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 30:dsad022, 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 114:271-278, 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) 13:jkad177, 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 31: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.

Yuan, Y., Zhong, T., Wang, Y., Yang, J., Gui, L., Shen, Y., Zhou, J., Chung-Davidson, Y.W., Li, W., Xu, J., Li, J., Li, M., Ren, J. :

Chromosome-scale genome assemblies of sexually dimorphic male and female Acrossocheilus fasciatus. Sci Data 11:653, 2024. Pubmed reference: 38906919. DOI: 10.1038/s41597-024-03504-9.

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 114:44-51, 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.

Lan, T., Yang, S., Li, H., Zhang, Y., Li, R., Sahu, S.K., Deng, W., Liu, B., Shi, M., Wang, S., Du, H., Huang, X., Lu, H., Liu, S., Deng, T., Chen, J., Wang, Q., Han, L., Zhou, Y., Li, Q., Li, D., Kristiansen, K., Wan, Q.H., Liu, H., Fang, S.G. :

Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives. Proc Natl Acad Sci U S A 121:e2406343121, 2024. Pubmed reference: 39186654. DOI: 10.1073/pnas.2406343121.

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 54:659-661, 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.

Alectoris rufa (red-legged partridge) :

2024

Eleiwa, A., Nadal, J., Vilaprinyo, E., Marin-Sanguino, A., Sorribas, A., Basallo, O., Lucido, A., Richart, C., Pena, R.N., Ros-Freixedes, R., Usie, A., Alves, R. :

Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge. Sci Rep 14:19531, 2024. Pubmed reference: 39174643. DOI: 10.1038/s41598-024-70018-0.

González-Prendes, R., Pena, R.N., Richart, C., Nadal, J., Ros-Freixedes, R. :

Long-read de novo assembly of the red-legged partridge (Alectoris rufa) genome. Sci Data 11:908, 2024. Pubmed reference: 39191744. DOI: 10.1038/s41597-024-03659-5.

Allactaga sibirica (Mongolian five-toed jerboa) :

2024

Chai, S., Chong, Y., Yin, D., Qiu, Q., Xu, S., Yang, G. :

Genomic insights into adaptation to bipedal saltation and desert-like habitats of jerboas. Sci China Life Sci 67:2003-2015, 2024. Pubmed reference: 38902451. DOI: 10.1007/s11427-023-2516-9.

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 27:686-696, 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.

Amphibia (amphibians) :

2024

Pyron, R.A., Pirro, S., Hains, T., Colston, T.J., Myers, E.A., O'Connell, K.A., Beamer, D.A. :

The draft genome sequences of 50 salamander species (Caudata, Amphibia). Biodivers Genomes 2024, 2024. Pubmed reference: 38725637. DOI: 10.56179/001c.116891.

Kosch, T.A., Torres-Sánchez, M., Liedtke, H.C., Summers, K., Yun, M.H., Crawford, A.J., Maddock, S.T., Ahammed, M.S., Araújo, V.L.N., Bertola, L.V., Bucciarelli, G., Carné, A., Carneiro, C.M., Chan, K.O., Chen, Y., Crottini, A., da Silva, J.M., Denton, R.D., Dittrich, C., Themudo, G.E., Farquharson, K.A., Forsdick, N.J., Gilbert, E., Jing, C., Katzenback, B.A., Kotharambath, R., Levis, N.A., Márquez, R., Mazepa, G., Mulder, K.P., Müller, H., O'Connell, M.J., Orozco-terWengel, P., Palomar, G., Petzold, A., Pfennig, D.W., Pfennig, K.S., Reichert, M.S., Robert, J., Scherz, M.D., Siu-Ting, K., Snead, A.A., Stöck, M., Stuckert, A.M.M., Stynoski, J.L., Tarvin, R.D., Valero, K.C.W. :

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. bioRxiv , 2024. Pubmed reference: 39005434. DOI: 10.1101/2024.06.27.601086.

Kosch, T.A., Torres-Sánchez, M., Liedtke, H.C., Summers, K., Yun, M.H., Crawford, A.J., Maddock, S.T., Ahammed, M.S., Araújo, V.L.N., Bertola, L.V., Bucciarelli, G.M., Carné, A., Carneiro, C.M., Chan, K.O., Chen, Y., Crottini, A., da Silva, J.M., Denton, R.D., Dittrich, C., Espregueira Themudo, G., Farquharson, K.A., Forsdick, N.J., Gilbert, E., Che, J., Katzenback, B.A., Kotharambath, R., Levis, N.A., Márquez, R., Mazepa, G., Mulder, K.P., Müller, H., O'Connell, M.J., Orozco-terWengel, P., Palomar, G., Petzold, A., Pfennig, D.W., Pfennig, K.S., Reichert, M.S., Robert, J., Scherz, M.D., Siu-Ting, K., Snead, A.A., Stöck, M., Stuckert, A.M.M., Stynoski, J.L., Tarvin, R.D., Wollenberg Valero, K.C. :

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BMC Genomics 25:1025, 2024. Pubmed reference: 39487448. DOI: 10.1186/s12864-024-10899-7.

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:giad016, 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) 13:jkad171, 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:evad183, 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.

2024

Zhou, Y., Mabrouk, I., Ma, J., Liu, Q., Song, Y., Xue, G., Li, X., Wang, S., Liu, C., Hu, J., Sun, Y. :

Chromosome-level genome sequencing and multi-omics of the Hungarian White Goose (Anser anser domesticus) reveals novel miRNA-mRNA regulation mechanism of waterfowl feather follicle development. Poult Sci 103:S0032-5791(24)00512-1:103933, 2024. Pubmed reference: 38943801. DOI: 10.1016/j.psj.2024.103933.

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) :

2024

Zhao, H., Zhou, H., Sun, G., Dong, B., Zhu, W., Mu, X., Li, X., Wang, J., Zhao, M., Yang, W., Zhang, G., Ji, R., Geng, T., Gong, D., Meng, H., Wang, J. :

Telomere-to-telomere genome assembly of the goose Anser cygnoides. Sci Data 11:741, 2024. Pubmed reference: 38972874. DOI: 10.1038/s41597-024-03567-8.

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.

ranchSATdb: A genome-wide simple sequence repeat (SSR) markers database of livestock species for mutant germplasm characterization and improving farm animal health. Genes (Basel) 14:1481, 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 33:703-714, 2023. Pubmed reference: 37156619. DOI: 10.1101/gr.276779.122.

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) :

2024

Warren, W.C., Rice, E.S., X, M., 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. G3 (Bethesda) 14:jkae103, 2024. Pubmed reference: 38771704. DOI: 10.1093/g3journal/jkae103.

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.

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 41: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) 13:jkad156, 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 52:263-274, 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 186:2959-2976.e22, 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) :

2024

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 58:S2090-1232(23)00143-1:93-104, 2024. 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) 13:jkad044, 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.

Lan, D., Fu, W., Ji, W., Mipam, T.D., Xiong, X., Ying, S., Xiong, Y., Sheng, P., Ni, J., Bai, L., Shan, T., Kong, X., Li, J. :

Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks. J Anim Sci Biotechnol 15:64, 2024. Pubmed reference: 38706000. DOI: 10.1186/s40104-024-01027-2.

Guo, S., Wang, X., Zhao, S., Zhao, E. :

Whole-genome resequencing reveals the uniqueness of Subei yak. J Anim Sci 102:skae152, 2024. Pubmed reference: 38832496. DOI: 10.1093/jas/skae152.

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) 13:2963, 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.

Benfica, L.F., Brito, L.F., do Bem, R.D., de Oliveira, L.F., Mulim, H.A., Braga, L.G., Cyrillo, J.N.S.G., Bonilha, S.F.M., Mercadante, M.E.Z. :

Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations. Front Genet 15:1377130, 2024. Pubmed reference: 38694873. DOI: 10.3389/fgene.2024.1377130.

Tijjani, A., Kambal, S., Terefe, E., Njeru, R., Ogugo, M., Ndambuki, G., Missohou, A., Traore, A., Salim, B., Ezeasor, C., D'andre H, C., Obishakin, E.T., Diallo, B., Talaki, E., Abdoukarim, I.Y., Nash, O., Osei-Amponsah, R., Ravaorimanana, S., Issa, Y., Zegeye, T., Mukasa, C., Tiambo, C., Prendergast, J.G.D., Kemp, S.J., Han, J., Marshall, K., Hanotte, O. :

Genomic reference resource for African cattle: Genome sequences and high-density array variants. Sci Data 11:801, 2024. Pubmed reference: 39030190. DOI: 10.1038/s41597-024-03589-2.

