.D. :

Genetic and physical mapping of sex-linked AFLP markers in Nile tilapia (Oreochromis niloticus). Mar Biotechnol (NY) 13:557-62, 2011. Pubmed reference: 20953654. DOI: 10.1007/s10126-010-9326-7.

2005

Lee, B.Y., Lee, W.J., Streelman, J.T., Carleton, K.L., Howe, A.E., Hulata, G., Slettan, A., Stern, J.E., Terai, Y., Kocher, T.D. :

A second-generation genetic linkage map of tilapia (Oreochromis spp.). Genetics 170:237-44, 2005. Pubmed reference: 15716505. DOI: 10.1534/genetics.104.035022.

2004

Ezaz, M.T., Harvey, S.C., Boonphakdee, C., Teale, A.J., McAndrew, B.J., Penman, D.J. :

Isolation and physical mapping of sex-linked AFLP markers in nile tilapia (Oreochromis niloticus L.). Mar Biotechnol (NY) 6:435-45, 2004. Pubmed reference: 15791488. DOI: 10.1007/s10126-004-3004-6.

2000

McConnell, S.K., Beynon, C., Leamon, J., Skibinski, D.O. :

Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed. Anim Genet 31:214-8, 2000. Pubmed reference: 10895314.

1998

Kocher, T.D., Lee, W.J., Sobolewska, H., Penman, D., McAndrew, B. :

A genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus). Genetics 148:1225-32, 1998. Pubmed reference: 9539437.

Ornithorhynchus anatinus (platypus) :

2021

Zhou, Y., Shearwin-Whyatt, L., Li, J., Song, Z., Hayakawa, T., Stevens, D., Fenelon, J.C., Peel, E., Cheng, Y., Pajpach, F., Bradley, N., Suzuki, H., Nikaido, M., Damas, J., Daish, T., Perry, T., Zhu, Z., Geng, Y., Rhie, A., Sims, Y., Wood, J., Haase, B., Mountcastle, J., Fedrigo, O., Li, Q., Yang, H., Wang, J., Johnston, S.D., Phillippy, A.M., Howe, K., Jarvis, E.D., Ryder, O.A., Kaessmann, H., Donnelly, P., Korlach, J., Lewin, H.A., Graves, J., Belov, K., Renfree, M.B., Grutzner, F., Zhou, Q., Zhang, G. :

Platypus and echidna genomes reveal mammalian biology and evolution. Nature 592:756-762, 2021. Pubmed reference: 33408411. DOI: 10.1038/s41586-020-03039-0.

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

2018

Martin, H.C., Batty, E.M., Hussin, J., Westall, P., Daish, T., Kolomyjec, S., Piazza, P., Bowden, R., Hawkins, M., Grant, T., Moritz, C., Grutzner, F., Gongora, J., Donnelly, P. :

Insights into Platypus Population Structure and History from Whole-Genome Sequencing. Mol Biol Evol 35:1238-1252, 2018. Pubmed reference: 29688544. DOI: 10.1093/molbev/msy041.

Orycteropus afer (aardvark) :

2003

Yang, F., Alkalaeva, E.Z., Perelman, P.L., Pardini, A.T., Harrison, W.R., O'Brien, P.C., Fu, B., Graphodatsky, A.S., Ferguson-Smith, M.A., Robinson, T.J. :

Oryctolagus cuniculus (rabbit) :

2023

Ballan, M., Bovo, S., Bertolini, F., Schiavo, G., Schiavitto, M., Negrini, R., Fontanesi, L. :

Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds. J Anim Breed Genet 140:663-678, 2023. Pubmed reference: 37435689. DOI: 10.1111/jbg.12818.

2021

Yang, N., Zhao, B., Chen, Y., D'Alessandro, E., Chen, C., Ji, T., Wu, X., Song, C. :

Distinct retrotransposon evolution profile in the genome of rabbit (Oryctolagus cuniculus). Genome Biol Evol 13, 2021. Pubmed reference: 34270728. DOI: 10.1093/gbe/evab168.

2018

Zhou, L., Xiao, Q., Bi, J., Wang, Z., Li, Y. :

RabGTD: a comprehensive database of rabbit genome and transcriptome. Database (Oxford) 2018, 2018. Pubmed reference: 30010730. DOI: 10.1093/database/bay075.

2016

Fontanesi, L., Di Palma, F., Flicek, P., Smith, A.T., Thulin, C.G., Alves, P.C. :

2015

Sternstein, I., Reissmann, M., Maj, D., Bieniek, J., Brockmann, G.A. :

A comprehensive linkage map and QTL map for carcass traits in a cross between Giant Grey and New Zealand White rabbits. BMC Genet 16:16, 2015. Pubmed reference: 25887754. DOI: 10.1186/s12863-015-0168-1.

2014

Carneiro, M., Rubin, C.J., Di Palma, F., Albert, F.W., Alföldi, J., Martinez Barrio, A., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., Younis, S., Afonso, S., Aken, B., Alves, J.M., Barrell, D., Bolet, G., Boucher, S., Burbano, H.A., Campos, R., Chang, J.L., Duranthon, V., Fontanesi, L., Garreau, H., Heiman, D., Johnson, J., Mage, R.G., Peng, Z., Queney, G., Rogel-Gaillard, C., Ruffier, M., Searle, S., Villafuerte, R., Xiong, A., Young, S., Forsberg-Nilsson, K., Good, J.M., Lander, E.S., Ferrand, N., Lindblad-Toh, K., Andersson, L. :

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345:1074-1079, 2014. Pubmed reference: 25170157. DOI: 10.1126/science.1253714.

Lohmueller, K.E. :

Evolution. On the origin of Peter Rabbit. Science 345:1000-1, 2014. Pubmed reference: 25170135. DOI: 10.1126/science.1258775.

2012

Fontanesi, L., Martelli, P.L., Scotti, E., Russo, V., Rogel-Gaillard, C., Casadio, R., Vernesi, C. :

Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization. Genomics 100:245-51, 2012. Pubmed reference: 22800765. DOI: 10.1016/j.ygeno.2012.07.001.

1983

Soulié, J., de Grouchy, J. :

New gene assignments in the rabbit (Oryctolagus cuniculus). Comparison with other species. Hum Genet 63:48-52, 1983. Pubmed reference: 6572613. DOI: 10.1007/BF00285397.

1941

Castle, W.E., Sawin, P.B. :

Genetic linkage in the rabbit. Proc Natl Acad Sci U S A 27:519-23, 1941. Pubmed reference: 16588495.

1936

Castle, W.E. :

Further Data on Linkage in Rabbits. Proc Natl Acad Sci U S A 22:222-5, 1936. Pubmed reference: 16577699.

Oryzias latipes (Japanese medaka) :

1999

Ohtsuka, M., Makino, S., Yoda, K., Wada, H., Naruse, K., Mitani, H., Shima, A., Ozato, K., Kimura, M., Inoko, H. :

Construction of a linkage map of the medaka (Oryzias latipes) and mapping of the Da mutant locus defective in dorsoventral patterning Genome Research 9:1277-1287, 1999. Pubmed reference: 10613850.

Oryzias melastigma (Indian medaka) :

2020

Liang, P., Saqib, H.S.A., Ni, X., Shen, Y. :

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). BMC Genomics 21:640, 2020. Pubmed reference: 32938378. DOI: 10.1186/s12864-020-07042-7.

Oryzias sinensis (Chinese medaka) :

2024

Dong, Z., Wang, J., Chen, G., Guo, Y., Zhao, N., Wang, Z., Zhang, B. :

A high-quality chromosome-level genome assembly of the Chinese medaka Oryzias sinensis. Sci Data 11:322, 2024. Pubmed reference: 38548787. DOI: 10.1038/s41597-024-03173-8.

Ostrea denselamellosa :

2023

Dong, Z., Bai, Y., Liu, S., Yu, H., Kong, L., Du, S., Li, Q. :

A chromosome-level genome assembly of Ostrea denselamellosa provides initial insights into its evolution. Genomics :110582, 2023. Pubmed reference: 36796653. DOI: 10.1016/j.ygeno.2023.110582.

Otis tarda (great bustard) :

2023

Luo, H., Jiang, X., Li, B., Wu, J., Shen, J., Xu, Z., Zhou, X., Hou, M., Huang, Z., Ou, X., Xu, L. :

A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes). Commun Biol 6:746, 2023. Pubmed reference: 37463976. DOI: 10.1038/s42003-023-05137-x.

Otocolobus manul (Pallas's cat) :

2023

Flack, N., Drown, M., Walls, C., Pratte, J., McLain, A., Faulk, C. :

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform 5:lqad033, 2023. Pubmed reference: 37025970. DOI: 10.1093/nargab/lqad033.

Ovibos moschatus (muskox) :

2023

Li, M., Li, X., Wu, Z., Zhang, G., Wang, N., Dou, M., Liu, S., Yang, C., Meng, G., Sun, H., Hvilsom, C., Xie, G., Li, Y., Li, Z.H., Wang, W., Jiang, Y., Heller, R., Wang, Y. :

Convergent molecular evolution of thermogenesis and circadian rhythm in Arctic ruminants. Proc Biol Sci 290:20230538, 2023. Pubmed reference: 37253422. DOI: 10.1098/rspb.2023.0538.

Ovis aries (sheep) :

2024

Qiao, G., Xu, P., Guo, T., He, X., Yue, Y., Yang, B. :

Genome-wide detection of structural variation in some sheep breeds using whole-genome long-read sequencing data. J Anim Breed Genet , 2024. Pubmed reference: 38247268. DOI: 10.1111/jbg.12846.

Li, M., Lu, Y., Gao, Z., Yue, D., Hong, J., Wu, J., Xi, D., Deng, W., Chong, Y. :

Pan-Omics in sheep: Unveiling genetic landscapes. Animals (Basel) 14:273, 2024. Pubmed reference: 38254442. DOI: 10.3390/ani14020273.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., Zhang, Y., Dai, X., Gao, Y., Zhang, Z., Fang, W., Yang, Y., Fu, W., Cao, C., Yang, P., Ghanatsaman, Z.A., Negari, N.J., Nanaei, H.A., Yue, X., Song, Y., Lan, X., Deng, W., Wang, X., Pan, C., Xiang, R., Ibeagha-Awemu, E.M., Heslop-Harrison, P.J.S., Rosen, B.D., Lenstra, J.A., Gan, S., Jiang, Y. :

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Res 33:463-477, 2023. Pubmed reference: 37310928. DOI: 10.1101/gr.277372.122.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome , 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Woolley, S.A., Salavati, M., Clark, E.L. :

Recent advances in the genomic resources for sheep. Mamm Genome , 2023. Pubmed reference: 37752302. DOI: 10.1007/s00335-023-10018-z.

Xie, S., Isaacs, K., Becker, G., Murdoch, B.M. :

A computational framework for improving genetic variants identification from 5,061 sheep sequencing data. J Anim Sci Biotechnol 14:127, 2023. Pubmed reference: 37779189. DOI: 10.1186/s40104-023-00923-3.

2022

Davenport, K.M., Bickhart, D.M., Worley, K., Murali, S.C., Salavati, M., Clark, E.L., Cockett, N.E., Heaton, M.P., Smith, T.P.L., Murdoch, B.M., Rosen, B.D. :

An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome. Gigascience 11, 2022. Pubmed reference: 35134925. DOI: 10.1093/gigascience/giab096.

Lv, F.H., Cao, Y.H., Liu, G.J., Luo, L.Y., Lu, R., Liu, M.J., Li, W.R., Zhou, P., Wang, X.H., Shen, M., Gao, L., Yang, J.Q., Yang, H., Yang, Y.L., Liu, C.B., Wan, P.C., Zhang, Y.S., Pi, W.H., Ren, Y.L., Shen, Z.Q., Wang, F., Wang, Y.T., Li, J.Q., Salehian-Dehkordi, H., Hehua, E., Liu, Y.G., Chen, J.F., Wang, J.K., Deng, X.M., Esmailizadeh, A., Dehghani-Qanatqestani, M., Charati, H., Nosrati, M., Štěpánek, O., Rushdi, H.E., Olsaker, I., Curik, I., Gorkhali, N.A., Paiva, S.R., Caetano, A.R., Ciani, E., Amills, M., Weimann, C., Erhardt, G., Amane, A., Mwacharo, J.M., Han, J.L., Hanotte, O., Periasamy, K., Johansson, A.M., Hallsson, J.H., Kantanen, J., Coltman, D.W., Bruford, M.W., Lenstra, J.A., Li, M.H. :

Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression, and agronomically important loci. Mol Biol Evol 39:msab353, 2022. Pubmed reference: 34893856. DOI: 10.1093/molbev/msab353.

Qiao, G., Xu, P., Guo, T., Wu, Y., Lu, X., Zhang, Q., He, X., Zhu, S., Zhao, H., Lei, Z., Sun, W., Yang, B., Yue, Y. :

Genetic basis of Dorper sheep (Ovis aries) revealed by long-Read de novo genome assembly. Front Genet 13:846449, 2022. Pubmed reference: 35480318. DOI: 10.3389/fgene.2022.846449.

2021

Salehian-Dehkordi, H., Xu, Y.X., Xu, S.S., Li, X., Luo, L.Y., Liu, Y.J., Wang, D.F., Cao, Y.H., Shen, M., Gao, L., Chen, Z.H., Glessner, J.T., Lenstra, J.A., Esmailizadeh, A., Li, M.H., Lv, F.H. :

Genome-wide detection of copy number variations and their association with distinct phenotypes in the world's sheep. Front Genet 12:670582, 2021. Pubmed reference: 34093663. DOI: 10.3389/fgene.2021.670582.

Wang, Z.H., Zhu, Q.H., Li, X., Zhu, J.W., Tian, D.M., Zhang, S.S., Kang, H.L., Li, C.P., Dong, L.L., Zhao, W.M., Li, M.H. :

iSheep: an integrated resource for sheep genome, variant and phenotype. Front Genet 12:714852, 2021. Pubmed reference: 34490043. DOI: 10.3389/fgene.2021.714852.

2020

Salavati, M., Caulton, A., Clark, R., Gazova, I., Smith, T.P.L., Worley, K.C., Cockett, N.E., Archibald, A.L., Clarke, S.M., Murdoch, B.M., Clark, E.L. :

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0). Front Genet 11:580580, 2020. Pubmed reference: 33193703. DOI: 10.3389/fgene.2020.580580.

2014

Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J.F., Faraut, T., Wu, C., Muzny, D.M., Li, Y., Zhang, W., Stanton, J.A., Brauning, R., Barris, W.C., Hourlier, T., Aken, B.L., Searle, S.M.J., Adelson, D.L., Bian, C., Cam, G.R., Chen, Y., Cheng, S., DeSilva, U., Dixen, K., Dong, Y., Fan, G., Franklin, I.R., Fu, S., Guan, R., Highland, M.A., Holder, M.E., Huang, G., Ingham, A.B., Jhangiani, S.N., Kalra, D., Kovar, C.L., Lee, S.L., Liu, W., Liu, X., Lu, C., Lv, T., Mathew, T., McWilliam, S., Menzies, M., Pan, S., Robelin, D., Servin, B., Townley, D., Wang, W., Wei, B., White, S.N., Yang, X., Ye, C., Yue, Y., Zeng, P., Zhou, Q., Hansen, J.B., Kristensen, K., Gibbs, R.A., Flicek, P., Warkup, C.C., Jones, H.E., Oddy, V.H., Nicholas, F.W., McEwan, J.C., Kijas, J., Wang, J., Worley, K.C., Archibald, A.L., Cockett, N., Xu, X., Wang, W., Dalrymple, B.P. :

The sheep genome illuminates biology of the rumen and lipid metabolism. Science 344:1168-1173, 2014. Pubmed reference: 24904168. DOI: 10.1126/science.1252806.

2010

International Sheep Genomics Consortium, Archibald, A.L., Cockett, N.E., Dalrymple, B.P., Faraut, T., Kijas, J.W., Maddox, J.F., McEwan, J.C., Oddy, V.H., Raadsma, H.W., Wade, C., Wang, J., Wang, W., Xun, X. :

The sheep genome reference sequence: a work in progress. Anim Genet 41:449-53, 2010. Pubmed reference: 20809919. DOI: 10.1111/j.1365-2052.2010.02100.x.

2007

Dalrymple, B.P., Kirkness, E.F., Nefedov, M., McWilliam, S., Ratnakumar, A., Barris, W., Zhao, S., Shetty, J., Maddox, J.F., O'Grady, M., Nicholas, F., Crawford, A.M., Smith, T., de Jong, P.J., McEwan, J., Oddy, V.H., Cockett, N.E. :

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biol 8:R152, 2007. Pubmed reference: 17663790. DOI: 10.1186/gb-2007-8-7-r152.

2006

Beraldi, D., McRae, AF., Gratten, J., Slate, J., Visscher, PM., Pemberton, JM. :

Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries). Genetics 173:1521-37, 2006. Pubmed reference: 16868121. DOI: 10.1534/genetics.106.057141.

Cockett, N.E. :

The sheep genome. Genome Dyn 2:79-85, 2006. Pubmed reference: 18753771. DOI: 10.1159/000095096.

2001

Maddox, J.F., Davies, K.P., Crawford, A.M., Hulme, D.J., Vaiman, D., Cribiu, E.P., Freking, B.A., Beh, K.J., Cockett, N.E., Kang, N., Riffkin, C.D., Drinkwater, R., Moore, S.S., Dodds, K.G., Lumsden, J.M., van Stijn, T.C., Phua, S.H., Adelson, D.L., Burkin, H.R., Broom, J.E., Buitkamp, J., Cambridge, L., Cushwa, W.T., Gerard, E., Galloway, S.M., Harrison, B., Hawken, R.J., Hiendleder, S., Henry, H.M., Medrano, J.F., Paterson, K.A., Schibler, L., Stone, R.T., van Hest, B. :

An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res 11:1275-89, 2001. Pubmed reference: 11435411. DOI: 10.1101/gr.135001.

1998

De Gortari, M.J., Freking, B.A., Cuthbertson, R.P., Kappes, S.M., Keele, J.W., Stone, R.T., Leymaster, K.A., Dodds, K.G., Crawford, A.M., Beattie, C.W. :

A second-generation linkage map of the sheep genome Mammalian Genome 9:204-209, 1998. Pubmed reference: 9501303.

1996

Galloway, S.M., Hanrahan, V., Dodds, K.G., Potts, M.D., Crawford, A.M., Hill, D.F. :

A linkage map of the ovine x chromosome Genome Research 6:667-677, 1996. Pubmed reference: 8858342.

Comparative genome organization of vertebrates Mammalian Genome 7:717-734, 1996. Pubmed reference: 8854859.

1995

Crawford, A.M., Dodds, K.G., Ede, A.J., Pierson, C.A., Montgomery, G.W., Garmonsway, H.G., Beattie, A.E., Davies, K., Maddox, J.F., Kappes, S.W., Stone, R.T., Nguyen, T.C., Penty, J.M., Lord, E.A., Broom, J.E., Buitkamp, J., Schwaiger, W., Epplen, J.T., Matthew, P., Matthews, M.E., Hulme, D.J., Beh, K.J., McGraw, R.A., Beattie, C.W. :

An autosomal genetic linkage map of the sheep genome Genetics 140:703-724, 1995. Pubmed reference: 7498748.

1994

Echard, G., Broad, T.E., Hill, D., Pearce, P. :

Present Status of the Ovine Gene Map (Ovis aries) - Comparison with the Bovine Map (Bos taurus) Mammalian Genome 5:324-332, 1994. Pubmed reference: 8043945.

Crawford, A.M., Montgomery, G.W., Pierson, C.A., Brown, T., Dodds, K.G., Sunden, S.L.F., Henry, H.M., Ede, A.J., Swarbrick, P.A., Berryman, T., Penty, J.M., Hill, D.F. :

Sheep linkage mapping: Nineteen linkage groups derived from the analysis of paternal half-sib families Genetics 137:573-579, 1994. Pubmed reference: 8070667.

Broad, T.E., Hill, D.F. :

Mapping the Sheep Genome - Practice, Progress and Promise British Veterinary Journal 150:237-252, 1994. Pubmed reference: 7913869. DOI: 10.1016/S0007-1935(05)80004-1.

Beattie, C.W. :

Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.

1931

Wassin, B. :

Linkage studies in sheep Journal of Heredity 22:9-13, 1931.

Ovis canadensis (bighorn sheep) :

2024

Deakin, S., Coltman, D.W. :

Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (Ovis canadensis canadensis). PeerJ 12:e16946, 2024. Pubmed reference: 38426129. DOI: 10.7717/peerj.16946.

Ovis orientalis (Asiatic mouflon) :

2022

2020

Su, R., Qiao, X., Gao, Y., Li, X., Jiang, W., Chen, W., Fan, Y., Zheng, B., Zhang, Y., Liu, Z., Wang, R., Wang, Z., Wang, Z., Wan, W., Dong, Y., Li, J. :

Draft genome of the European mouflon (Ovis orientalis musimon). Front Genet 11:533611, 2020. Pubmed reference: 33329689. DOI: 10.3389/fgene.2020.533611.

Pagetopsis macropterus :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Pan troglodytes (chimpanzee) :

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Pangasianodon hypophthalmus (striped catfish) :

2021

Gao, Z., You, X., Zhang, X., Chen, J., Xu, T., Huang, Y., Lin, X., Xu, J., Bian, C., Shi, Q. :

A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus). Genomics 113:3349-3356, 2021. Pubmed reference: 34343676. DOI: 10.1016/j.ygeno.2021.07.026.

Panthera pardus (leopard) :

2024

Li, H.M., Liu, B.Y., Shi, M.H., Zhang, L., Yang, S.C., Sahu, S.K., Cui, L.Y., Liu, S.L., Dussex, N., Ma, Y., Liu, D., Kong, W.Y., Lu, H.R., Zhao, Y., Dalén, L., Liu, H., Lan, T.M., Jiang, G.S., Xu, Y.C. :

Haplotype-resolved and chromosome-scale genomes provide insights into co-adaptation between the Amur tiger and Amur leopard. Zool Res 45:2095-8137(2024)03-0464-04:464-467, 2024. Pubmed reference: 38583937. DOI: 10.24272/j.issn.2095-8137.2023.232.

2023

Mochales-Riaño, G., Fontsere, C., de Manuel, M., Talavera, A., Burriel-Carranza, B., Tejero-Cicuéndez, H., AlGethami, R.H.M., Shobrak, M., Marques-Bonet, T., Carranza, S. :

Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr). iScience 26:107481, 2023. Pubmed reference: 37601769. DOI: 10.1016/j.isci.2023.107481.

Panthera tigris (tiger) :

2013

Cho, Y.S., Hu, L., Hou, H., Lee, H., Xu, J., Kwon, S., Oh, S., Kim, H.M., Jho, S., Kim, S., Shin, Y.A., Kim, B.C., Kim, H., Kim, C.U., Luo, S.J., Johnson, W.E., Koepfli, K.P., Schmidt-Küntzel, A., Turner, J.A., Marker, L., Harper, C., Miller, S.M., Jacobs, W., Bertola, L.D., Kim, T.H., Lee, S., Zhou, Q., Jung, H.J., Xu, X., Gadhvi, P., Xu, P., Xiong, Y., Luo, Y., Pan, S., Gou, C., Chu, X., Zhang, J., Liu, S., He, J., Chen, Y., Yang, L., Yang, Y., He, J., Liu, S., Wang, J., Kim, C.H., Kwak, H., Kim, J.S., Hwang, S., Ko, J., Kim, C.B., Kim, S., Bayarlkhagva, D., Paek, W.K., Kim, S.J., O'Brien, S.J., Wang, J., Bhak, J. :

The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun 4:2433, 2013. Pubmed reference: 24045858. DOI: 10.1038/ncomms3433.

Pantherophis alleghaniensis :

2023

Burbrink, F.T., Harrington, S.M., Bobo, D., Myers, E.A. :

Considering admixture when producing draft genomes: an example in North American ratsnakes (P. alleghaniensis/P. obsoletus). G3 (Bethesda) , 2023. Pubmed reference: 37228097. DOI: 10.1093/g3journal/jkad113.

Pantherophis guttatus (corn snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

2020

Ullate-Agote, A., Burgelin, I., Debry, A., Langrez, C., Montange, F., Peraldi, R., Daraspe, J., Kaessmann, H., Milinkovitch, M.C., Tzika, A.C. :

Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles. Proc Natl Acad Sci U S A 117:26307-26317, 2020. Pubmed reference: 33020272. DOI: 10.1073/pnas.2003724117.

2014

Ullate-Agote, A., Milinkovitch, M.C., Tzika, A.C. :

The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. Int J Dev Biol 58:881-8, 2014. Pubmed reference: 26154328. DOI: 10.1387/ijdb.150060at.

Papio (baboons) :

2023

Sørensen, E.F., Harris, R.A., Zhang, L., Raveendran, M., Kuderna, L.F.K., Walker, J.A., Storer, J.M., Kuhlwilm, M., Fontsere, C., Seshadri, L., Bergey, C.M., Burrell, A.S., Bergman, J., Phillips-Conroy, J.E., Shiferaw, F., Chiou, K.L., Chuma, I.S., Keyyu, J.D., Fischer, J., Gingras, M.C., Salvi, S., Doddapaneni, H., Schierup, M.H., Batzer, M.A., Jolly, C.J., Knauf, S., Zinner, D., Farh, K.K., Marques-Bonet, T., Munch, K., Roos, C., Rogers, J. :

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 380:eabn8153, 2023. Pubmed reference: 37262153. DOI: 10.1126/science.abn8153.

Paracanthobrama guichenoti :

2021

Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :

Paralichthys orbignyanus :

2024

Villarreal, F., Burguener, G.F., Sosa, E.J., Stocchi, N., Somoza, G.M., Turjanski, A.G., Blanco, A., Viñas, J., Mechaly, A.S. :

Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure. BMC Genomics 25:297, 2024. Pubmed reference: 38509481. DOI: 10.1186/s12864-024-10081-z.

Parapercis pulchella (harlequin sandsmelt) :

2024

Yao, A., Kohtsuka, H., Miura, T. :

Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (Parapercis pulchella). Mar Genomics 73:S1874-7787(24)00004-7:101086, 2024. Pubmed reference: 38365348. DOI: 10.1016/j.margen.2024.101086.

Passer domesticus (House sparrow) :

2023

Magallanes-Alba, M.E., Baricalla, A., Rego, N., Brun, A., Karasov, W.H., Caviedes-Vidal, E. :

Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation. Biol Methods Protoc 8:bpad013, 2023. Pubmed reference: 37521110. DOI: 10.1093/biomethods/bpad013.