Ayalew, W., Xiaoyun, W., Tarekegn, G.M., Naboulsi, R., Sisay Tessema, T., Van Damme, R., Bongcam-Rudloff, E., Chu, M., Liang, C., Edea, Z., Enquahone, S., Ping, Y. :

Whole genome sequences of 70 indigenous Ethiopian cattle. Sci Data 11:584, 2024. Pubmed reference: 38839789. DOI: 10.1038/s41597-024-03342-9.

S, V., D, B., Kg, T., A, G., Smk, K. :

Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India. Anim Biosci , 2024. Pubmed reference: 39210813. DOI: 10.5713/ab.23.0525.

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 34:4885-4899, 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 45:1399-1408, 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 33:1284-1298, 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.

Dang, D., Zhang, L., Gao, L., Peng, L., Chen, J., Yang, L. :

Analysis of genomic copy number variations through whole-genome scan in Yunling cattle. Front Vet Sci 11:1413504, 2024. Pubmed reference: 39104544. DOI: 10.3389/fvets.2024.1413504.

Bos primigenius (aurochs) :

2024

Erven, J.A.M., Scheu, A., Pereira Verdugo, M., Cassidy, L., Chen, N., Gehlen, B., Street, M., Madsen, O., Mullin, V.E. :

A high coverage Mesolithic aurochs genome and effective leveraging of ancient cattle genomes using whole genome imputation. Mol Biol Evol 41:msae076, 2024. Pubmed reference: 38662789. DOI: 10.1093/molbev/msae076.

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 34:300-309, 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.

Erven, J.A.M., Scheu, A., Pereira Verdugo, M., Cassidy, L., Chen, N., Gehlen, B., Street, M., Madsen, O., Mullin, V.E. :

Smith, T., Olagunju, T., Rosen, B., Neibergs, H., Becker, G., Davenport, K., Elsik, C., Hadfield, T., Koren, S., Kuhn, K., Rhie, A., Shira, K., Skibiel, A., Stegemiller, M., Thorne, J., Villamediana, P., Cockett, N., Murdoch, B. :

The first complete T2T Assemblies of cattle and sheep Y-Chromosomes uncover remarkable divergence in structure and gene content. Res Sq , 2024. Pubmed reference: 38712074. DOI: 10.21203/rs.3.rs-4033388/v1.

Wang, Y., Huang, Y., Zhen, Y., Wang, J., Wang, L., Chen, N., Wu, F., Zhang, L., Shen, Y., Bi, C., Li, S., Pool, K., Blache, D., Maloney, S.K., Liu, D., Yang, Z., Li, C., Yu, X., Zhang, Z., Chen, Y., Xue, C., Gu, Y., Huang, W., Yan, L., Wei, W., Wang, Y., Zhang, J., Zhang, Y., Sun, Y., Wang, S., Zhao, X., Luo, C., Wang, H., Ding, L., Yang, Q.Y., Zhou, P., Wang, M. :

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Delledonne, A., Punturiero, C., Ferrari, C., Bernini, F., Milanesi, R., Bagnato, A., Strillacci, M.G. :

Copy number variant scan in more than four thousand Holstein cows bred in Lombardy, Italy. PLoS One 19:e0303044, 2024. Pubmed reference: 38771855. DOI: 10.1371/journal.pone.0303044.

Gao, Z., Lu, Y., Chong, Y., Li, M., Hong, J., Wu, J., Wu, D., Xi, D., Deng, W. :

Beef cattle genome project: Advances in genome sequencing, assembly, and functional genes discovery. Int J Mol Sci 25:7147, 2024. Pubmed reference: 39000250. DOI: 10.3390/ijms25137147.

Genomic reference resource for African cattle: Genome sequences and high-density array variants. Sci Data 11:801, 2024. Pubmed reference: 39030190. DOI: 10.1038/s41597-024-03589-2.

Chang, W.J., Baker, M.S., Laritsky, E., Gunasekara, C.J., Maduranga, U., Galliou, J.C., McFadden, J.W., Waltemyer, J.R., Berggren-Thomas, B., Tate, B.N., Zhang, H., Rosen, B.D., Van Tassell, C.P., Liu, G.E., Coarfa, C., Ren, Y.A., Waterland, R.A. :

Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. Genome Biol 25:185, 2024. Pubmed reference: 39004763. DOI: 10.1186/s13059-024-03307-6.

Ayalew, W., Xiaoyun, W., Tarekegn, G.M., Naboulsi, R., Sisay Tessema, T., Van Damme, R., Bongcam-Rudloff, E., Chu, M., Liang, C., Edea, Z., Enquahone, S., Ping, Y. :

Whole genome sequences of 70 indigenous Ethiopian cattle. Sci Data 11:584, 2024. Pubmed reference: 38839789. DOI: 10.1038/s41597-024-03342-9.

Boschiero, C., Neupane, M., Yang, L., Schroeder, S.G., Tuo, W., Ma, L., Baldwin, R.L., Van Tassell, C.P., Liu, G.E. :

A pilot detection and associate study of gene presence-absence variation in Holstein cattle. Animals (Basel) 14:1921, 2024. Pubmed reference: 38998033. DOI: 10.3390/ani14131921.

Jin, S., Won, J.I., Kim, H.J., Park, B., Kim, S.W., Kim, U.H., Kang, S.S., Lee, H.J., Moon, S.J., Park, M.S., Sim, Y.T., Jang, S.S., Kim, N.Y. :

Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle. J Anim Sci Technol 66:717-725, 2024. Pubmed reference: 39165748. DOI: 10.5187/jast.2024.e10.

Olagunju, T.A., Rosen, B.D., Neibergs, H.L., Becker, G.M., Davenport, K.M., Elsik, C.G., Hadfield, T.S., Koren, S., Kuhn, K.L., Rhie, A., Shira, K.A., Skibiel, A.L., Stegemiller, M.R., Thorne, J.W., Villamediana, P., Cockett, N.E., Murdoch, B.M., Smith, T.P.L. :

Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content. Nat Commun 15:8277, 2024. Pubmed reference: 39333471. DOI: 10.1038/s41467-024-52384-5.

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) 13:jkad108, 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 34:418-436, 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 33:1848-1864, 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 112:565, 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 52:785-798, 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 160:85-93, 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:giaa021, 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 51:675-682, 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 Mamm Genome 8:21-8, 1997. Pubmed reference: 9021143. DOI: 10.1007/s003359900340.

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 Res 7:235-49, 1997. Pubmed reference: 9074927. DOI: 10.1101/gr.7.3.235.

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.

2024

Pineda, P.S., Flores, E.B., Villamor, L.P., Parac, C.J.M., Khatkar, M.S., Thu, H.T., Smith, T.P.L., Rosen, B.D., Ajmone-Marsan, P., Colli, L., Williams, J.L., Low, W.Y. :

Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project. Gigascience 13:giae053, 2024. Pubmed reference: 39250077. DOI: 10.1093/gigascience/giae053.

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 34:418-436, 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:giad063, 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 114:418-427, 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) :

2024

Vijh, R.K., Sharma, U., Arora, R., Kapoor, P., Raheja, M., Sharma, R., Ahlawat, S., Dureja, V. :

Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids. Gene 921:148541, 2024. Pubmed reference: 38723784. DOI: 10.1016/j.gene.2024.148541.

Guo, L., Dao, L., Liu, B., Wang, J., Liu, Z., Ma, F., Morigen, B., Chang, C., Bai, Y., Guo, Y., Shi, C., Cao, J., Zhang, W. :

Development and application of a 1K functional liquid chip for lactation performance in Bactrian camels. Front Vet Sci 11:1359923, 2024. Pubmed reference: 39021409. DOI: 10.3389/fvets.2024.1359923.

2023

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

Genome-wide identification and characterization of microsatellite markers in Bactrian Camel. Genomics 115:110726, 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) :

2024

Vijh, R.K., Sharma, U., Arora, R., Kapoor, P., Raheja, M., Sharma, R., Ahlawat, S., Dureja, V. :

Bahbahani, H., Mohammad, Z., Al-Ateeqi, A., Almathen, F. :

A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data. Sci Rep 14:25573, 2024. Pubmed reference: 39462079. DOI: 10.1038/s41598-024-77773-0.

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 115:480-486, 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:giad018, 2023. Pubmed reference: 36994871. DOI: 10.1093/gigascience/giad018.

Canis lupus familiaris (dog) :

2024

Nguyen, A.K., Schall, P.Z., Kidd, J.M. :

A map of canine sequence variation relative to a Greenland wolf outgroup. Mamm Genome 35:565-576, 2024. Pubmed reference: 39088040. DOI: 10.1007/s00335-024-10056-1.