Passer montanus (Eurasian tree sparrow) :

2023

Wang, S., Shen, Y., Lin, Z., Miao, Y., Wang, C., Zhang, W., Zhang, Y. :

New genes driven by segmental duplications share a testis-specific expression pattern in the chromosome-level genome assembly of tree sparrow. Integr Zool , 2023. Pubmed reference: 38014459. DOI: 10.1111/1749-4877.12789.

Passerculus sandwichensis (Savannah sparrow) :

2024

Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., King, B.L., Thomas, W.K., Kovach, A.I., Nachman, M.W., Bowie, R.C.K. :

Pavo cristatus (Indian peafowl) :

2023

Chakraborty, A., Mondal, S., Mahajan, S., Sharma, V.K. :

High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl. Heliyon 9:e18571, 2023. Pubmed reference: 37576271. DOI: 10.1016/j.heliyon.2023.e18571.

Pelochelys cantorii (Cantor's giant softshell turtle) :

2023

Hong, X., Liu, H., Wang, Y., Li, M., Ji, L., Wang, K., Wei, C., Li, W., Chen, C., Yu, L., Zhu, X., Liu, X. :

A chromosome-level genome assembly of the Asian giant softshell turtle Pelochelys cantorii. Sci Data 10:754, 2023. Pubmed reference: 37914689. DOI: 10.1038/s41597-023-02667-1.

Pelteobagrus vachellii :

2023

Gong, G., Ke, W., Liao, Q., Xiong, Y., Hu, J., Mei, J. :

A chromosome-level genome assembly of the darkbarbel catfish Pelteobagrus vachelli. Sci Data 10:598, 2023. Pubmed reference: 37684295. DOI: 10.1038/s41597-023-02509-0.

Penaeus monodon (black tiger shrimp) :

2018

Huerlimann, R., Wade, N.M., Gordon, L., Montenegro, J.D., Goodall, J., McWilliam, S., Tinning, M., Siemering, K., Giardina, E., Donovan, D., Sellars, M.J., Cowley, J.A., Condon, K., Coman, G.J., Khatkar, M.S., Raadsma, H.W., Maes, G.E., Zenger, K.R., Jerry, D.R. :

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. Sci Rep 8:13553, 2018. Pubmed reference: 30202061. DOI: 10.1038/s41598-018-31148-4.

Perdix hodgsoniae (Tibetan partridge) :

2023

Zhou, C., Zheng, X., Feng, K., Peng, K., Zhang, Y., Zhao, G., Meng, Y., Zhang, L., Yue, B., Wu, Y. :

The draft genome of the Tibetan partridge (Perdix hodgsoniae) provides insights into its phylogenetic position and high-altitude adaptation. J Hered 114:175-188, 2023. Pubmed reference: 36546409. DOI: 10.1093/jhered/esac069.

Periophthalmus magnuspinnatus :

2023

Bian, C., Huang, Y., Li, R., Xu, P., You, X., Lv, Y., Ruan, Z., Chen, J., Xu, J., Shi, Q. :

Periophthalmus modestus (shuttles hoppfish) :

2023

Bian, C., Huang, Y., Li, R., Xu, P., You, X., Lv, Y., Ruan, Z., Chen, J., Xu, J., Shi, Q. :

Perisoreus infaustus :

2009

Jaari, S., Li, M.H., Merilä, J. :

A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution. BMC Genomics 10:1, 2009. Pubmed reference: 19121221. DOI: 10.1186/1471-2164-10-1.

Perognathus longimembris (little pocket mouse) :

2023

Kozak, K.M., Escalona, M., Chumchim, N., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., Seligmann, W., Conroy, C., Patton, J.L., Bowie, R.C.K., Nachman, M.W. :

A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris. J Hered , 2023. Pubmed reference: 37793045. DOI: 10.1093/jhered/esad060.

Peromyscus polionotus (oldfield mouse) :

2022

Wooldridge, T.B., Kautt, A.F., Lassance, J.M., McFadden, S., Domingues, V.S., Mallarino, R., Hoekstra, H.E. :

An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice. Proc Natl Acad Sci U S A 119:e2202862119, 2022. Pubmed reference: 35776547. DOI: 10.1073/pnas.2202862119.

Petromyzon marinus (sea lamprey) :

2023

Timoshevskaya, N., Eşkut, K.I., Timoshevskiy, V.A., Robb, S.M.C., Holt, C., Hess, J.E., Parker, H.J., Baker, C.F., Miller, A.K., Saraceno, C., Yandell, M., Krumlauf, R., Narum, S.R., Lampman, R.T., Gemmell, N.J., Mountcastle, J., Haase, B., Balacco, J.R., Formenti, G., Pelan, S., Sims, Y., Howe, K., Fedrigo, O., Jarvis, E.D., Smith, J.J. :

An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes. Cell Rep 42:112263, 2023. Pubmed reference: 36930644. DOI: 10.1016/j.celrep.2023.112263.

Phacochoerus africanus (Common warthog) :

2023

Feng, W., Zhou, L., Zhao, P., Du, H., Diao, C., Zhang, Y., Liu, Z., Jin, W., Yu, J., Han, J., Okoth, E., Mrode, R., Liu, J.F. :

Comparative genomic analysis of warthog and Sus scrofa identifies adaptive genes associated with African swine fever. Biology (Basel) 12:1001, 2023. Pubmed reference: 37508430. DOI: 10.3390/biology12071001.

Phascolarctos cinereus (koala) :

2023

Hogg, C.J., Silver, L., McLennan, E.A., Belov, K. :

Koala genome survey: An open data resource to improve conservation planning. Genes (Basel) 14:546, 2023. Pubmed reference: 36980819. DOI: 10.3390/genes14030546.

2018

Johnson, R.N., O'Meally, D., Chen, Z., Etherington, G.J., Ho, S.Y.W., Nash, W.J., Grueber, C.E., Cheng, Y., Whittington, C.M., Dennison, S., Peel, E., Haerty, W., O'Neill, R.J., Colgan, D., Russell, T.L., Alquezar-Planas, D.E., Attenbrow, V., Bragg, J.G., Brandies, P.A., Chong, A.Y., Deakin, J.E., Di Palma, F., Duda, Z., Eldridge, M.D.B., Ewart, K.M., Hogg, C.J., Frankham, G.J., Georges, A., Gillett, A.K., Govendir, M., Greenwood, A.D., Hayakawa, T., Helgen, K.M., Hobbs, M., Holleley, C.E., Heider, T.N., Jones, E.A., King, A., Madden, D., Graves, J.A.M., Morris, K.M., Neaves, L.E., Patel, H.R., Polkinghorne, A., Renfree, M.B., Robin, C., Salinas, R., Tsangaras, K., Waters, P.D., Waters, S.A., Wright, B., Wilkins, M.R., Timms, P., Belov, K. :

Adaptation and conservation insights from the koala genome. Nat Genet 50:1102-1111, 2018. Pubmed reference: 29967444. DOI: 10.1038/s41588-018-0153-5.

Phocoena sinus (vaquita) :

2021

Morin, P.A., Archer, F.I., Avila, C.D., Balacco, J.R., Bukhman, Y.V., Chow, W., Fedrigo, O., Formenti, G., Fronczek, J.A., Fungtammasan, A., Gulland, F.M.D., Haase, B., Peter Heide-Jorgensen, M., Houck, M.L., Howe, K., Misuraca, A.C., Mountcastle, J., Musser, W., Paez, S., Pelan, S., Phillippy, A., Rhie, A., Robinson, J., Rojas-Bracho, L., Rowles, T.K., Ryder, O.A., Smith, C.R., Stevenson, S., Taylor, B.L., Teilmann, J., Torrance, J., Wells, R.S., Westgate, A.J., Jarvis, E.D. :

Reference genome and demographic history of the most endangered marine mammal, the vaquita. Mol Ecol Resour 21:1008-1020, 2021. Pubmed reference: 33089966. DOI: 10.1111/1755-0998.13284.

Phodopus roborovskii (desert hamster) :

2022

Andreotti, S., Altmüller, J., Quedenau, C., Borodina, T., Nouailles, G., Teixeira Alves, L.G., Landthaler, M., Bieniara, M., Trimpert, J., Wyler, E. :

De novo-whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome: An animal model for severe/critical COVID-19. Genome Biol Evol 14, 2022. Pubmed reference: 35778793. DOI: 10.1093/gbe/evac100.

Phrynocephalus forsythii :

2023

Qi, Y., Zhao, W., Zhao, Y., Niu, C., Cao, S., Zhang, Y. :

Chromosome-level genome assembly of Phrynocephalus forsythii using third-generation DNA sequencing and Hi-C analysis. DNA Res , 2023. Pubmed reference: 36882113. DOI: 10.1093/dnares/dsad003.

Phrynosoma blainvillii :

2023

Richmond, J.Q., McGuire, J.A., Escalona, M., Marimuthu, M.P.A., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Fisher, R.N., Wang, I.J., Shaffer, H.B. :

Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii. J Hered , 2023. Pubmed reference: 37195437. DOI: 10.1093/jhered/esad032.

Phyllostomus discolor (pale spear-nosed bat) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Picus viridis (Eurasian green woodpecker) :

2024

Forest, T., Achaz, G., Marbouty, M., Bignaud, A., Thierry, A., Koszul, R., Milhes, M., Lledo, J., Pons, J.M., Fuchs, J. :

Chromosome-level genome assembly of the European green woodpecker Picus viridis. G3 (Bethesda) :jkae042, 2024. Pubmed reference: 38537260. DOI: 10.1093/g3journal/jkae042.

Plecoglossus altivelis (ayu) :

2023

Nakamoto, M., Sakamoto, T. :

Improvement of the ayu (Plecoglossus altivelis) draft genome using Hi-C sequencing. BMC Res Notes 16:92, 2023. Pubmed reference: 37254197. DOI: 10.1186/s13104-023-06362-7.

2021

Nakamoto, M., Uchino, T., Koshimizu, E., Kuchiishi, Y., Sekiguchi, R., Wang, L., Sudo, R., Endo, M., Guiguen, Y., Schartl, M., Postlethwait, J.H., Sakamoto, T. :

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis. PLoS Genet 17:e1009705, 2021. Pubmed reference: 34437539. DOI: 10.1371/journal.pgen.1009705.

Plectropomus leopardus (leopard coralgrouper) :

2023

Han, W., Wu, S., Ding, H., Wang, M., Wang, M., Bao, Z., Wang, B., Hu, J. :

Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper. Sci Data 10:156, 2023. Pubmed reference: 36949049. DOI: 10.1038/s41597-023-02051-z.

Plotosus lineatus (striped eel catfish) :

2023

Shao, F., Wu, Z.C., Xu, Y., Li, P., Peng, Z.G. :

Genome of striped eel catfish (Plotosus lineatus) provides insights into the adaptive evolution of amphidromous fish. Zool Res 44:349-352, 2023. Pubmed reference: 36849790. DOI: 10.24272/j.issn.2095-8137.2022.387.

Podarcis lilfordi (Lilford's wall lizard) :

2023

Gomez-Garrido, J., Cruz, F., Alioto, T.S., Feiner, N., Uller, T., Gut, M., Sanchez Escudero, I., Tavecchia, G., Rotger, A., Otalora Acevedo, K.E., Baldo, L. :

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain). DNA Res , 2023. Pubmed reference: 37137526. DOI: 10.1093/dnares/dsad008.

Podarcis raffoneae (Aeolian wall lizard) :

2023

Gabrielli, M., Benazzo, A., Biello, R., Ancona, L., Fuselli, S., Iannucci, A., Balacco, J., Mountcastle, J., Tracey, A., Ficetola, G.F., Salvi, D., Sollitto, M., Fedrigo, O., Formenti, G., Jarvis, E.D., Gerdol, M., Ciofi, C., Trucchi, E., Bertorelle, G. :

A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei. J Hered , 2023. Pubmed reference: 36866448. DOI: 10.1093/jhered/esad014.

Poecilia reticulata (guppy) :

2023

Charlesworth, D., Qiu, S., Bergero, R., Gardner, J., Keegan, K., Yong, L., Hastings, A., Konczal, M. :

Has recombination changed during the recent evolution of the guppy Y chromosome? Genetics , 2023. Pubmed reference: 37956094. DOI: 10.1093/genetics/iyad198.

Poeciliopsis occidentalis (Sonoran topminnow) :

2023

Mussmann, S.M., Harrison, A.S., Wilson, W.D. :

Development of twenty-one novel microsatellite loci for Gila topminnow, Poeciliopsis occidentalis occidentalis. Mol Biol Rep , 2023. Pubmed reference: 36939964. DOI: 10.1007/s11033-023-08376-7.

Poeciliopsis prolifica (blackstripe livebearer) :

2023

Zhang, Y., Reynoso, Y., Reznick, D., Wang, X. :

Whole genome assembly and annotation of blackstripe livebearer Poeciliopsis prolifica. Genome Biol Evol , 2023. Pubmed reference: 37949830. DOI: 10.1093/gbe/evad195.

Pogonophryne albipinna :

2023

Jo, E., Choi, S., Lee, S.J., Kim, J., Choi, E.K., Cho, M., Kim, J., Chung, S., Lee, J., Kim, J.H., Park, H. :

Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna. Sci Data 10:891, 2023. Pubmed reference: 38086886. DOI: 10.1038/s41597-023-02811-x.

Prionailurus bengalensis (leopard cat) :

2020

Bredemeyer, K.R., Harris, A.J., Li, G., Zhao, L., Foley, N.M., Roelke-Parker, M., O'Brien, S.J., Lyons, L.A., Warren, W.C., Murphy, W.J. :

Prionailurus viverrinus (fishing cat) :

2024

Carroll, R.A., Rice, E.S., Murphy, W.J., Lyons, L.A., Thibaud-Nissen, F., Coghill, L.M., Swanson, W.F., Terio, K.A., Boyd, T., Warren, W.C. :

A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants. Sci Rep 14:8073, 2024. Pubmed reference: 38580653. DOI: 10.1038/s41598-024-56003-7.

Protobothrops mucrosquamatus (Chinese habu) :

2023

Niu, X., Lu, H., Shi, M., Wang, S., Zhou, Y., Liu, H. :

Genome assembly and annotation of the Brown-Spotted Pit viper Protobothrops mucrosquamatus. GigaByte 2023:gigabyte97, 2023. Pubmed reference: 38023064. DOI: 10.46471/gigabyte.97.

Protopterus annectens (West African lungfish) :

2023

Zhang, R., Liu, Q., Pan, S., Zhang, Y., Qin, Y., Du, X., Yuan, Z., Lu, Y., Song, Y., Zhang, M., Zhang, N., Ma, J., Zhang, Z., Jia, X., Wang, K., He, S., Liu, S., Ni, M., Liu, X., Xu, X., Yang, H., Wang, J., Seim, I., Fan, G. :

A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization. Nat Commun 14:5630, 2023. Pubmed reference: 37699889. DOI: 10.1038/s41467-023-41309-3.

Protosalanx hyalocranius (clearhead icefish) :

2017

Liu, K., Xu, D., Li, J., Bian, C., Duan, J., Zhou, Y., Zhang, M., You, X., You, Y., Chen, J., Yu, H., Xu, G., Fang, D.A., Qiang, J., Jiang, S., He, J., Xu, J., Shi, Q., Zhang, Z., Xu, P. :

Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. Gigascience 6:1-6, 2017. Pubmed reference: 28327943. DOI: 10.1093/gigascience/giw012.

Psammodynastes pulverulentus :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Pseudocaranx georgianus (silver trevally) :

2021

Catanach, A., Ruigrok, M., Bowatte, D., Davy, M., Storey, R., Valenza-Troubat, N., López-Girona, E., Hilario, E., Wylie, M.J., Chagné, D., Wellenreuther, M. :

The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus. BMC Genomics 22:785, 2021. Pubmed reference: 34727894. DOI: 10.1186/s12864-021-08102-2.

Pseudochaenichthys georgianus (South Georgia icefish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Pteronura brasiliensis (giant otter) :

2019

Beichman, A.C., Koepfli, K.P., Li, G., Murphy, W., Dobrynin, P., Kliver, S., Tinker, M.T., Murray, M.J., Johnson, J., Lindblad-Toh, K., Karlsson, E.K., Lohmueller, K.E., Wayne, R.K. :

Ptyas mucosa (Dhaman) :

2023

Wang, J., Wang, S., Huang, S., Wang, Q., Lan, T., Jiang, M., Wu, H., Yuan, Y. :

The genome assembly and annotation of the Oriental rat snake Ptyas mucosa. GigaByte 2023:gigabyte92, 2023. Pubmed reference: 37753478. DOI: 10.46471/gigabyte.92.

Puma yagouaroundi (jaguarundi) :

2021

Tamazian, G., Dobrynin, P., Zhuk, A., Zhernakova, D.V., Perelman, P.L., Serdyukova, N.A., Graphodatsky, A.S., Komissarov, A., Kliver, S., Cherkasov, N., Scott, A.F., Mohr, D.W., Koepfli, K.P., O'Brien, S.J., Krasheninnikova, K. :

Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi. J Hered 112:540-548, 2021. Pubmed reference: 34146095. DOI: 10.1093/jhered/esab036.

Puntigrus tetrazona (Sumatra barb) :

2021

Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :

Pusa sibirica (Baikal seal) :

2023

Yakupova, A., Tomarovsky, A., Totikov, A., Beklemisheva, V., Logacheva, M., Perelman, P.L., Komissarov, A., Dobrynin, P., Krasheninnikova, K., Tamazian, G., Serdyukova, N.A., Rayko, M., Bulyonkova, T., Cherkasov, N., Pylev, V., Peterfeld, V., Penin, A., Balanovska, E., Lapidus, A. :

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal. Genes (Basel) 14, 2023. Pubmed reference: 36980891. DOI: 10.3390/genes14030619.

Rallus crepitans (clapper rail) :

2023

Elizondo, E.C., Faircloth, B.C., Brumfield, R.T., Shakya, S.B., Ellis, V.A., Schmidt, C.J., Kovach, A.I., Shriver, W.G. :

A high quality de novo genome assembly for clapper rail (Rallus crepitans). G3 (Bethesda) , 2023. Pubmed reference: 37130071. DOI: 10.1093/g3journal/jkad097.

Rallus limicola :

2023

Hall, L.A., Wang, I.J., Escalona, M., Beraut, E., Sacco, S., Sahasrabudhe, R., Nguyen, O., Toffelmier, E., Shaffer, H.B., Beissinger, S.R. :

Reference genome of the Virginia rail, Rallus limicola. J Hered , 2023. Pubmed reference: 37105531. DOI: 10.1093/jhered/esad026.

Rangifer tarandus (reindeer) :

2024

Yi, W., Hu, M., Shi, L., Li, T., Sun, H., Qin, L., Yan, S. :

Analysis of genetic variants in protein-coding genes of Aoluguya reindeer based on the whole-genome data. Anim Genet , 2024. Pubmed reference: 38319118. DOI: 10.1111/age.13402.

2023

Poisson, W., Prunier, J., Carrier, A., Gilbert, I., Mastromonaco, G., Albert, V., Taillon, J., Bourret, V., Droit, A., Côté, S.D., Robert, C. :

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights. BMC Genomics 24:142, 2023. Pubmed reference: 36959567. DOI: 10.1186/s12864-023-09189-5.

Shi, L., Shi, Z., Hu, M., Wu, M., Quan, X., Qin, L., Zhao, Z., Sun, H., Tian, L., Yan, S. :

Whole genome sequencing of Aoluguya reindeer (Rangifer tarandus) in China. Front Genet 14:1243795, 2023. Pubmed reference: 37600663. DOI: 10.3389/fgene.2023.1243795.

Pokharel, K., Weldenegodguad, M., Dudeck, S., Honkatukia, M., Lindeberg, H., Mazzullo, N., Paasivaara, A., Peippo, J., Soppela, P., Stammler, F., Kantanen, J. :

Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia. Sci Rep 13:23019, 2023. Pubmed reference: 38155192. DOI: 10.1038/s41598-023-50253-7.

2022

Carrier, A., Prunier, J., Poisson, W., Trottier-Lavoie, M., Gilbert, I., Cavedon, M., Pokharel, K., Kantanen, J., Musiani, M., Côté, S.D., Albert, V., Taillon, J., Bourret, V., Droit, A., Robert, C. :

Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus). BMC Genomics 23:687, 2022. Pubmed reference: 36199020. DOI: 10.1186/s12864-022-08899-6.

Rhinatrema bivittatum (two-lined caecilian) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Rhinichthys cobitis (loach minnow) :

2023

Alexandre, N.M., Cameron, A.C., Tian, D., Chatla, K., Kolora, S.R.R., Whiteman, N.K., Turner, T.F., Reinthal, P.N. :

Rhinolophus ferrumequinum (greater horseshoe bat) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Rissa tridactyla (black-legged kittiwake) :

2023

Sozzoni, M., Ferrer Obiol, J., Formenti, G., Tigano, A., Paris, J.R., Balacco, J.R., Jain, N., Tilley, T., Collins, J., Sims, Y., Wood, J., Benowitz-Fredericks, Z.M., Field, K.A., Seyoum, E., Gatt, M.C., Léandri-Breton, D.J., Nakajima, C., Whelan, S., Gianfranceschi, L., Hatch, S.A., Elliott, K.H., Shoji, A., Cecere, J.G., Jarvis, E.D., Pilastro, A., Rubolini, D. :

A chromosome-level reference genome for the black-legged kittiwake (Rissa tridactyla), a declining circumpolar seabird. Genome Biol Evol , 2023. Pubmed reference: 37590950. DOI: 10.1093/gbe/evad153.

Saccostrea glomerata :

2018

Powell, D., Subramanian, S., Suwansa-Ard, S., Zhao, M., O'Connor, W., Raftos, D., Elizur, A. :

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves. DNA Res 25:655-665, 2018. Pubmed reference: 30295708. DOI: 10.1093/dnares/dsy032.

Salamandra salamandra (fire salamander) :

2023

Libro, P., Chiocchio, A., De Rysky, E., Di Martino, J., Bisconti, R., Castrignanò, T., Canestrelli, D. :

De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage. Sci Data 10:330, 2023. Pubmed reference: 37244908. DOI: 10.1038/s41597-023-02217-9.

Salmo salar (Atlantic salmon) :

2023

MacLeod-Bigley, M.L., Boulding, E.G. :

High-density linkage maps detail sex-specific regions of suppressed recombination near fusions of polymorphic chromosomes in purebred and hybrid North American Atlantic salmon (Salmo salar). Genome , 2023. Pubmed reference: 36944224. DOI: 10.1139/gen-2022-0065.

Gao, G., Waldbieser, G.C., Youngblood, R.C., Zhao, D., Pietrak, M.R., Allen, M.S., Stannard, J.A., Buchanan, J.T., Long, R.L., Milligan, M., Burr, G., Mejía-Guerra, K., Sheehan, M.J., Scheffler, B.E., Rexroad, C.E., Peterson, B.C., Palti, Y. :

The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50 K SNP array for the St John River aquaculture strain of North American Atlantic salmon. G3 (Bethesda) , 2023. Pubmed reference: 37335943. DOI: 10.1093/g3journal/jkad138.

2016

Lien, S., Koop, B.F., Sandve, S.R., Miller, J.R., Kent, M.P., Nome, T., Hvidsten, T.R., Leong, J.S., Minkley, D.R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R.A., von Schalburg, K., Rondeau, E.B., Di Genova, A., Samy, J.K., Olav Vik, J., Vigeland, M.D., Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., de Jong, P., Moen, T., Baranski, M., Palti, Y., Smith, D.R., Yorke, J.A., Nederbragt, A.J., Tooming-Klunderud, A., Jakobsen, K.S., Jiang, X., Fan, D., Hu, Y., Liberles, D.A., Vidal, R., Iturra, P., Jones, S.J., Jonassen, I., Maass, A., Omholt, S.W., Davidson, W.S. :

The Atlantic salmon genome provides insights into rediploidization. Nature 533:200-5, 2016. Pubmed reference: 27088604. DOI: 10.1038/nature17164.

2014

Houston, R.D., Taggart, J.B., Cézard, T., Bekaert, M., Lowe, N.R., Downing, A., Talbot, R., Bishop, S.C., Archibald, A.L., Bron, J.E., Penman, D.J., Davassi, A., Brew, F., Tinch, A.E., Gharbi, K., Hamilton, A. :

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar). BMC Genomics 15:90, 2014. Pubmed reference: 24524230. DOI: 10.1186/1471-2164-15-90.

Gonen, S., Lowe, N.R., Cezard, T., Gharbi, K., Bishop, S.C., Houston, R.D. :

Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing. BMC Genomics 15:166, 2014. Pubmed reference: 24571138. DOI: 10.1186/1471-2164-15-166.

Salmo trutta (brown trout) :

2019

Saint-Pé, K., Leitwein, M., Tissot, L., Poulet, N., Guinand, B., Berrebi, P., Marselli, G., Lascaux, J.M., Gagnaire, P.A., Blanchet, S. :

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics. BMC Genomics 20:582, 2019. Pubmed reference: 31307373. DOI: 10.1186/s12864-019-5958-9.

2017

Leitwein, M., Guinand, B., Pouzadoux, J., Desmarais, E., Berrebi, P., Gagnaire, P.A. :

A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity. G3 (Bethesda) 7:1365-1376, 2017. Pubmed reference: 28235829. DOI: 10.1534/g3.116.038497.

Salvelinus alpinus (Arctic char) :

2023

Pappas, F., Kurta, K., Vanhala, T., Jeuthe, H., Hagen, Ø., Beirão, J., Palaiokostas, C. :

Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia. Evol Appl 16:797-813, 2023. Pubmed reference: 37124091. DOI: 10.1111/eva.13537.

Salvelinus fontinalis (brook trout) :

2023

Mamoozadeh, N.R., Whiteley, A.R., Letcher, B.H., Kazyak, D.C., Tarsa, C., Meek, M.H. :

A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis). Mol Ecol Resour , 2023. Pubmed reference: 37584304. DOI: 10.1111/1755-0998.13853.

Sarcophilus harrisii (Tasmanian devil) :

2023

Stammnitz, M.R., Gori, K., Kwon, Y.M., Harry, E., Martin, F.J., Billis, K., Cheng, Y., Baez-Ortega, A., Chow, W., Comte, S., Eggertsson, H., Fox, S., Hamede, R., Jones, M., Lazenby, B., Peck, S., Pye, R., Quail, M.A., Swift, K., Wang, J., Wood, J., Howe, K., Stratton, M.R., Ning, Z., Murchison, E.P. :

The evolution of two transmissible cancers in Tasmanian devils. Science 380:283-293, 2023. Pubmed reference: 37079675. DOI: 10.1126/science.abq6453.