Nguyen, A.K., Blacksmith, M.S., Kidd, J.M. :

Duplications and retrogenes are numerous and widespread in modern canine genomic assemblies. Genome Biol Evol 16:evae142, 2024. Pubmed reference: 38946312. DOI: 10.1093/gbe/evae142.

Bougiouri, K., Aninta, S.G., Charlton, S., Harris, A., Carmagnini, A., Piličiauskienė, G., Feuerborn, T.R., Scarsbrook, L., Tabadda, K., Blaževičius, P., Parker, H.G., Gopalakrishnan, S., Larson, G., Ostrander, E.A., Irving-Pease, E.K., Frantz, L.A.F., Racimo, F. :

Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years. bioRxiv , 2024. Pubmed reference: 38903121. DOI: 10.1101/2024.03.15.585179.

Nebenführ, M., Prochotta, D., Ben Hamadou, A., Janke, A., Gerheim, C., Betz, C., Greve, C., Bolz, H.J. :

High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome. GigaByte 2024:gigabyte134, 2024. Pubmed reference: 39314919. DOI: 10.46471/gigabyte.134.

Zhou, T., Pu, S.Y., Zhang, S.J., Zhou, Q.J., Zeng, M., Lu, J.S., Lu, X., Wang, Y.N., Wang, G.D. :

Dog10K: an integrated Dog10K database summarizing canine multi-omics. Nucleic Acids Res :gkae928, 2024. Pubmed reference: 39436034. DOI: 10.1093/nar/gkae928.

Liu, Y., Wang, Y., Sun, J., Kong, D., Zhou, B., Ding, M., Meng, Y., Duan, G., Cui, Y., Fan, Z., Zhang, Y.P., Zhao, W., Tang, B. :

iDog: a multi-omics resource for canids study. Nucleic Acids Res :gkae1031, 2024. Pubmed reference: 39526388. DOI: 10.1093/nar/gkae1031.

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 64:515-520, 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) 13:jkad203, 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 43:1-18, 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:giaa027, 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 Mamm Genome 11:120-30, 2000. Pubmed reference: 10656926. DOI: 10.1007/s003350010024.

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 J Hered 90:3-6, 1999. Pubmed reference: 9987895. DOI: 10.1093/jhered/90.1.3.

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. DOI: 10.1093/jhered/90.1.15.

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.

Meng, Y., Zhang, W., Cheng, Y., Wu, Y., Wu, H., He, M., Chen, S., Man, C., Gao, H., Du, L., Chen, Q., Wang, F. :

Development and verification of a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets. BMC Genom Data 25:44, 2024. Pubmed reference: 38714950. DOI: 10.1186/s12863-024-01228-8.

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

He, Q., Zhang, F., Zhang, X., Yao, W., Wu, J., Niu, H., Wang, Y., Luo, J. :

Chromosome-level dairy goat genome reveals the regulatory landscape of lactation. Int J Biol Macromol 280:135968, 2024. Pubmed reference: 39322167. DOI: 10.1016/j.ijbiomac.2024.135968.

Liu, J., Shi, Y., Mo, D., Luo, L., Xu, S., Lv, F. :

The goat pan-genome reveals patterns of gene loss during domestication. J Anim Sci Biotechnol 15:132, 2024. Pubmed reference: 39367490. DOI: 10.1186/s40104-024-01092-7.

Wang, Z., Lv, Q., Li, W., Huang, W., Gong, G., Yan, X., Liu, B., Chen, O., Wang, N., Zhang, Y., Wang, R., Li, J., Tian, S., Su, R. :

Chromosome-level genome assembly of the cashmere goat. Sci Data 11:1107, 2024. Pubmed reference: 39384835. DOI: 10.1038/s41597-024-03932-7.

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 54:421-424, 2023. Pubmed reference: 36849788. DOI: 10.1111/age.13311.

Arslan, M. :

Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus). Mamm Genome 34:437-448, 2023. Pubmed reference: 37004528. DOI: 10.1007/s00335-023-09990-3.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 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.

Capricornis milneedwardsii (Chinese serow) :

2024

Li, A., Yang, Q., Li, R., Cai, K., Zhu, L., Wang, X., Cheng, G., Wang, X., Lei, Y., Jiang, Y., Zan, L. :

Chromosome-level genome assembly for the Chinese serow (Capricornis milneedwardsii) provides insights into its taxonomic status and evolution. Ecol Evol 14:e70400, 2024. Pubmed reference: 39385836. DOI: 10.1002/ece3.70400.

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 54:792-797, 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 30:dsad018, 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.

Ceratotherium simum (white rhinoceros) :

2008

Trifonov, V.A., Stanyon, R., Nesterenko, A.I., Fu, B., Perelman, P.L., O'Brien, P.C., Stone, G., Rubtsova, N.V., Houck, M.L., Robinson, T.J., Ferguson-Smith, M.A., Dobigny, G., Graphodatsky, A.S., Yang, F. :

Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla. Chromosome Res 16:89-107, 2008. Pubmed reference: 18293107. DOI: 10.1007/s10577-007-1201-7.

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) 11:2614, 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.

Cervus nippon (sika deer) :

2024

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Wang, Q., Han, R., Xing, H., Li, H. :

A consensus genome of sika deer (Cervus nippon) and transcriptome analysis provided novel insights on the regulation mechanism of transcript factor in antler development. BMC Genomics 25:617, 2024. Pubmed reference: 38890595. DOI: 10.1186/s12864-024-10522-9.

Li, Z., Xu, Z., Zhu, L., Qin, T., Ma, J., Feng, Z., Yue, H., Guan, Q., Zhou, B., Han, G., Zhang, G., Li, C., Jia, S., Qiu, Q., Hao, D., Wang, Y., Wang, W. :

High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration. Genome Res :gr.279448.124, 2024. Pubmed reference: 39542648. DOI: 10.1101/gr.279448.124.

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. :

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) 14: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.

Coregonus clupeaformis (lake whitefish) :

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 cf. rhombifer :

2024

Meredith, R.W., Milián-García, Y., Gatesy, J., Russello, M.A., Amato, G. :

Draft assembly and annotation of the Cuban crocodile (Crocodylus rhombifer) genome. BMC Genom Data 25:53, 2024. Pubmed reference: 38844844. DOI: 10.1186/s12863-024-01240-y.

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 114:681-689, 2023. Pubmed reference: 37493092. DOI: 10.1093/jhered/esad045.

Crotalus ruber (red diamond rattlesnake) :

2024

Hirst, S.R., Rautsaw, R.M., VanHorn, C.M., Beer, M.A., McDonald, P.J., Rosales-García, R.A., Lopez, B.R., Rubio Rincón, A., Franz-Chávez, H., Vásquez-Cruz, V., Kelly-Hernández, A., Storfer, A., Borja, M., Castañeda-Gaytán, G., Frandsen, P.B., Parkinson, C.L., Strickland, J.L., Margres, M.J. :

Where the 'ruber' meets the road: Using the genome of the Red Diamond Rattlesnake to unravel the evolutionary processes driving venom evolution. Genome Biol Evol 16:evae198, 2024. Pubmed reference: 39255072. DOI: 10.1093/gbe/evae198.

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) :

2024

Zhao, H., Fang, D.A., Wang, Y., Zhang, M., Wang, A., Xu, Y., Xu, D. :

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.

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.

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

Chromosome-level genome assembly and annotation of the Patagonian toothfish Dissostichus eleginoides. Sci Data 11:1240, 2024. Pubmed reference: 39550355. DOI: 10.1038/s41597-024-04119-w.

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 115:212-220, 2024. Pubmed reference: 38245832. DOI: 10.1093/jhered/esae003.

Tian, R., Zhang, Y., Kang, H., Zhang, F., Jin, Z., Wang, J., Zhang, P., Zhou, X., Lanyon, J.M., Sneath, H.L., Woolford, L., Fan, G., Li, S., Seim, I. :

Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria. Nat Commun 15:5568, 2024. Pubmed reference: 38956050. DOI: 10.1038/s41467-024-49769-x.

Dysomma anguillare (shortbelly eel) :

2024

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 62:2296-2313, 2024. Pubmed reference: 37906301. DOI: 10.1007/s10528-023-10543-1.

Echeneis naucrates (live sharksucker) :

2024

Gao, T., Liu, K., Liu, Q., Wang, D. :

An improved chromosome-level genome assembly and annotation of Echeneis naucrates. Sci Data 11:452, 2024. Pubmed reference: 38704456. DOI: 10.1038/s41597-024-03309-w.