Sardinella longiceps (Indian oil sardine) :

2023

Sukumaran, S., Sebastian, W., Gopalakrishnan, A., Mathew, O.K., Vysakh, V.G., Rohit, P., Jena, J.K. :

The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps. Sci Data 10:565, 2023. Pubmed reference: 37626109. DOI: 10.1038/s41597-023-02481-9.

Sarotherodon galilaeus (mango tilapia) :

2023

Fiteha, Y.G., Rashed, M.A., Ali, R.A.M., Magdy, M. :

Characterization and phylogenetic analysis of the complete mitochondrial genome of Mango tilapia (Sarotherodon galilaeus: Cichlidae). Mol Biol Rep , 2023. Pubmed reference: 36781609. DOI: 10.1007/s11033-023-08288-6.

Scaptonyx fusicaudus (long-tailed mole) :

2023

Wang, X., Liu, Y., Liao, R., Liu, S. :

The complete mitochondrial genome of the long-tailed mole: Scaptonyx fusicaudus (Eulipotyphla, Talpidae). Mitochondrial DNA B Resour 8:264-265, 2023. Pubmed reference: 36816057. DOI: 10.1080/23802359.2022.2032438.

Scarus forsteni (Forsten's parrotfish) :

2024

Liang, Y., Xian, L., Pan, J., Zhu, K., Guo, H., Liu, B., Zhang, N., Ou-Yang, Y., Zhang, Q., Zhang, D. :

De novo genome assembly of the Whitespot Parrotfish (Scarus forsteni): A valuable scaridae genomic resource. Genes (Basel) 15:249, 2024. Pubmed reference: 38397238. DOI: 10.3390/genes15020249.

Sceloporus occidentalis (western fence lizard) :

2023

Bishop, A.P., Westeen, E.P., Yuan, M.L., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Chumchim, N., Toffelmier, E., Fisher, R.N., Shaffer, H.B., Wang, I.J. :

Assembly of the largest squamate reference genome to date: the western fence lizard, Sceloporus occidentalis. J Hered , 2023. Pubmed reference: 37335574. DOI: 10.1093/jhered/esad037.

Sciaenops ocellatus (red drum) :

2023

Xiao, Y., Liu, J., Wei, J., Xiao, Z., Li, J., Ma, Y. :

Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration. Sci Data 10:774, 2023. Pubmed reference: 37935724. DOI: 10.1038/s41597-023-02699-7.

Sciurus niger (fox squirrel) :

2021

Kang, L., Michalak, P., Hallerman, E., Moncrief, N.D. :

A draft genome assembly for the Eastern fox squirrel, Sciurus niger. G3 (Bethesda) :jkab315, 2021. Pubmed reference: 34550334. DOI: 10.1093/g3journal/jkab315.

Scomber colias (Atlantic chub mackerel) :

2022

Machado, A.M., Gomes-Dos-Santos, A., Fonseca, M.M., da Fonseca, R.R., Veríssimo, A., Felício, M., Capela, R., Alves, N., Santos, M., Salvador-Caramelo, F., Domingues, M., Ruivo, R., Froufe, E., Castro, L.F.C. :

A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource. GigaByte 2022:gigabyte40, 2022. Pubmed reference: 36824513. DOI: 10.46471/gigabyte.40.

Scomber japonicus (chub mackerel) :

2023

Lee, Y.H., Abueg, L., Kim, J.K., Kim, Y.W., Fedrigo, O., Balacco, J., Formenti, G., Howe, K., Tracey, A., Wood, J., Thibaud-Nissen, F., Nam, B.H., No, E.S., Kim, H.R., Lee, C., Jarvis, E.D., Kim, H. :

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean. Sci Data 10:880, 2023. Pubmed reference: 38066002. DOI: 10.1038/s41597-023-02782-z.

Scotinomys teguina (Alston's brown mouse) :

2023

Smith, S.K., Frazel, P.W., Khodadadi-Jamayran, A., Zappile, P., Marier, C., Okhovat, M., Brown, S., Long, M.A., Heguy, A., Phelps, S.M. :

De novo assembly and annotation of the singing mouse genome. BMC Genomics 24:569, 2023. Pubmed reference: 37749493. DOI: 10.1186/s12864-023-09678-7.

Semaprochilodus insignis :

2023

Yang, X., Song, Y., Zhang, R., Yu, M., Guo, X., Guo, H., Du, X., Sun, S., Li, C., Mao, X., Fan, G., Liu, X. :

Semicossyphus pulcher :

2022

Bernardi, G., DeBiasse, M., Escalona, M., Marimuthu, M.P.A., Nguyen, O., Sacco, S., Beraut, E., Miller, C., Toffelmier, E., Shaffer, H.B. :

Reference genome of the California sheephead, Semicossyphus pulcher (Labridae, Perciformes), a keystone fish predator in kelp forest ecosystems. J Hered 113:649-656, 2022. Pubmed reference: 35778264. DOI: 10.1093/jhered/esac032.

Semotilus atromaculatus (creek chub) :

2023

Meuser, A.V., Pitura, A.R., Mandeville, E.G. :

A high-quality reference genome for the common creek chub, Semotilus atromaculatus. G3 (Bethesda) :jkad283, 2023. Pubmed reference: 38128526. DOI: 10.1093/g3journal/jkad283.

Seriola lalandi (yellowtail amberjack) :

2021

Li, S., Liu, K., Cui, A., Hao, X., Wang, B., Wang, H.Y., Jiang, Y., Wang, Q., Feng, B., Xu, Y., Shao, C., Liu, X. :

A Chromosome-Level Genome Assembly of Yellowtail Kingfish (Seriola lalandi). Front Genet 12:825742, 2021. Pubmed reference: 35126476. DOI: 10.3389/fgene.2021.825742.

Setipinna tenuifilis (common hairfin anchovy) :

2023

Liu, B., Li, J., Peng, Y., Zhang, K., Liu, Q., Jin, X., Zheng, S., Wang, Y., Gong, L., Liu, L., Lü, Z., Liu, Y. :

Chromosome-level genome assembly and population genomic analysis reveal evolution and local adaptation in common hairfin anchovy (Setipinna tenuifilis). Mol Ecol , 2023. Pubmed reference: 37434292. DOI: 10.1111/mec.17067.

Setophaga petechia (yellow warbler) :

2024

Tsai, W.L.E., Escalona, M., Garrett, K.L., Terrill, R.S., Sahasrabudhe, R., Nguyen, O., Beraut, E., Seligmann, W., Fairbairn, C.W., Harrigan, R.J., McCormack, J.E., Alfaro, M.E., Smith, T.B., Bay, R.A. :

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). J Hered :esae008, 2024. Pubmed reference: 38401156. DOI: 10.1093/jhered/esae008.

Siniperca chuatsi (mandarin fish) :

2021

Ding, W., Zhang, X., Zhao, X., Jing, W., Cao, Z., Li, J., Huang, Y., You, X., Wang, M., Shi, Q., Bing, X. :

A chromosome-level genome assembly of the Mandarin fish (Siniperca chuatsi). Front Genet 12:671650, 2021. Pubmed reference: 34249093. DOI: 10.3389/fgene.2021.671650.

Guo, W., He, S., Liang, X., Tian, C., Dou, Y., Lv, L. :

A high-density genetic linkage map for Chinese perch (Siniperca chuatsi) using 2.3K genotyping-by-sequencing SNPs. Anim Genet 52:311-320, 2021. Pubmed reference: 33598959. DOI: 10.1111/age.13046.

Sistrurus catenatus (massasauga) :

2023

Mathur, S., Mason, A.J., Bradburd, G.S., Gibbs, H.L. :

Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake. Proc Natl Acad Sci U S A 120:e2303043120, 2023. Pubmed reference: 37844221. DOI: 10.1073/pnas.2303043120.

Sparidentex hasta (sobaity seabream) :

2022

Karam, Q., Kumar, V., Shajan, A.B., Al-Nuaimi, S., Sattari, Z., El-Dakour, S. :

De-novo genome assembly and annotation of sobaity seabream Sparidentex hasta. Front Genet 13:988488, 2022. Pubmed reference: 36386818. DOI: 10.3389/fgene.2022.988488.

Sparus aurata (gilthead seabream) :

2023

Bertolini, F., Ribani, A., Capoccioni, F., Buttazzoni, L., Bovo, S., Schiavo, G., Caggiano, M., Rothschild, M.F., Fontanesi, L. :

Whole genome sequencing provides information on the genomic architecture and diversity of cultivated gilthead seabream (Sparus aurata) broodstock nuclei. Genes (Basel) 14:839, 2023. Pubmed reference: 37107597. DOI: 10.3390/genes14040839.

Spondylurus culebrae :

2024

Rivera, D., Henderson, J.B., Lam, A.W., Hostetter, N.J., Collazo, J.A., Bell, R.C. :

High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks Spondylurus nitidus and S. culebrae. Genome Biol Evol :evae079, 2024. Pubmed reference: 38619022. DOI: 10.1093/gbe/evae079.

Spondylurus nitidus :

2024

Rivera, D., Henderson, J.B., Lam, A.W., Hostetter, N.J., Collazo, J.A., Bell, R.C. :

Squalus acanthias (spiny dogfish) :

2023

Wagner, C.I., Kopp, M.E.L., Thorburn, J., Jones, C.S., Hoarau, G., Noble, L.R. :

Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome. G3 (Bethesda) , 2023. Pubmed reference: 37395764. DOI: 10.1093/g3journal/jkad146.

Squamata (squamates) :

2023

Pinto, B.J., Gamble, T., Smith, C.H., Wilson, M.A. :

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. J Hered , 2023. Pubmed reference: 37018459. DOI: 10.1093/jhered/esad023.

Pinto, B.J., Gamble, T., Smith, C.H., Wilson, M.A. :

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. bioRxiv , 2023. Pubmed reference: 37034614. DOI: 10.1101/2023.01.20.524006.

Staurois parvus :

2023

Holtz, M.A., Racicot, R., Preininger, D., Stuckert, A.M.M., Mangiamele, L.A. :

Genome assembly of the foot-flagging frog, Staurois parvus: a resource for understanding mechanisms of behavior. G3 (Bethesda) , 2023. Pubmed reference: 37625789. DOI: 10.1093/g3journal/jkad193.

Steno bredanensis (rough-toothed dolphin) :

2023

Huang, X., Fan, H., Zhou, W., Yang, G., Wei, F. :

The rough-toothed dolphin genome provides new insights into the genetic mechanism of its rough teeth. Integr Zool , 2023. Pubmed reference: 37212019. DOI: 10.1111/1749-4877.12723.

Strigops habroptilus (kakapo) :

2023

Wold, J.R., Guhlin, J.G., Dearden, P.K., Santure, A.W., Steeves, T.E. :

The promise and challenges of characterising genome-wide structural variants: A case study in a critically endangered parrot. Mol Ecol Resour , 2023. Pubmed reference: 36916824. DOI: 10.1111/1755-0998.13783.

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

2015

Koepfli, K.P., Paten, B. :

The Genome 10K Project: a way forward. Annu Rev Anim Biosci 3:57-111, 2015. Pubmed reference: 25689317. DOI: 10.1146/annurev-animal-090414-014900.

Strix aluco (tawny owl) :

2024

Baltazar-Soares, M., Karell, P., Wright, D., Nilsson, J.Å., Brommer, J.E. :

Genomic basis of melanin-associated phenotypes suggests colour-specific environmental adaptations in tawny owls. Mol Ecol 33:e17247, 2024. Pubmed reference: 38173194. DOI: 10.1111/mec.17247.

Struthio camelus (African ostrich) :

2018

Papoli Yazdi, H., Ellegren, H. :

A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution. Genome Biol Evol , 2018. Pubmed reference: 30099482. DOI: 10.1093/gbe/evy163.

Suncus etruscus (white-toothed pygmy shrew) :

2024

Bukhman, Y.V., Meyer, S., Chu, L.F., Abueg, L., Antosiewicz-Bourget, J., Balacco, J., Brecht, M., Dinatale, E., Fedrigo, O., Formenti, G., Fungtammasan, A., Giri, S.J., Hiller, M., Howe, K., Kihara, D., Mamott, D., Mountcastle, J., Pelan, S., Rabbani, K., Sims, Y., Tracey, A., Wood, J.M.D., Jarvis, E.D., Thomson, J.A., Chaisson, M.J.P., Stewart, R. :

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Sci Data 11:176, 2024. Pubmed reference: 38326333. DOI: 10.1038/s41597-024-03011-x.

Sus scrofa (pig) :

2024

Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H. :

A compendium of genetic regulatory effects across pig tissues. Nat Genet , 2024. Pubmed reference: 38177344. DOI: 10.1038/s41588-023-01585-7.

Du, H., Diao, C., Zhuo, Y., Zheng, X., Hu, Z., Lu, S., Jin, W., Zhou, L., Liu, J.F. :

Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity. Genomics 116:S0888-7543(24)00002-8:110782, 2024. Pubmed reference: 38176574. DOI: 10.1016/j.ygeno.2024.110782.

Miao, J., Wei, X., Cao, C., Sun, J., Xu, Y., Zhang, Z., Wang, Q., Pan, Y., Wang, Z. :

Pig pangenome graph reveals functional features of non-reference sequences. J Anim Sci Biotechnol 15:32, 2024. Pubmed reference: 38389084. DOI: 10.1186/s40104-023-00984-4.

Zong, W., Zhao, R., Wang, X., Zhou, C., Wang, J., Chen, C., Niu, N., Zheng, Y., Chen, L., Liu, X., Hou, X., Zhao, F., Wang, L., Wang, L., Song, C., Zhang, L. :

Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. DNA Res :dsae008, 2024. Pubmed reference: 38447059. DOI: 10.1093/dnares/dsae008.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Jiang, Y.F., Wang, S., Wang, C.L., Xu, R.H., Wang, W.W., Jiang, Y., Wang, M.S., Jiang, L., Dai, L.H., Wang, J.R., Chu, X.H., Zeng, Y.Q., Fang, L.Z., Wu, D.D., Zhang, Q., Ding, X.D. :

Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 26:106119, 2023. Pubmed reference: 36852268. DOI: 10.1016/j.isci.2023.106119.

Zhang, F., Velez-Irizarry, D., Ernst, C.W., Huang, W. :

Mapping splice QTLs reveals distinct transcriptional and post-transcriptional regulatory variation of gene expression and identifies putative alternative splicing variation mediating complex trait variation in pigs. BMC Genomics 24:240, 2023. Pubmed reference: 37142954. DOI: 10.1186/s12864-023-09314-4.

Ding, R., Savegnago, R., Liu, J., Long, N., Tan, C., Cai, G., Zhuang, Z., Wu, J., Yang, M., Qiu, Y., Ruan, D., Quan, J., Zheng, E., Yang, H., Li, Z., Tan, S., Bedhane, M., Schnabel, R., Steibel, J., Gondro, C., Yang, J., Huang, W., Wu, Z. :

The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs. Commun Biol 6:577, 2023. Pubmed reference: 37253973. DOI: 10.1038/s42003-023-04933-9.

Qian, R., Xie, F., Zhang, W., Kong, J., Zhou, X., Wang, C., Li, X. :

Genome-wide detection of CNV regions between Anqing six-end-white and Duroc pigs. Mol Cytogenet 16:12, 2023. Pubmed reference: 37400846. DOI: 10.1186/s13039-023-00646-0.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome , 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Tong, X., Chen, D., Hu, J., Lin, S., Ling, Z., Ai, H., Zhang, Z., Huang, L. :

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences. Nat Commun 14:5126, 2023. Pubmed reference: 37612277. DOI: 10.1038/s41467-023-40434-3.

Benjamin, N.R., Crooijmans, R.P.M.A., Jordan, L.R., Bolt, C.R., Schook, L.B., Schachtschneider, K.M., Groenen, M.A.M., Roca, A.L. :

Swine global genomic resources: insights into wild and domesticated populations. Mamm Genome , 2023. Pubmed reference: 37805667. DOI: 10.1007/s00335-023-10012-5.

Li, J., Zhao, T., Guan, D., Pan, Z., Bai, Z., Teng, J., Zhang, Z., Zheng, Z., Zeng, J., Zhou, H., Fang, L., Cheng, H. :

Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits. Cell Genom 3:100390, 2023. Pubmed reference: 37868039. DOI: 10.1016/j.xgen.2023.100390.

Li, Z., Liu, X., Wang, C., Li, Z., Jiang, B., Zhang, R., Tong, L., Qu, Y., He, S., Chen, H., Mao, Y., Li, Q., Pook, T., Wu, Y., Zan, Y., Zhang, H., Li, L., Wen, K., Chen, Y. :

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation. Genome Res , 2023. Pubmed reference: 37914227. DOI: 10.1101/gr.277638.122.

Kwon, D., Park, N., Wy, S., Lee, D., Chai, H.H., Cho, I.C., Lee, J., Kwon, K., Kim, H., Moon, Y., Kim, J., Park, W., Kim, J. :

A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa). Sci Data 10:761, 2023. Pubmed reference: 37923776. DOI: 10.1038/s41597-023-02661-7.

Zeng, H., Zhang, W., Lin, Q., Gao, Y., Teng, J., Xu, Z., Cai, X., Zhong, Z., Wu, J., Liu, Y., Diao, S., Wei, C., Gong, W., Pan, X., Li, Z., Huang, X., Chen, X., Du, J. :

PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs. Nucleic Acids Res , 2023. Pubmed reference: 37956339. DOI: 10.1093/nar/gkad1080.

2022

Chen, J., Zhong, J., He, X., Li, X., Ni, P., Safner, T., Šprem, N., Han, J. :

The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications. Anim Genet 53:281-292, 2022. Pubmed reference: 35238061. DOI: 10.1111/age.13181.

Crespo-Piazuelo, D., Acloque, H., González-Rodríguez, O., Mongellaz, M., Mercat, M.J., Bink, M.C.A.M., Huisman, A.E., Ramayo-Caldas, Y., Sánchez, J.P., Ballester, M. :

Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues. Gigascience 12, 2022. Pubmed reference: 37354463. DOI: 10.1093/gigascience/giad042.

2021

Pan, Z., Yao, Y., Yin, H., Cai, Z., Wang, Y., Bai, L., Kern, C., Halstead, M., Chanthavixay, G., Trakooljul, N., Wimmers, K., Sahana, G., Su, G., Lund, M.S., Fredholm, M., Karlskov-Mortensen, P., Ernst, C.W., Ross, P., Tuggle, C.K., Fang, L., Zhou, H. :

Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat Commun 12:5848, 2021. Pubmed reference: 34615879. DOI: 10.1038/s41467-021-26153-7.

Wang, D., Yang, L., Ning, C., Liu, J.F., Zhao, X. :

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs. BMC Genomics 22:736, 2021. Pubmed reference: 34641784. DOI: 10.1186/s12864-021-08030-1.

Zhang, Y., Fan, G., Liu, X., Skovgaard, K., Sturek, M., Heegaard, P.M.H. :

The genome of the naturally evolved obesity-prone Ossabaw miniature pig. iScience 24:103081, 2021. Pubmed reference: 34585119. DOI: 10.1016/j.isci.2021.103081.

2020

Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Girón, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Schwartz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P.L., Archibald, A.L. :

An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience 9:giaa051, 2020. Pubmed reference: 32543654. DOI: 10.1093/gigascience/giaa051.

2018

Keel, B.N., Nonneman, D.J., Lindholm-Perry, A.K., Oliver, W.T., Rohrer, G.A. :

Porcine single nucleotide polymorphisms and their functional effect: an update. BMC Res Notes 11:860, 2018. Pubmed reference: 30514360. DOI: 10.1186/s13104-018-3973-6.

2014

Fernández, A.I., Muñoz, M., Alves, E., Folch, J.M., Noguera, J.L., Enciso, M.P., Rodríguez, M.d.e.l. .C., Silió, L. :

Recombination of the porcine X chromosome: a high density linkage map. BMC Genet 15:148, 2014. Pubmed reference: 25526890. DOI: 10.1186/s12863-014-0148-x.

2012

Freeman, T.C., Ivens, A., Baillie, J.K., Beraldi, D., Barnett, M.W., Dorward, D., Downing, A., Fairbairn, L., Kapetanovic, R., Raza, S., Tomoiu, A., Alberio, R., Wu, C., Su, A.I., Summers, K.M., Tuggle, C.K., Archibald, A.L., Hume, D.A. :

A gene expression atlas of the domestic pig. BMC Biol 10:90, 2012. Pubmed reference: 23153189. DOI: 10.1186/1741-7007-10-90.

Tortereau, F., Servin, B., Frantz, L., Megens, H.J., Milan, D., Rohrer, G., Wiedmann, R., Beever, J., Archibald, A.L., Schook, L.B., Groenen, M.A. :

A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics 13:586, 2012. Pubmed reference: 23152986. DOI: 10.1186/1471-2164-13-586.

Groenen, M.A., Archibald, A.L., Uenishi, H., Tuggle, C.K., Takeuchi, Y., Rothschild, M.F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H.J., Li, S., Larkin, D.M., Kim, H., Frantz, L.A., Caccamo, M., Ahn, H., Aken, B.L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C.W., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S.H., Chow, W., Clark, R.C., Clee, C., Crooijmans, R.P., Dawson, H.D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z.Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G.J., Fowler, K.E., Fredholm, M., Fritz, E., Gilbert, J.G., Giuffra, E., Gorodkin, J., Griffin, D.K., Harrow, J.L., Hayward, A., Howe, K., Hu, Z.L., Humphray, S.J., Hunt, T., Hornshøj, H., Jeon, J.T., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J.H., Kim, K.W., Kim, T.H., Larson, G., Lee, K., Lee, K.T., Leggett, R., Lewin, H.A., Li, Y., Liu, W., Loveland, J.E., Lu, Y., Lunney, J.K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M.P., Narayan, J., Nguyen, D.T., Ni, P., Oh, S.J., Onteru, S., Panitz, F., Park, E.W., Park, H.S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J.M., Rodriguez-Zas, S., Rohrer, G.A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J.G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B.R., Sperber, G., Stadler, P., Sweedler, J.V., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C., Schook, L.B. :

Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393-8, 2012. Pubmed reference: 23151582. DOI: 10.1038/nature11622.

2010

Archibald, A.L., Bolund, L., Churcher, C., Fredholm, M., Groenen, M.A., Harlizius, B., Lee, K.T., Milan, D., Rogers, J., Rothschild, M.F., Uenishi, H., Wang, J., Schook, L.B. :

Pig genome sequence--analysis and publication strategy. BMC Genomics 11:438, 2010. Pubmed reference: 20642822. DOI: 10.1186/1471-2164-11-438.

2009

Ramos, A.M., Crooijmans, R.P., Affara, N.A., Amaral, A.J., Archibald, A.L., Beever, J.E., Bendixen, C., Churcher, C., Clark, R., Dehais, P., Hansen, M.S., Hedegaard, J., Hu, Z.L., Kerstens, H.H., Law, A.S., Megens, H.J., Milan, D., Nonneman, D.J., Rohrer, G.A., Rothschild, M.F., Smith, T.P., Schnabel, R.D., Van Tassell, C.P., Taylor, J.F., Wiedmann, R.T., Schook, L.B., Groenen, M.A. :

Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4:e6524, 2009. Pubmed reference: 19654876. DOI: 10.1371/journal.pone.0006524.

Amaral, A.J., Megens, H.J., Kerstens, H.H., Heuven, H.C., Dibbits, B., Crooijmans, R.P., den Dunnen, J.T., Groenen, M.A. :

Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics 10:374, 2009. Pubmed reference: 19674453. DOI: 10.1186/1471-2164-10-374.

2007

Humphray, S.J., Scott, C.E., Clark, R., Marron, B., Bender, C., Camm, N., Davis, J., Jenks, A., Noon, A., Patel, M., Sehra, H., Yang, F., Rogatcheva, M.B., Milan, D., Chardon, P., Rohrer, G., Nonneman, D., de Jong, P., Meyers, S.N., Archibald, A., Beever, J.E., Schook, L.B., Rogers, J. :

A high utility integrated map of the pig genome. Genome Biol 8:R139, 2007. Pubmed reference: 17625002. DOI: 10.1186/gb-2007-8-7-r139.

2005

Schook, L.B., Beever, J.E., Rogers, J., Humphray, S., Archibald, A., Chardon, P., Milan, D., Rohrer, G., Eversole, K. :

Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome. Comp Funct Genomics 6:251-5, 2005. Pubmed reference: 18629187. DOI: 10.1002/cfg.479.

2003

Karsenty, E., Barillot, E., Tosser-Klopp, G., Lahbib-Mansais, Y., Milan, D., Hatey, F., Cirera, S., Sawera, M., Jorgensen, C.B., Chowdhary, B., Fredholm, M., Wimmers, K., Ponsuksili, S., Davoli, R., Fontanesi, L., Braglia, S., Zambonelli, P., Bigi, D., Neuenschwander, S., Gellin, J. :

The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa) Nucleic Acids Research 31:138-41, 2003. Pubmed reference: 12519967.

Martins-Wess, F., Milan, D., Drogemuller, C., Vobeta-Nemitz, R., Brenig, B., Robic, A., Yerle, M., Leeb, T. :

A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1 BMC Genomics 4:20, 2003. Pubmed reference: 12744726. DOI: 10.1186/1471-2164-4-20.

Rothschild, M.F. :

From a sow's ear to a silk purse: real progress in porcine genomics. Cytogenet Genome Res 102:95-9, 2003. Pubmed reference: 14970686. DOI: 75732.

2002

Jiang, Z.H., Melville, J.S., Cao, H.H., Kumar, S., Filipski, A., Gibbins, A.M.V. :

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome Genome 45:769-776, 2002. Pubmed reference: 12175081.

Yerle, M., Pinton, P., Delcros, C., Arnal, N., Milan, D., Robic, A. :

Generation and characterization of a 12,,000-rad radiation hybrid panel for fine mapping in pig Cytogenetic & Genome Research 97:219-228, 2002.

Rink, A., Santschi, E.M., Eyer, K.M., Roelofs, B., Hess, M., Godfrey, M., Karajusuf, E.K., Yerle, M., Milan, D., Beattie, C.W. :

A first-generation EST RH comparative map of the porcine and human genome Mammalian Genome 13:578-87, 2002. Pubmed reference: 12420136. DOI: 10.1007/s00335-002-2192-5.

1999

Hawken, R.J., Murtaugh, J., Flickinger, G.H., Yerle, M., Robic, A., Milan, D., Gellin, J., Beattie, C.W., Schook, L.B., Alexander, L.J. :

A first-generation porcine whole-genome radiation hybrid map Mammalian Genome 10:824-830, 1999. Pubmed reference: 10430669.