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) 13:701, 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 114:529-538, 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 22:e13917, 2023. Pubmed reference: 37395176. DOI: 10.1111/acel.13917.

Eliomys quercinus (garden dormouse) :

2024

Byerly, P.A., von Thaden, A., Leushkin, E., Hilgers, L., Liu, S., Winter, S., Schell, T., Gerheim, C., Ben Hamadou, A., Greve, C., Betz, C., Bolz, H.J., Büchner, S., Lang, J., Meinig, H., Famira-Parcsetich, E.M., Stubbe, S.P., Mouton, A., Bertolino, S., Verbeylen, G., Briner, T., Freixas, L., Vinciguerra, L., Mueller, S.A., Nowak, C., Hiller, M. :

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe. Genome Res , 2024. Pubmed reference: 39542649. DOI: 10.1101/gr.279066.124.

Elopichthys bambusa (yellowcheek carp) :

2024

Li, S., Xiong, X., Qiu, S., Shen, Z., He, Y., Gao, Z., Wan, S. :

Chromosome-level genome assembly of the yellow-cheek carp Elopichthys bambusa. Sci Data 11:426, 2024. Pubmed reference: 38658574. DOI: 10.1038/s41597-024-03262-8.

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) 8:379, 2017. Pubmed reference: 29232880. DOI: 10.3390/genes8120379.

Entelurus aequoreus (snake pipefish) :

None

[No authors listed] :

GigaByte 2024:gigabyte105, None. Pubmed reference: 38239770. DOI: 10.46471/gigabyte.105.

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) :

2024

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

Reference genome for the Northern bat (Eptesicus nilssonii), a most northern bat species. J Hered 115:149-154, 2024. Pubmed reference: 37791665. DOI: 10.1093/jhered/esad056.

Equus asinus (ass (donkey)) :

2024

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Yang, G., Gong, M., Yang, Q.M., Li, Y.D., Halima, J., Lei, C.Z., Jiang, Y., Dang, R.H. :

Improved chromosome-level donkey (Equus asinus) genome provides insights into genome and chromosome evolution. J Genet Genomics :S1673-8527(24)00295-9, 2024. Pubmed reference: 39542171. DOI: 10.1016/j.jgg.2024.11.002.

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.

2021

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

Transcriptome atlas of 16 donkey tissues. Front Genet 12:682734, 2021. Pubmed reference: 34434218. DOI: 10.3389/fgene.2021.682734.

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.

2016

Sun, Y., Jiang, Q., Yang, C., Wang, X., Tian, F., Wang, Y., Ma, Y., Ju, Z., Huang, J., Zhou, X., Zhong, J., Wang, C. :

Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis. Curr Genet 62:383-90, 2016. Pubmed reference: 26527116. DOI: 10.1007/s00294-015-0531-9.

2015

Bertolini, F., Scimone, C., Geraci, C., Schiavo, G., Utzeri, V.J., Chiofalo, V., Fontanesi, L. :

Next generation semiconductor based sequencing of the donkey (Equus asinus) genome provided comparative sequence data against the horse genome and a few millions of single nucleotide polymorphisms. PLoS One 10:e0131925, 2015. Pubmed reference: 26151450. DOI: 10.1371/journal.pone.0131925.

2009

Di Meo, G.P., Perucatti, A., Peretti, V., Incarnato, D., Ciotola, F., Liotta, L., Raudsepp, T., Di Berardino, D., Chowdhary, B., Iannuzzi, L. :

The 450-band resolution G- and R-banded standard karyotype of the donkey (Equus asinus, 2n = 62). Cytogenet Genome Res 125:266-71, 2009. Pubmed reference: 19864889. DOI: 10.1159/000235932.

2000

Raudsepp, T., Christensen, K., Chowdhar, B.P. :

Cytogenetics of donkey chromosomes: nomenclature proposal based on GTG-banded chromosomes and depiction of NORs and telomeric sites. Chromosome Res 8:659-70, 2000. Pubmed reference: 11196129. DOI: 10.1023/a:1026707002538.

1996

Xu, X., Gullberg, A., Arnason, U. :

The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs. J Mol Evol 43:438-46, 1996. Pubmed reference: 8875857. DOI: 10.1007/BF02337515.

Equus caballus (horse) :

2024

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Pokharel, K., Weldenegodguad, M., Reilas, T., Kantanen, J. :

EquCab_Finn: A new reference genome assembly for the domestic horse, Finnhorse. Anim Genet 55:766-771, 2024. Pubmed reference: 38986537. DOI: 10.1111/age.13463.

Bailey, E., Finno, C.J., Cullen, J.N., Kalbfleisch, T., Petersen, J.L. :

Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations. Sci Rep 14:22930, 2024. Pubmed reference: 39358442. DOI: 10.1038/s41598-024-73645-9.

Ahlawat, S., Niranjan, S.K., Arora, R., Vijh, R.K., Kumar, A., Sharma, U., Raheja, M., Popli, K., Yadav, S., Mehta, S.C. :

Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies. Funct Integr Genomics 24:195, 2024. Pubmed reference: 39441226. DOI: 10.1007/s10142-024-01482-0.

Assanbayev, T., Akilzhanov, R., Sharapatov, T., Bektayev, R., Samatkyzy, D., Karabayev, D., Gabdulkayum, A., Daniyarov, A., Rakhimova, S., Kozhamkulov, U., Sarbassov, D., Akilzhanova, A., Kairov, U. :

Whole genome sequencing and de novo genome assembly of the Kazakh native horse Zhabe. Front Genet 15:1466382, 2024. Pubmed reference: 39529846. DOI: 10.3389/fgene.2024.1466382.

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 23:1656-1672, 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 54:662-663, 2023. Pubmed reference: 37336519. DOI: 10.1111/age.13338.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 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) 14:1422, 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.

2013

Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P.L., Fumagalli, M., Vilstrup, J.T., Raghavan, M., Korneliussen, T., Malaspinas, A.S., Vogt, J., Szklarczyk, D., Kelstrup, C.D., Vinther, J., Dolocan, A., Stenderup, J., Velazquez, A.M., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G.D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J.F., Weinstock, J., Gregersen, K., Røed, K.H., Eisenmann, V., Rubin, C.J., Miller, D.C., Antczak, D.F., Bertelsen, M.F., Brunak, S., Al-Rasheid, K.A., Ryder, O., Andersson, L., Mundy, J., Krogh, A., Gilbert, M.T., Kjær, K., Sicheritz-Ponten, T., Jensen, L.J., Olsen, J.V., Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J., Willerslev, E. :

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499:74-8, 2013. Pubmed reference: 23803765. DOI: 10.1038/nature12323.

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. DOI: 10.1023/b:chro.0000009298.02689.8a.

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. DOI: 10.1016/j.ygeno.2003.07.002.

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. DOI: 10.1046/j.1365-2052.2003.00973.x.

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. DOI: 10.1046/j.1365-2052.2003.00951_1.x.

Yang, F., Fu, B., O'Brien, P.C., Robinson, T.J., Ryder, O.A., Ferguson-Smith, M.A. :

Karyotypic relationships of horses and zebras: results of cross-species chromosome painting. Cytogenet Genome Res 102:235-43, 2003. Pubmed reference: 14970709. DOI: 10.1159/000075755.

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. DOI: 10.1023/a:1016608806205.

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. DOI: 10.1007/s003350010146.

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. DOI: 10.1101/gr.9.12.1239.

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. DOI: 10.1046/j.1365-2052.1999.00510.x.

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. DOI: 10.1046/j.1365-2052.1999.00377.x.

1998

Bailey, E., Binns, M.M. :

The Horse Gene Map. ILAR J 39:171-176, 1998. Pubmed reference: 11528075. DOI: 10.1093/ilar.39.2-3.171.

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. DOI: 10.1101/gr.8.9.951.

Equus grevyi (Grevy's zebra) :

2008

2007

Musilova, P., Kubickova, S., Zrnova, E., Horin, P., Vahala, J., Rubes, J. :

Karyotypic relationships among Equus grevyi, Equus burchelli and domestic horse defined using horse chromosome arm-specific probes. Chromosome Res 15:807-13, 2007. Pubmed reference: 17874215. DOI: 10.1007/s10577-007-1164-8.

Equus hemionus (onager) :

2009

Musilova, P., Kubickova, S., Horin, P., Vodicka, R., Rubes, J. :

Karyotypic relationships in Asiatic asses (kulan and kiang) as defined using horse chromosome arm-specific and region-specific probes. Chromosome Res 17:783-90, 2009. Pubmed reference: 19731053. DOI: 10.1007/s10577-009-9069-3.

2008

1978

Ryder, O.A. :

Chromosomal polymorphism in Equus hemionus. Cytogenet Cell Genet 21:177-83, 1978. Pubmed reference: 149653. DOI: 10.1159/000130895.

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 19:1199-1210, 2023. Pubmed reference: 38151756. DOI: 10.1111/1749-4877.12795.

2021

Zeng, L., Liu, H.Q., Tu, X.L., Ji, C.M., Gou, X., Esmailizadeh, A., Wang, S., Wang, M.S., Wang, M.C., Li, X.L., Charati, H., Adeola, A.C., Moshood Adedokun, R.A., Oladipo, O., Olaogun, S.C., Sanke, O.J., Godwin F, M., Cecily Ommeh, S., Agwanda, B., Kasiiti Lichoti, J., Han, J.L., Zheng, H.K., Wang, C.F., Zhang, Y.P., Frantz, L.A.F., Wu, D.D. :

Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zool Res 42:2095-8137(2021)04-0450-11:450-460, 2021. Pubmed reference: 34156172. DOI: 10.24272/j.issn.2095-8137.2021.095.

2011

Luo, Y., Chen, Y., Liu, F., Jiang, C., Gao, Y. :

Mitochondrial genome sequence of the Tibetan wild ass (Equus kiang). Mitochondrial DNA 22:6-8, 2011. Pubmed reference: 21732718. DOI: 10.3109/19401736.2011.588221.

2009

Musilova, P., Kubickova, S., Horin, P., Vodicka, R., Rubes, J. :

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. Pubmed reference: 38464182. DOI: 10.1101/2024.02.20.581252.

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). G3 (Bethesda) 14:jkae113, 2024. Pubmed reference: 38805182. DOI: 10.1093/g3journal/jkae113.

2023

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

Equus quagga (plains zebra) :

2007

Musilova, P., Kubickova, S., Zrnova, E., Horin, P., Vahala, J., Rubes, J. :

2003

Yang, F., Fu, B., O'Brien, P.C., Robinson, T.J., Ryder, O.A., Ferguson-Smith, M.A. :

Karyotypic relationships of horses and zebras: results of cross-species chromosome painting. Cytogenet Genome Res 102:235-43, 2003. Pubmed reference: 14970709. DOI: 10.1159/000075755.

Equus zebra (mountain zebra) :

2002

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

Comparative mapping in equids: the asine X chromosome is rearranged compared to horse and Hartmann's mountain zebra. Cytogenet Genome Res 96:206-9, 2002. Pubmed reference: 12438800. DOI: 10.1159/000063050.

2001

Richard, F., Messaoudi, C., Lombard, M., Dutrillaux, B. :

Chromosome homologies between man and mountain zebra (Equus zebra hartmannae) and description of a new ancestral synteny involving sequences homologous to human chromosomes 4 and 8. Cytogenet Cell Genet 93:291-6, 2001. Pubmed reference: 11528128. DOI: 10.1159/000057000.

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 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Felis catus (domestic cat) :

2024

Matsumoto, Y., Yik-Lok Chung, C., Isobe, S., Sakamoto, M., Lin, X., Chan, T.F., Hirakawa, H., Ishihara, G., Lam, H.M., Nakayama, S., Sasamoto, S., Tanizawa, Y., Watanabe, A., Watanabe, K., Yagura, M., Niimura, Y., Nakamura, Y. :

Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats. J Adv Res , 2024. Pubmed reference: 39490737. DOI: 10.1016/j.jare.2024.10.023.

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 52:675-682, 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) 6:1607-16, 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 45:614-5, 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. DOI: 10.1093/jhered/esg008.

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. DOI: 10.1126/science.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 14:1248-60, 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 15:evad131, 2023. Pubmed reference: 37481259. DOI: 10.1093/gbe/evad131.

Gadus morhua (Atlantic cod) :

2024

Jentoft, S., Tørresen, O.K., Tooming-Klunderud, A., Skage, M., Kollias, S., Jakobsen, K.S. :

The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758). Wellcome Open Res 9:189, 2024. Pubmed reference: 39224768. DOI: 10.12688/wellcomeopenres.21122.1.

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.

Gallirallus australis (weka) :

2024

Gaspar, J., Trewick, S.A., Gibb, G.C. :

De-novo assembly of four rail (Aves: Rallidae) genomes: A resource for comparative genomics. Ecol Evol 14:e11694, 2024. Pubmed reference: 39026944. DOI: 10.1002/ece3.11694.

Gallirallus philippensis (buff-banded rail) :

2024

Gaspar, J., Trewick, S.A., Gibb, G.C. :

De-novo assembly of four rail (Aves: Rallidae) genomes: A resource for comparative genomics. Ecol Evol 14:e11694, 2024. Pubmed reference: 39026944. DOI: 10.1002/ece3.11694.

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.

Wu, S., 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., Ge, C., Su, Z., Wang, K. :

Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents. BMC Genomics 25:430, 2024. Pubmed reference: 38693501. DOI: 10.1186/s12864-024-10316-z.

Degalez, F., Bardou, P., Lagarrigue, S. :

GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations. NAR Genom Bioinform 6:lqae101, 2024. Pubmed reference: 39157583. DOI: 10.1093/nargab/lqae101.

Qiu, H., Ning, T., Gong, W., Sun, H., Mu, G., Li, J. :

Comprehensive sequencing of the genome and transcriptome of the Xishuangbanna game fowl. Sci Data 11:1163, 2024. Pubmed reference: 39438465. DOI: 10.1038/s41597-024-04014-4.

Ren, J., Kou, W., Xu, Y., Lu, M., Gong, M., Wang, X., Zhang, X., Liu, Z., Li, H., Yang, Q., Shah, A.M., Zhu, F., Hou, Z.C., Xu, N., Jiang, Y., Wang, F. :

Pan-genome analyses add ∼1000 genes to the "complete" genome assembly of chicken. J Genet Genomics :S1673-8527(24)00283-2, 2024. Pubmed reference: 39510408. DOI: 10.1016/j.jgg.2024.10.009.

2023

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 101:skad064, 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) 14:1198, 2023. Pubmed reference: 37372379. DOI: 10.3390/genes14061198.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 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.

2022

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.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.D., 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.D., 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.D., Schneider, V.A., 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 162:405-528, 2022. Pubmed reference: 36716736. DOI: 10.1159/000529376.

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 22:1-6, 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 51:337-56, 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. DOI: 10.1093/bfgp/3.1.60.

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. DOI: 10.1093/ilar.39.2-3.229.

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 Genet 11:190-4, 1995. Pubmed reference: 7785078. DOI: 10.1016/s0168-9525(00)89042-3.

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. DOI: 10.1093/genetics/34.3.333.

1933

Hutt, F.B. :

Genetics of the fowl. II. a four-gene autosomal linkage group. Genetics 18:82-94, 1933. Pubmed reference: 17246679. DOI: 10.1093/genetics/18.1.82.

Warren, D.C. :

Nine independently inherited autosomal factors in the domestic fowl. Genetics 18:68-81, 1933. Pubmed reference: 17246678. DOI: 10.1093/genetics/18.1.68.

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:giz090, 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 23:1108-1123, 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 186:2959-2976.e22, 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.

Gorilla gorilla (western gorilla) :

2024

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., Solar, S.J., Antipov, D., Pickett, B.D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J.M., Lin, J., Sequeira, A.N., Mangan, R.J., Hickey, G., Anez, G.M., Balachandran, P., Bankevich, A., Beck, C.R., Biddanda, A., Borchers, M., Bouffard, G.G., Brannan, E., Brooks, S.Y., Carbone, L., Carrel, L., Chan, A.P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G.H., de Gennaro, L., Gilbert, D., Green, R.E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R.S., Hartley, G.A., Harvey, W.T., Hiller, M., Hoekzema, K., Houck, M.L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A.P., Li, Q., Loftus, M., Loh, Y.H.E., Loucks, H., Ma, J., Mao, Y., Martinez, J.F.I., Masterson, P., McCoy, R.C., McGrath, B., McKinney, S., Meyer, B.S., Miga, K.H., Mohanty, S.K., Munson, K.M., Pal, K., Pennell, M., Pevzner, P.A., Porubsky, D., Potapova, T., Ringeling, F.R., Rocha, J.L., Ryder, O.A., Sacco, S., Saha, S., Sasaki, T., Schatz, M.C., Schork, N.J., Shanks, C., Smeds, L., Son, D.R., Steiner, C., Sweeten, A.P., Tassia, M.G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S.A., Zhu, Y., Jarvis, E.D., Gerton, J.L., Rivas-González, I., Paten, B., Szpiech, Z.A., Huber, C.D., Lenz, T.L., Konkel, M.K., Yi, S.V., Canzar, S., Watson, C.T., Sudmant, P.H., Molloy, E., Garrison, E., Lowe, C.B., Ventura, M., O'Neill, R.J., Koren, S., Makova, K.D., Phillippy, A.M., Eichler, E.E. :

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

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) :

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) 25:580-587, 2023. Pubmed reference: 37351707. DOI: 10.1007/s10126-023-10227-2.