Mikawa, S., Akita, T., Hisamatsu, N., Inage, Y., Ito, Y., Kobayashi, E., Kusumoto, H., Matsumoto, T., Mikami, H., Minezawa, M., Miyake, M., Shimanuki, S., Sugiyama, C., Uchida, Y., Wada, Y., Yanai, S., Yasue, H. :

A linkage map of 243 DNA markers in an intercross of Gottingen miniature and Meishan pigs Animal Genetics 30:407-417, 1999. Pubmed reference: 10612229.

1998

Yerle, M., Pinton, P., Robic, A., Alfonso, A., Palvadeau, Y., Delcros, C., Hawken, R., Alexander, L., Beattie, C., Schook, L., Milan, D., Gellin, J. :

Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs Cytogenetics & Cell Genetics 82:182-188, 1998.

1997

Ambady, S., Mendiola, J.R., Louis, C.F., Janzen, M.A., Schook, L.B., Buoen, L., Lunney, J.K., Grimm, D.R., Deleon, F.A.P. :

Development and use of a microdissected swine chromosome 6 dna library Cytogenetics & Cell Genetics 76:27-33, 1997.

Rohrer, G.A., Alexander, L.J., Beattie, C.W., Wilkie, P., Flickinger, G.H., Schook, L.B., Paszek, A.A., Andersson, L., Mariani, P., Marklund, L., Fredholm, M., Hoyheim, B., Archibald, A.L., Nielsen, V.H., Milan, D., Groenen, M.A.M. :

A consensus linkage map for swine chromosome 7 Animal Genetics 28:223-229, 1997.

Yerle, M., Lahbibmansais, Y., Pinton, P., Robic, A., Goureau, A., Milan, D., Gellin, J. :

The cytogenetic map of the domestic pig (sus scrofa domestica) [Review] Mammalian Genome 8:592-607, 1997. Pubmed reference: 9250869.

Andersson, L. :

The use of a wild pig x domestic pig intercross to map phenotypic trait loci Journal of Heredity 88:380-383, 1997. Pubmed reference: 9378913.

1996

Fronicke, L., Chowdhary, B.P., Scherthan, H., Gustavsson, I. :

A comparative map of the porcine and human genomes demonstrates zoo-FISH and gene mapping-based chromosomal homologies Mammalian Genome 7:285-290, 1996. Pubmed reference: 8661700.

Rohrer, G.A., Alexander, L.J., Hu, Z.L., Smith, T.P.L., Keele, J.W., Beattie, C.W. :

A comprehensive map of the porcine genome Genome Research 6:371-391, 1996. Pubmed reference: 8743988.

Marklund, L., Johansson Moller, M., Høyheim, B., Davies, W., Fredholm, M., Juneja, R.K., Mariani, P., Coppieters, W., Ellegren, H., Andersson, L. :

A comprehensive linkage map of the pig based on a wild pig-Large White intercross. Anim Genet 27:255-69, 1996. Pubmed reference: 8856923.

Rettenberger, G., Bruch, J., Hameister, H. :

A comparative mapping approach to the pig genome Journal of Animal Breeding & Genetics-Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 113:331-338, 1996.

Comparative genome organization of vertebrates Mammalian Genome 7:717-734, 1996. Pubmed reference: 8854859.

1995

Archibald, A.L., Haley, C.S., Brown, J.F., Couperwhite, S., McQueen, H.A., Nicholson, D., Coppieters, W., Weghe, A. van de, Stratil, A., Wintero, A.K., Fredholm, M., Larsen, N.J., Nielsen, V.H., Milan, D., Woloszyn, N., Robic, A., Dalens, M., Riquet, J., Gellin, J., Caritez, J.C., Burgaud, G., Ollivier, L., Bidanel, J.P., Vaiman, M., Renard, C., Geldermann, H., Davoli, R., Ruyter, D., Verstege, E.J.M., Groenen, M.A.M., Davies, W., Hoyheim, B., Keiserud, A., Andersson, L., Ellegren, H., Johansson, M., Marklund, L., Miller, J.R., Dear, D.V.A., Signer, E., Jeffreys, A.J., Moran, C., Le Tissier, P., Muladno, Rothschild, M.F., Tuggle, C.K., Vaske, D., Helm, J., Liu, H.-C., Rahman, A., Yu, T.-P., Larson, R.G., Schmitz, C.B. :

The PiGMaP consortium linkage map of the pig (Sus scrofa) Mammalian Genome 6:157-175, 1995. Pubmed reference: 7749223.

Yerle, M., Lahbibmansais, Y., Mellink, C., Goureau, A., Pinton, P., Echard, G., Gellin, J., Zijlstra, C., Dehaan, N., Bosma, A.A., Chowdhary, B., Gu, F., Gustavsson, I., Thomsen, P.D., Christensen, K., Rettenberger, G., Hameister, H., Schmitz, A., Chaput, B., Frelat, G. :

The PiGMaP consortium cytogenetic map of the domestic pig (Sus scrofa domestica) Mammalian Genome 6:176-186, 1995. Pubmed reference: 7749224.

Rettenberger, G., Klett, C., Zechner, U., Kunz, J., Vogel, W., Hameister, H. :

Visualization of the conservation of synteny between humans and pigs by heterologous chromosomal painting Genomics 26:372-378, 1995. Pubmed reference: 7601464.

Ollivier, L. :

Genetic differences in recombination frequency in the pig (sus scrofa) Genome 38:1048-1051, 1995. Pubmed reference: 8536996.

1994

Rohrer, G.A., Alexander, L.J., Keele, J.W., Smith, T.P., Beattie, C.W. :

A Microsatellite Linkage Map of the Porcine Genome Genetics 136:231-245, 1994. Pubmed reference: 8138161.

Ellegren, H., Chowdhary, B.P., Johansson, M., Marklund, L., Fredholm, M., Gustavsson, I., Andersson, L. :

A primary linkage map of the porcine genome reveals a low rate of genetic recombination Genetics 137:1089-1100, 1994. Pubmed reference: 7982563.

Beattie, C.W. :

Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.

1992

Echard, G., Milan, D., Yerle, M., Lahbibmansais, Y., Gellin, J. :

The Gene Map of the Pig (Sus-Scrofa-Domestica L) - A Review Cytogenetics and Cell Genetics 61:146-151, 1992. Pubmed reference: 1395726.

None

[No authors listed] :

, None. Pubmed reference: 38056526.

Sylvia atricapilla (blackcap) :

2023

Bours, A., Pruisscher, P., Bascón-Cardozo, K., Odenthal-Hesse, L., Liedvogel, M. :

The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons. Sci Rep 13:16471, 2023. Pubmed reference: 37777595. DOI: 10.1038/s41598-023-43090-1.

Syngnathus scovelli (Gulf pipefish) :

2023

Ramesh, B., Small, C.M., Healey, H., Johnson, B., Barker, E., Currey, M., Bassham, S., Myers, M., Cresko, W.A., Jones, A.G. :

Improvements to the Gulf pipefish Syngnathus scovelli genome. GigaByte 2023:gigabyte76, 2023. Pubmed reference: 36969711. DOI: 10.46471/gigabyte.76.

Tachyglossus aculeatus (Australian echidna) :

2021

Platypus and echidna genomes reveal mammalian biology and evolution. Nature 592:756-762, 2021. Pubmed reference: 33408411. DOI: 10.1038/s41586-020-03039-0.

Tachysurus fulvidraco × Tachysurus vachelli (hybrid yellow catfish) :

2021

Zhou, H., Duan, G., Jiang, H., Ling, J., Hu, Y., Zhang, Y., Wang, H., Pan, T., Chen, X. :

High-density genetic map and QTL mapping for body color of the yellow catfish (Tachysurus fulvidraco♀ × T. vachellii♂). Anim Genet , 2021. Pubmed reference: 33503316. DOI: 10.1111/age.13042.

Taeniopygia guttata (zebra finch) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

2008

Stapley, J., Birkhead, TR., Burke, T., Slate, J. :

A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution. Genetics 179:651-67, 2008. Pubmed reference: 10506561.

Tanypteryx hageni :

2023

Tolman, E.R., Beatty, C.D., Bush, J., Kohli, M., Moreno, C.M., Ware, J.L., Webber, K.S., Khan, R., Maheshwari, C., Weisz, D., Dudchenko, O., Aiden, E.L., Frandsen, P.B. :

A chromosome-length assembly of the black petaltail (Tanypteryx hageni) dragonfly. Genome Biol Evol , 2023. Pubmed reference: 36807678. DOI: 10.1093/gbe/evad024.

Tautogolabrus adspersus (cunner) :

2023

Nugent, C.M., Kess, T., Brachmann, M.K., Langille, B.L., Duffy, S.J., Lehnert, S.J., Wringe, B.F., Bentzen, P., Bradbury, I.R. :

Whole-genome sequencing reveals fine-scale environment-associated divergence near the range limits of a temperate reef fish. Mol Ecol , 2023. Pubmed reference: 37430462. DOI: 10.1111/mec.17063.

Thunnus albacares (yellowfin tuna) :

2024

Dimens, P.V., Jones, K.L., Margulies, D., Scholey, V., Cusatti, S., McPeak, B., Hildahl, T.E., Saillant, E.A.E. :

Genomic resources for the Yellowfin tuna Thunnus albacares. Mol Biol Rep 51:232, 2024. Pubmed reference: 38281308. DOI: 10.1007/s11033-023-09117-6.

Thymallus thymallus (grayling) :

2019

Sävilammi, T., Primmer, C.R., Varadharajan, S., Guyomard, R., Guiguen, Y., Sandve, S.R., Vøllestad, L.A., Papakostas, S., Lien, S. :

The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids. G3 (Bethesda) , 2019. Pubmed reference: 30833292. DOI: 10.1534/g3.118.200919.

Thyrsites atun (snoek) :

2023

Mthethwa, S., Bester-van der Merwe, A., Roodt-Wilding, R. :

The complete mitochondrial genome of the South African snoek Thyrsites atun (Euphrasén, 1791) (Perciformes, Gempylidae). Mitochondrial DNA B Resour 8:288-291, 2023. Pubmed reference: 36845005. DOI: 10.1080/23802359.2023.2179353.

Trachinotus ovatus (derbio) :

2023

Luo, H., Zhang, Y., Liu, F., Zhao, Y., Peng, J., Xu, Y., Chen, X., Huang, Y., Ji, C., Liu, Q., He, P., Feng, P., Yang, C., Wei, P., Ma, Z., Qin, J., Zhou, S., Dai, S., Zhang, Y., Zhao, Z., Liu, H., Zheng, H., Zhang, J., Lin, Y., Chen, X. :

The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth. J Adv Res :S2090-1232(23)00369-7, 2023. Pubmed reference: 38043610. DOI: 10.1016/j.jare.2023.11.030.

Trachurus trachurus (Atlantic horse mackerel) :

2022

Genner, M., Collins, R. :

The genome sequence of the Atlantic horse mackerel, Trachurus trachurus (Linnaeus 1758). Wellcome Open Res 7:118, 2022. Pubmed reference: 36874570. DOI: 10.12688/wellcomeopenres.17813.1.

Tragopan temminckii (Temminck's tragopan) :

2023

Li, X., Wang, X., Yu, X., Yang, C., Lin, L., Huang, Y. :

The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 24:751, 2023. Pubmed reference: 38062370. DOI: 10.1186/s12864-023-09857-6.

Tremarctos ornatus (spectacled bear) :

2021

Saremi, N.F., Oppenheimer, J., Vollmers, C., O'Connell, B., Milne, S.A., Byrne, A., Yu, L., Ryder, O.A., Green, R.E., Shapiro, B. :

An annotated draft genome for the Andean bear, Tremarctos ornatus. J Hered 112:377-384, 2021. Pubmed reference: 33882130. DOI: 10.1093/jhered/esab021.

Trematomus bernacchii (emerald rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Trematomus hansoni (striped rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Trematomus loennbergii (deepwater notothen) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Trematomus scotti (blackfin notothen) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Trichomycterus rosablanca (Andean cavefish) :

2024

Cadena, C.D., Pabón, L., DoNascimiento, C., Abueg, L., Tilley, T., O-Toole, B., Absolon, D., Sims, Y., Formenti, G., Fedrigo, O., Jarvis, E.D., Torres, M. :

A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments. J Hered :esae019, 2024. Pubmed reference: 38513109. DOI: 10.1093/jhered/esae019.

Trichosurus vulpecula (common brushtail) :

2023

Bond, D.M., Ortega-Recalde, O., Laird, M.K., Hayakawa, T., Richardson, K.S., Reese, F.C.B., Kyle, B., McIsaac-Williams, B.E., Robertson, B.C., van Heezik, Y., Adams, A.L., Chang, W.S., Haase, B., Mountcastle, J., Driller, M., Collins, J., Howe, K., Go, Y., Thibaud-Nissen, F., Lister, N.C., Waters, P.D., Fedrigo, O., Jarvis, E.D., Gemmell, N.J., Alexander, A., Hore, T.A. :

The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes. Nat Commun 14:6364, 2023. Pubmed reference: 37848431. DOI: 10.1038/s41467-023-41784-8.

Trimeresurus albolabris (white-lipped tree viper) :

2024

Niu, X., Lv, Y., Chen, J., Feng, Y., Cui, Y., Lu, H., Liu, H. :

The genome assembly and annotation of the white-lipped tree pit viper Trimeresurus albolabris. GigaByte 2024:gigabyte106, 2024. Pubmed reference: 38313188. DOI: 10.46471/gigabyte.106.