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.

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 114:436-443, 2023. Pubmed reference: 37119047. DOI: 10.1093/jhered/esad025.

[No authors listed] :

Correction to: Reference genome of the black rail. J Hered 114:585, 2023. Pubmed reference: 37354561. DOI: 10.1093/jhered/esad038.

Lates japonicus :

2024

Hashiguchi, Y., Mishina, T., Takeshima, H., Nakayama, K., Tanoue, H., Takeshita, N., Takahashi, H. :

Draft genome of akame (Lates japonicus) reveals possible genetic mechanisms for long-term persistence and adaptive evolution with low genetic diversity. Genome Biol Evol 16:evae174, 2024. Pubmed reference: 39109913. DOI: 10.1093/gbe/evae174.

Leiocassis longirostris (Chinese longsnout catfish) :

2024

Liu, Y., Zhai, G., Su, J., Gong, Y., Yang, B., Lu, Q., Xi, L., Zheng, Y., Cao, J., Liu, H., Jin, J., Zhang, Z., Yang, Y., Zhu, X., Wang, Z., Gong, G., Mei, J., Yin, Z., Gozlan, R.E., Xie, S., Han, D. :

The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores. Genome Res 34:981-996, 2024. Pubmed reference: 39122473. DOI: 10.1101/gr.278476.123.

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:giac026, 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.

Lepidosiren paradoxa (South American lungfish) :

2024

Schartl, M., Woltering, J.M., Irisarri, I., Du, K., Kneitz, S., Pippel, M., Brown, T., Franchini, P., Li, J., Li, M., Adolfi, M., Winkler, S., de Freitas Sousa, J., Chen, Z., Jacinto, S., Kvon, E.Z., Correa de Oliveira, L.R., Monteiro, E., Baia Amaral, D., Burmester, T., Chalopin, D., Suh, A., Myers, E., Simakov, O., Schneider, I., Meyer, A. :

The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature 634:96-103, 2024. Pubmed reference: 39143221. DOI: 10.1038/s41586-024-07830-1.

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) 13:jkad095, 2023. Pubmed reference: 37119803. DOI: 10.1093/g3journal/jkad095.

Leptobotia elongata (royal clown loach) :

2024

Wen, Z., Wei, X., Chen, J., Li, Y., Zhou, B., Zhang, C., Fu, P., Prathomya, P., Li, R., Lv, Y., Li, Y., Zeng, W., He, Y., Zhou, L., Fan, J., Shi, Q., Zhang, X. :

Chromosome-level genome assemblies of vulnerable male and female elongate loach (Leptobotia elongata). Sci Data 11:924, 2024. Pubmed reference: 39181886. DOI: 10.1038/s41597-024-03789-w.

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. :

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

Lutjanus argentimaculatus (mangrove red snapper) :

2024

Shekhar, M.S., Katneni, V.K., Jangam, A.K., Krishnan, K., Prabhudas, S.K., Jayaraman, R., Angel, J.R.J., Kailasam, M. :

Genome assembly, full-length transcriptome, and isoform diversity of Red Snapper, Lutjanus argentimaculatus. Sci Data 11:796, 2024. Pubmed reference: 39025998. DOI: 10.1038/s41597-024-03633-1.

Lycaon pictus (African hunting dog) :

2024

Kliver, S., Kovacic, I., Mak, S., Sinding, M.S., Stagegaard, J., Petersen, B., Nesme, J., Gilbert, M.T.P. :

A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus). J Hered :esae052, 2024. Pubmed reference: 39316562. DOI: 10.1093/jhered/esae052.

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) :

2024

Wang, J., Wang, M., Moshiri, A., Harris, R.A., Raveendran, M., Nguyen, T., Kim, S., Young, L., Wang, K., Wiseman, R., O'Connor, D.H., Johnson, Z., Martinez, M., Montague, M.J., Sayers, K., Lyke, M., Vallender, E., Stout, T., Li, Y., Thomasy, S.M., Rogers, J., Chen, R. :

Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models. Nat Commun 15:5658, 2024. Pubmed reference: 38969634. DOI: 10.1038/s41467-024-49922-6.

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 33:91-99, 2022. Pubmed reference: 34999909. DOI: 10.1007/s00335-021-09922-z.

Macropodus opercularis (paradise fish) :

2024

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 Macropodus opercularis (the paradise fish). Sci Data 11:540, 2024. Pubmed reference: 38796485. DOI: 10.1038/s41597-024-03277-1.

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.

Macrotis lagotis (bilby) :

2024

Hogg, C.J., Edwards, R.J., Farquharson, K.A., Silver, L.W., Brandies, P., Peel, E., Escalona, M., Jaya, F.R., Thavornkanlapachai, R., Batley, K., Bradford, T.M., Chang, J.K., Chen, Z., Deshpande, N., Dziminski, M., Ewart, K.M., Griffith, O.W., Marin Gual, L., Moon, K.L., Travouillon, K.J., Waters, P., Whittington, C.M., Wilkins, M.R., Helgen, K.M., Lo, N., Ho, S.Y.W., Ruiz Herrera, A., Paltridge, R., Marshall Graves, J.A., Renfree, M., Shapiro, B., Ottewell, K. :

Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 8:1311-1326, 2024. Pubmed reference: 38945974. DOI: 10.1038/s41559-024-02436-2.

Author Correction: Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 8:1776, 2024. Pubmed reference: 39075174. DOI: 10.1038/s41559-024-02519-0.

Macrotis leucura (lesser bilby) :

2024

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:msad190, 2023. Pubmed reference: 37794645. DOI: 10.1093/molbev/msad190.

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:giad051, 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 16:evae067, 2024. Pubmed reference: 38566597. DOI: 10.1093/gbe/evae067.

Meriones unguiculatus (Mongolian gerbil) :

2024

Guo, Y., Cui, Y., Sun, M., Zhu, X., Zhang, Y., Lu, J., Li, C., Lv, J., Guo, M., Liu, X., Chen, Z., Du, X., Huo, X. :

Establishment and application of a novel genetic detection panel for SNPs in Mongolian gerbils. Genes (Basel) 15:817, 2024. Pubmed reference: 38927752. DOI: 10.3390/genes15060817.

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 40:msad115, 2023. Pubmed reference: 37183864. DOI: 10.1093/molbev/msad115.

Mesocricetus auratus (golden hamster) :

Yin, D., Chen, C., Lin, D., Hua, Z., Ying, C., Zhang, J., Zhao, C., Liu, Y., Cao, Z., Zhang, H., Wang, C., Liang, L., Xu, P., Jian, J., Liu, K. :

Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise. Gigascience 13:giae067, 2024. Pubmed reference: 39283687. DOI: 10.1093/gigascience/giae067.

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 141:507-520, 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 (hihi) :

2024

Tan, H.Z., Scherer, P., Stuart, K.C., Bailey, S., Lee, K.D., Brekke, P., Ewen, J.G., Whibley, A., Santure, A.W. :

A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta). Heredity (Edinb) 133:262-275, 2024. Pubmed reference: 39095652. DOI: 10.1038/s41437-024-00711-3.

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 19:997-1014, 2019. Pubmed reference: 30945415. DOI: 10.1111/1755-0998.13017.

Nyctalus aviator :

2024

Geng, Y., Liu, Y., Zhang, Y., Gong, L., Han, Y., Huang, Z., Ke, C., Wu, H., Lin, A., Feng, J., Jiang, T. :

A chromosome-level genome assembly of an avivorous bat species (Nyctalus aviator). Sci Data 11:480, 2024. Pubmed reference: 38730001. DOI: 10.1038/s41597-024-03322-z.

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) :

Liu, S., Martin, K.E., Snelling, W.M., Long, R., Leeds, T.D., Vallejo, R.L., Wiens, G.D., Palti, Y. :

Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout. G3 (Bethesda) 14:jkae168, 2024. Pubmed reference: 39041837. DOI: 10.1093/g3journal/jkae168.

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.

2021

Gao, G., Magadan, S., Waldbieser, G.C., Youngblood, R.C., Wheeler, P.A., Scheffler, B.E., Thorgaard, G.H., Palti, Y. :

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout. G3 (Bethesda) 11:jkab052, 2021. Pubmed reference: 33616628. DOI: 10.1093/g3journal/jkab052.