Turnix suscitator (barred buttonquail) :

2023

Dey, P., Ray, S.D., Pramod, P., Singh, R.P. :

Dataset from genome sequencing, assembly and mining of microsatellite markers in barred-button quail (Turnix suscitator). Data Brief 48:109288, 2023. Pubmed reference: 37383822. DOI: 10.1016/j.dib.2023.109288.

Tympanuchus pallidicinctus (lesser prairie-chicken) :

2023

Black, A.N., Bondo, K.J., Mularo, A., Hernandez, A., Yu, Y., Stein, C.M., Gregory, A., Fricke, K.A., Prendergast, J., Sullins, D., Haukos, D., Whitson, M., Grisham, B., Lowe, Z., DeWoody, J.A. :

A highly-contiguous and annotated genome assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus). Genome Biol Evol , 2023. Pubmed reference: 36916502. DOI: 10.1093/gbe/evad043.

Urocyon cinereoargenteus (gray fox) :

2024

Armstrong, E.E., Bissell, K.L., Fatima, H.S., Heikkinen, M.A., Jessup, A., Junaid, M.O., Lee, D.H., Lieb, E.C., Liem, J.T., Martin, E.M., Moreno, M., Otgonbayar, K., Romans, B.W., Royar, K., Adler, M.B., Needle, D.B., Harkess, A., Kelley, J.L., Mooney, J.A., Mychajliw, A.M. :

Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3 (Bethesda) :jkae034, 2024. Pubmed reference: 38366575. DOI: 10.1093/g3journal/jkae034.

Urosaurus nigricaudus :

2023

Davalos-Dehullu, E., Baty, S.M., Fisher, R.N., Scott, P.A., Dolby, G.A., Munguia-Vega, A., Cortez, D. :

Chromosome-level genome assembly of the blacktail brush lizard, Urosaurus nigricaudus, reveals dosage compensation in an endemic lizard. Genome Biol Evol 15:evad210, 2023. Pubmed reference: 38056449. DOI: 10.1093/gbe/evad210.

Ursidae (bears) :

2022

Willey, C., Korstanje, R. :

Sequencing and assembling bear genomes: the bare necessities. Front Zool 19:30, 2022. Pubmed reference: 36451195. DOI: 10.1186/s12983-022-00475-8.

Ursus americanus (American black bear) :

2019

Srivastava, A., Kumar Sarsani, V., Fiddes, I., Sheehan, S.M., Seger, R.L., Barter, M.E., Neptune-Bear, S., Lindqvist, C., Korstanje, R. :

Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation. DNA Res 26:37-44, 2019. Pubmed reference: 30395234. DOI: 10.1093/dnares/dsy036.

Ursus arctos (brown bear) :

2023

Perry, B.W., Saxton, M.W., Jansen, H.T., Quackenbush, C.R., Evans Hutzenbiler, B.D., Robbins, C.T., Kelley, J.L., Cornejo, O.E. :

A multi-tissue gene expression dataset for hibernating brown bears. BMC Genom Data 24:33, 2023. Pubmed reference: 37291509. DOI: 10.1186/s12863-023-01136-3.

2021

Scarpulla, E., Boattini, A., Cozzo, M., Giangregorio, P., Ciucci, P., Mucci, N., Randi, E., Davoli, F. :

First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach. BMC Genomics 22:623, 2021. Pubmed reference: 34407764. DOI: 10.1186/s12864-021-07915-5.

Varanus komodoensis (Komodo dragon) :

2019

van Hoek, M.L., Prickett, M.D., Settlage, R.E., Kang, L., Michalak, P., Vliet, K.A., Bishop, B.M. :

The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters. BMC Genomics 20:684, 2019. Pubmed reference: 31470795. DOI: 10.1186/s12864-019-6029-y.

Vicugna pacos (alpaca) :

2021

Calderon, M., More, M.J., Gutierrez, G.A., Ponce de León, F.A. :

Development of a 76k alpaca (Vicugna pacos) single nucleotide polymorphisms (SNPs) microarray. Genes (Basel) 12, 2021. Pubmed reference: 33669871. DOI: 10.3390/genes12020291.

2020

Mendoza, M.N., Raudsepp, T., More, M.J., Gutiérrez, G.A., Ponce de León, F.A. :

Cytogenetic mapping of 35 new markers in the alpaca (Vicugna pacos). Genes (Basel) 11, 2020. Pubmed reference: 32397072. DOI: 10.3390/genes11050522.

2019

Richardson, M.F., Munyard, K., Croft, L.J., Allnutt, T.R., Jackling, F., Alshanbari, F., Jevit, M., Wright, G.A., Cransberg, R., Tibary, A., Perelman, P., Appleton, B., Raudsepp, T. :

Chromosome-level alpaca reference genome VicPac3.1 improves genomic insight into the biology of new world camelids. Front Genet 10:586, 2019. Pubmed reference: 31293619. DOI: 10.3389/fgene.2019.00586.

Mendoza, M.N., Raudsepp, T., Alshanbari, F., Gutiérrez, G., Ponce de León, F.A. :

Chromosomal localization of candidate genes for fiber growth and color in alpaca (Vicugna pacos). Front Genet 10:583, 2019. Pubmed reference: 31275359. DOI: 10.3389/fgene.2019.00583.

Vomeridens infuscipinnis :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Vulpes pallida (pale fox) :

2023

L Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R., Godinho, R. :

North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol , 2023. Pubmed reference: 37308700. DOI: 10.1038/s41559-023-02094-w.

Vulpes rueppellii (Rueppel's fox) :

2023

L Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R., Godinho, R. :

North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol , 2023. Pubmed reference: 37308700. DOI: 10.1038/s41559-023-02094-w.

Vulpes vulpes (red fox) :

2023

L Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R., Godinho, R. :

North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol , 2023. Pubmed reference: 37308700. DOI: 10.1038/s41559-023-02094-w.

2019

Rando, H.M., Wadlington, W.H., Johnson, J.L., Stutchman, J.T., Trut, L.N., Farré, M., Kukekova, A.V. :

The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 10, 2019. Pubmed reference: 31142040. DOI: 10.3390/genes10060409.

2018

Kukekova, A.V., Johnson, J.L., Xiang, X., Feng, S., Liu, S., Rando, H.M., Kharlamova, A.V., Herbeck, Y., Serdyukova, N.A., Xiong, Z., Beklemischeva, V., Koepfli, K.P., Gulevich, R.G., Vladimirova, A.V., Hekman, J.P., Perelman, P.L., Graphodatsky, A.S., O'Brien, S.J., Wang, X., Clark, A.G., Acland, G.M., Trut, L.N., Zhang, G. :

Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol 2:1479-1491, 2018. Pubmed reference: 30082739. DOI: 10.1038/s41559-018-0611-6.

Author Correction: Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol , 2018. Pubmed reference: 30104754. DOI: 10.1038/s41559-018-0664-6.

2011

Kukekova, A.V., Trut, L.N., Chase, K., Kharlamova, A.V., Johnson, J.L., Temnykh, S.V., Oskina, I.N., Gulevich, R.G., Vladimirova, A.V., Klebanov, S., Shepeleva, D.V., Shikhevich, S.G., Acland, G.M., Lark, K.G. :

Mapping Loci for fox domestication: deconstruction/reconstruction of a behavioral phenotype. Behav Genet 41:593-606, 2011. Pubmed reference: 21153916. DOI: 10.1007/s10519-010-9418-1.

2007

Kukekova, A.V., Trut, L.N., Oskina, I.N., Johnson, J.L., Temnykh, S.V., Kharlamova, A.V., Shepeleva, D.V., Gulievich, R.G., Shikhevich, S.G., Graphodatsky, A.S., Aguirre, G.D., Acland, G.M. :

A meiotic linkage map of the silver fox, aligned and compared to the canine genome. Genome Res 17:387-99, 2007. Pubmed reference: 17284676. DOI: 10.1101/gr.5893307.

1998

Rubtsov, N.B. :

The Fox Gene Map. ILAR J 39:182-188, 1998. Pubmed reference: 11528077.

Vulpes zerda (fennec fox) :

2023

L Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R., Godinho, R. :

North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol , 2023. Pubmed reference: 37308700. DOI: 10.1038/s41559-023-02094-w.

Xenopeltis unicolor (sunbeam snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell , 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Xiphophorus (swordtail and platyfish) :

2023

Lu, Y., Rice, E., Du, K., Kneitz, S., Naville, M., Dechaud, C., Volff, J.N., Boswell, M., Boswell, W., Hillier, L., Tomlinson, C., Milin, K., Walter, R.B., Schartl, M., Warren, W.C. :

High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res , 2023. Pubmed reference: 37147111. DOI: 10.1101/gr.277434.122.

Xyrichtys novacula (pearly razorfish) :

2023

Cruz, F., Gómez-Garrido, J., Gut, M., Alioto, T.S., Pons, J., Alós, J., Barcelo-Serra, M. :

Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome. DNA Res , 2023. Pubmed reference: 37797305. DOI: 10.1093/dnares/dsad021.

Zacco platypus (freshwater minnow) :

2024

Xu, X., Chen, J., Guan, W., Niu, B., Yi, S., Lou, B. :

A chromosome-level genome assembly of East Asia endemic minnow Zacco platypus. Sci Data 11:317, 2024. Pubmed reference: 38538602. DOI: 10.1038/s41597-024-03163-w.

Zonotrichia leucophrys :

2024

Wu, Z., Miedzinska, K., Krause, J.S., Pérez, J.H., Wingfield, J.C., Meddle, S.L., Smith, J. :

A chromosome-level genome assembly of a free-living white-crowned sparrow (Zonotrichia leucophrys gambelii). Sci Data 11:86, 2024. Pubmed reference: 38238322. DOI: 10.1038/s41597-024-02929-6.

The University of Sydney - OMIA - Online Mendelian Inheritance in Animals

Genetic map articles

Acanthopagrus schlegelii (black porgy) :

Acestrorhynchus altus :

Acinonyx jubatus (cheetah) :

Acomys cahirinus (Egyptian spiny mouse) :

Acridotheres tristis (common myna) :

Acrossocheilus fasciatus :

Actinemys marmorata (Pacific pond turtle) :

Agapornis roseicollis (peach-faced lovebird) :

Agelaius tricolor (tricolored blackbird) :

Ahaetulla prasina (Asian vine snakes) :

Ailuropoda melanoleuca (giant panda) :

Akarotaxis nudiceps :

Albula glossodonta (roundjaw bonefish) :

Alectoris chukar (chukar partridge) :

Alectoris magna (Przewalski's partridge) :

Alligator mississippiensis (American alligator) :

Amazona aestiva (blue-fronted amazon) :

Amazona vittata (Puerto Rican parrot) :

Amblyraja radiata (thorny skate) :

Amia calva (bowfin) :

Amphilophus citrinellus (Midas cichlid) :

Amphiprion bicinctus (twoband anemonefish) :

Amphiprion percula (orange clownfish) :

Anas platyrhynchos (Mallard) :

Andrias davidianus (Chinese giant salamander) :

Anolis apletophallus (slender anole) :

Anoplopoma fimbria (sablefish) :

Anser anser (domestic goose) :

Anser cygnoides (swan goose) :

Aphelocoma californica (Western scrub-jay) :

Apis mellifera (honey bee) :

Ara macao (scarlet macaw) :

Aratinga solstitialis (sun parakeet) :

Archilochus colubris :

Archocentrus centrarchus (flier cichlid) :

Arizona elegans occidentalis :

Aselliscus stoliczkanus (Stoliczka's Asian trident bat) :

Astatotilapia calliptera (eastern happy) :

Astyanax mexicanus (Mexican tetra) :

Ateles fusciceps (brown-headed spider monkey) :

Aythya baeri (Baer's pochard) :

Aythya fuligula (tufted duck) :

Aythya marila (greater scaup) :

Bahaba taipingensis (Chinese bahaba) :

Balaenoptera musculus (Blue whale) :

Bathydraco marri (deepwater dragon) :

Bison bison (American bison) :

Bison bonasus (European bison) :

Boaedon fuliginosus (brown house snake) :

Boleophthalmus pectinirostris (great blue-spotted mudskipper) :

Bombyx mori (domestic silkworm) :

Bos gaurus (gaur) :

Bos grunniens (domestic yak) :

Bos indicus (indicine cattle (zebu)) :

Bos indicus x Bos taurus (hybrid cattle) :

Bos taurus (taurine cattle) :

Bovichtus diacanthus :

Bovichtus variegatus (thornfish) :

Brachyistius frenatus (kelp perch) :

Bradypodion pumilum :

Bradypodion ventrale (Southern dwarf chameleon) :

Bubalus bubalis (water buffalo) :

Bungarus multicinctus (many-banded krait) :

Cairina moschata (Muscovy duck) :

Callipepla californica (California quail) :

Callithrix jacchus (white-tufted-ear marmoset) :

Calotes versicolor (garden lizard) :

Calotriton arnoldi (Montseny brook newt) :

Calotriton asper (Pyrenean brook newt) :

Calypte anna (Anna's hummingbird) :

Camelus bactrianus (Bactrian camel) :

Camelus dromedarius (Arabian camel) :

Campylomormyrus compressirostris :

Canis aureus (golden jackal) :

Canis latrans (coyote) :

Canis lupus (gray wolf) :

Canis lupus dingo (dingo) :

Canis lupus familiaris (dog) :