2019

Pearse, D.E., Barson, N.J., Nome, T., Gao, G., Campbell, M.A., Abadía-Cardoso, A., Anderson, E.C., Rundio, D.E., Williams, T.H., Naish, K.A., Moen, T., Liu, S., Kent, M., Moser, M., Minkley, D.R., Rondeau, E.B., Brieuc, M.S.O., Sandve, S.R., Miller, M.R., Cedillo, L., Baruch, K., Hernandez, A.G., Ben-Zvi, G., Shem-Tov, D., Barad, O., Kuzishchin, K., Garza, J.C., Lindley, S.T., Koop, B.F., Thorgaard, G.H., Palti, Y., Lien, S. :

Sex-dependent dominance maintains migration supergene in rainbow trout. Nat Ecol Evol 3:1731-1742, 2019. Pubmed reference: 31768021. DOI: 10.1038/s41559-019-1044-6.

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.

Opsanus beta (Gulf toadfish) :

2024

Kron, N.S., Young, B.D., Drown, M.K., McDonald, M.D. :

Long-read de novo genome assembly of Gulf toadfish (Opsanus beta). BMC Genomics 25:871, 2024. Pubmed reference: 39289604. DOI: 10.1186/s12864-024-10747-8.

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) :

2024

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

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:evab168, 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:bay075, 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. DOI: 10.1073/pnas.27.11.519.

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 141:403-414, 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.

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Lu, Z., Yuan, C., An, X., Chen, Z., Guo, T., Liu, J. :

Chromosome-level genome assembly of Guide Black-Fur sheep (Ovis aries). Sci Data 11:711, 2024. Pubmed reference: 38951548. DOI: 10.1038/s41597-024-03564-x.

You, X., Fang, Q., Chen, C., Cao, J., Fu, S., Zhang, T., Wang, S., He, X., He, J., Zhou, Y., Wang, B., Wang, L., Wang, Z., Sun, T., Yang, X., Te, R., Jian, J., Zhou, H., Dai, Y., Liu, Y. :

A near complete genome assembly of the East Friesian sheep genome. Sci Data 11:762, 2024. Pubmed reference: 38992134. DOI: 10.1038/s41597-024-03581-w.

You, X., Fang, Q., Chen, C., Cao, J., Fu, S., Zhang, T., Wang, S., He, X., He, J., Zhou, Y., Wang, B., Wang, L., Wang, Z., Sun, T., Yang, X., Te, R., Jian, J., Zhou, H., Dai, Y., Liu, Y. :

Author Correction: A near complete genome assembly of the East Friesian sheep genome. Sci Data 11:947, 2024. Pubmed reference: 39209856. DOI: 10.1038/s41597-024-03755-6.

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 34:418-436, 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 34:545-558, 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:giab096, 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.

Pagrus auratus (squirefish) :

2024

Blommaert, J., Sandoval-Castillo, J., Beheregaray, L., Wellenreuther, M. :

Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper. Genomics 116:110929, 2024. Pubmed reference: 39216708. DOI: 10.1016/j.ygeno.2024.110929.

Pampus argenteus (silver pomfret) :

2024

Hu, J., Zhang, Y., Li, Y., Li, Y., Zhang, M., Huang, W., Xu, S., Wang, D., Wang, X., Liu, J., Wang, Y., Yan, X. :

Two high quality chromosome-scale genome assemblies of female and male silver pomfret (Pampus argenteus). Sci Data 11:1100, 2024. Pubmed reference: 39379396. DOI: 10.1038/s41597-024-03914-9.

Pan paniscus (pygmy chimpanzee) :

2024

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

Pan troglodytes (chimpanzee) :

2024

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

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) :

2024

Das, A., Suvo, M.S.H., Shaha, M., Gupta, M.D. :

Genome sequencing of captive white tigers from Bangladesh. BMC Genom Data 25:52, 2024. Pubmed reference: 38844863. DOI: 10.1186/s12863-024-01239-5.

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) 13:jkad113, 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 186:2959-2976.e22, 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.

Pantholops hodgsonii (chiru) :

2024

Xu, B., Chen, J., Song, P., Gu, H., Jiang, F., Li, B., Wei, Q., Zhang, T. :

A high-quality chromosome-level reference genome assembly of Tibetan antelope (Pantholops hodgsonii). Sci Data 11:1215, 2024. Pubmed reference: 39532915. DOI: 10.1038/s41597-024-04089-z.

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.

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 19:1004-1008, 2023. Pubmed reference: 38014459. DOI: 10.1111/1749-4877.12789.

2024

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

Periophthalmus modestus (shuttles hoppfish) :

2024

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) :

2024

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 115:130-138, 2024. 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) :

2024

Lott, M.J., Frankham, G.J., Eldridge, M.D.B., Alquezar-Planas, D.E., Donnelly, L., Zenger, K.R., Leigh, K.A., Kjeldsen, S.R., Field, M.A., Lemon, J., Lunney, D., Crowther, M.S., Krockenberger, M.B., Fisher, M., Neaves, L.E. :

Reversing the decline of threatened koala (Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes. Ecol Evol 14:e11700, 2024. Pubmed reference: 39091325. DOI: 10.1002/ece3.11700.

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:evac100, 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 30:dsad003, 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 114:410-417, 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) 14:jkae042, 2024. Pubmed reference: 38537260. DOI: 10.1093/g3journal/jkae042.

Pipistrellus nathusii (Nathusius's pipistrelle) :

2024

Driller, M., Brown, T., Currie, S.E., Hiller, M., Winkler, S., Pippel, M., Voigt, C.C., Fickel, J., Mazzoni, C.J. :

A Haplotype-resolved reference genome of a long-distance migratory bat, Pipistrellus nathusii (Keyserling & Blasius, 1839). DNA Res 31:dsae018, 2024. Pubmed reference: 38847751. DOI: 10.1093/dnares/dsae018.

Plagiognathops microlepis (smallscale yellowfin) :

2024

Wu, Y., Sha, H., Luo, X., Zou, G., Liang, H. :

Chromosome-level genome assembly of Plagiognathops microlepis based on PacBio HiFi and Hi-C sequencing. Sci Data 11:802, 2024. Pubmed reference: 39030192. DOI: 10.1038/s41597-024-03645-x.

Liang, Y., Liu, H., Lu, W., Li, J., Fang, T., Gao, N., Chen, C., Zhao, X., Yang, K., Liu, H. :

Chromosome-level genome assembly of the smallscale yellowfin (Plagiognathops microlepis). Sci Data 11:1234, 2024. Pubmed reference: 39548126. DOI: 10.1038/s41597-024-04105-2.

Platalea minor (black-faced spoonbill) :

2024

[No authors listed] :

Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor. GigaByte 2024:1-13, 2024. Pubmed reference: 39071178. DOI: 10.46471/gigabyte.130.

Platichthys flesus (European flounder) :

2024

Pomianowski, K., Kulczykowska, E., Burzyński, A. :

Genome guided, organ-specific transcriptome assembly of the European flounder (P. flesus) from the Baltic Sea. Sci Data 11:1184, 2024. Pubmed reference: 39477936. DOI: 10.1038/s41597-024-04004-6.

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.

2024

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

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. :

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.

Pteronotus parnellii (Parnell's mustached bat) :

2024

Sánchez-de la Vega, G., Gasca-Pineda, J., Martínez-Cárdenas, A., Vernes, S.C., Teeling, E.C., Mai, M., Aguirre-Planter, E., Eguiarte, L.E., Phillips, C.D., Ortega, J. :

The genome sequence of the endemic Mexican common mustached bat, Pteronotus mexicanus. Miller, 1902 [Mormoopidae; Pteronotus]. Gene 929:148821, 2024. Pubmed reference: 39111456. DOI: 10.1016/j.gene.2024.148821.

2024

Wang, D., Rastas, P., Yi, X., Löytynoja, A., Kivikoski, M., Feng, X., Reid, K., Merilä, J. :

Improved assembly of the Pungitius pungitius reference genome. G3 (Bethesda) 14:jkae126, 2024. Pubmed reference: 38861393. DOI: 10.1093/g3journal/jkae126.

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) 14:619, 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) 13:jkad097, 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 114:428-435, 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 55:296-298, 2024. Pubmed reference: 38319118. DOI: 10.1111/age.13402.

Wu, B., Ren, Q., Yan, X., Zhao, F., Qin, T., Xin, P., Cui, X., Wang, K., Du, R., Røed, K.H., Côté, S.D., Yannic, G., Li, Z., Qiu, Q. :

Resequencing of reindeer genomes provides clues to their docile habits. Evol Lett 8:494-504, 2024. Pubmed reference: 39100238. DOI: 10.1093/evlett/qrae006.

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.

Ranitomeya imitator (mimic poison frog) :

2024

Stuckert, A.M.M., Chouteau, M., McClure, M., LaPolice, T.M., Linderoth, T., Nielsen, R., Summers, K., MacManes, M.D. :

The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system. Mol Ecol 33:e17438, 2024. Pubmed reference: 38923007. DOI: 10.1111/mec.17438.

Rhabdophis nuchalis (Hubei keelback) :

2024

Duan, M., Yang, S., Li, X., Tang, X., Cheng, Y., Luo, J., Wang, J., Song, H., Wang, Q., Zhu, G.X. :

Chromosome-level genome assembly and annotation of the Rhabdophis nuchalis (Hubei keelback). Sci Data 11:850, 2024. Pubmed reference: 39117633. DOI: 10.1038/s41597-024-03708-z.

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 affinis (intermediate horseshoe bat) :

2024

Zhao, L., Yuan, J., Wang, G., Jing, H., Huang, C., Xu, L., Xu, X., Sun, T., Chen, W., Mao, X., Li, G. :

Chromosome-level genome and population genomics of the intermediate horseshoe bat (Rhinolophus affinis) reveal the molecular basis of virus tolerance in Rhinolophus and echolocation call frequency variation. Zool Res 45:2095-8137(2024)05-1147-14:1147-1160, 2024. Pubmed reference: 39257377. DOI: 10.24272/j.issn.2095-8137.2024.027.

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 15:evad153, 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 66:175-192, 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) 13:jkad138, 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) :

2024

[No authors listed] :

Editorial Note: Design and characterization of an 87k SNP genotyping array for Arctic charr (Salvelinus alpinus). PLoS One 19:e0304369, 2024. Pubmed reference: 38833497. DOI: 10.1371/journal.pone.0304369.

Beemelmanns, A., Bouchard, R., Michaelides, S., Normandeau, E., Jeon, H.B., Chamlian, B., Babin, C., Hénault, P., Perrot, O., Harris, L.N., Zhu, X., Fraser, D., Bernatchez, L., Moore, J.S. :

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) :

2024

Beemelmanns, A., Bouchard, R., Michaelides, S., Normandeau, E., Jeon, H.B., Chamlian, B., Babin, C., Hénault, P., Perrot, O., Harris, L.N., Zhu, X., Fraser, D., Bernatchez, L., Moore, J.S. :

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) 14: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.

Serpentes (snakes) :

2024

Roberts, J.R., Bernstein, J.M., Austin, C.C., Hains, T., Mata, J., Kieras, M., Pirro, S., Ruane, S. :

Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics. J Hered 115:487-497, 2024. Pubmed reference: 38722259. DOI: 10.1093/jhered/esae026.

Setipinna tenuifilis (common hairfin anchovy) :

2024

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 33:e17067, 2024. 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 115:317-325, 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.

Sminthopsis crassicaudata (fat-tailed dunnart) :

2024

Ibeh, N., Feigin, C.Y., Frankenberg, S.R., McCarthy, D.J., Pask, A.J., Gallego Romero, I. :

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata). GigaByte 2024:gigabyte118, 2024. Pubmed reference: 38746537. DOI: 10.46471/gigabyte.118.

Somateria mollissima (common eider) :

2024

Tørresen, O.K., Kersten, O., Garmann-Aarhus, B., Helberg, M., Tooming-Klunderud, A., Skage, M., Boessenkool, S., Jakobsen, K.S. :

A chromosome-level genome assembly of the common eider, Somateria mollissima (Linnaeus, 1758). J Hered :esae042, 2024. Pubmed reference: 39231044. DOI: 10.1093/jhered/esae042.

Sorex fumeus (smoky shrew) :

2024

Cossette, M.L., Stewart, D.T., Shafer, A.B.A. :

Comparative genomics of the world's smallest mammals reveals links to echolocation, metabolism, and body size plasticity. Genome Biol Evol 16:evae225, 2024. Pubmed reference: 39431406. DOI: 10.1093/gbe/evae225.

Sorex maritimensis (Maritime shrew) :

2024

Cossette, M.L., Stewart, D.T., Shafer, A.B.A. :

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.

Spinibarbus caldwelli :

2024

Wu, L., Gu, S., Wen, P., Wu, L., Li, L., Guo, S., Ding, S. :

Chromosome-level genome assembly and annotation of the Spinibarbus caldwelli. Sci Data 11:933, 2024. Pubmed reference: 39198473. DOI: 10.1038/s41597-024-03796-x.

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 16: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) 13:jkad146, 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 114:445-458, 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) 13:jkad193, 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 18:601-615, 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 10:2049-2060, 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

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 52:D980-D989, 2024. Pubmed reference: 37956339. DOI: 10.1093/nar/gkad1080.

Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H. :

A compendium of genetic regulatory effects across pig tissues. Nat Genet 56:112-123, 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 31:dsae008, 2024. Pubmed reference: 38447059. DOI: 10.1093/dnares/dsae008.

Wang, Y., Gou, Y., Yuan, R., Zou, Q., Zhang, X., Zheng, T., Fei, K., Shi, R., Zhang, M., Li, Y., Gong, Z., Luo, C., Xiong, Y., Shan, D., Wei, C., Shen, L., Tang, G., Li, M., Zhu, L., Li, X., Jiang, Y. :

A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs. Int J Biol Macromol 270:131796, 2024. Pubmed reference: 38677688. DOI: 10.1016/j.ijbiomac.2024.131796.

Yang, L., Yin, H., Bai, L., Yao, W., Tao, T., Zhao, Q., Gao, Y., Teng, J., Xu, Z., Lin, Q., Diao, S., Pan, Z., Guan, D., Li, B., Zhou, H., Zhou, Z., Zhao, F., Wang, Q., Pan, Y., Zhang, Z., Li, K., Fang, L., Liu, G.E. :

Mapping and functional characterization of structural variation in 1060 pig genomes. Genome Biol 25:116, 2024. Pubmed reference: 38715020. DOI: 10.1186/s13059-024-03253-3.

Niu, Y., Fan, X., Yang, Y., Li, J., Lian, J., Wang, L., Zhang, Y., Tang, Y., Tang, Z. :

Haplotype-resolved assembly of a pig genome using single-sperm sequencing. Commun Biol 7:738, 2024. Pubmed reference: 38890535. DOI: 10.1038/s42003-024-06397-x.

Wy, S., Kwon, D., Park, W., Chai, H.H., Cho, I.C., Kim, J. :

A chromosome-level genome assembly of the Korean minipig (Sus scrofa). Sci Data 11:840, 2024. Pubmed reference: 39097649. DOI: 10.1038/s41597-024-03680-8.

Quan, J., Yang, M., Wang, X., Cai, G., Ding, R., Zhuang, Z., Zhou, S., Tan, S., Ruan, D., Wu, J., Zheng, E., Zhang, Z., Liu, L., Meng, F., Wu, J., Xu, C., Qiu, Y., Wang, S., Lin, M., Li, S., Ye, Y., Zhou, F., Lin, D., Li, X., Deng, S., Zhang, Y., Yao, Z., Gao, X., Yang, Y., Liu, Y., Zhan, Y., Liu, Z., Zhang, J., Ma, F., Yang, J., Chen, Q., Yang, J., Ye, J., Dong, L., Gu, T., Huang, S., Xu, Z., Li, Z., Yang, J., Huang, W., Wu, Z. :

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs. Nat Commun 15:5587, 2024. Pubmed reference: 38961076. DOI: 10.1038/s41467-024-49923-5.

Kwon, S.G., Bae, G.H., Hong, J.H., Choi, J.W., Choi, J.H., Lim, N.S., Jeon, C., Mali, N.M., Jun, M.S., Shin, J., Kim, J., Cho, E.S., Han, M.H., Oh, J.W. :

Comprehensive analysis of somatic mutations and structural variations in domestic pig. Mamm Genome 35:645-656, 2024. Pubmed reference: 39177814. DOI: 10.1007/s00335-024-10058-z.

Schwartz, J.C., Farrell, C.P., Freimanis, G., Sewell, A.K., Phillips, J.D., Hammond, J.A. :

A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation. Immunogenetics 76:361-380, 2024. Pubmed reference: 39294478. DOI: 10.1007/s00251-024-01355-7.

Du, H., Lu, S., Huang, Q., Zhou, L., Liu, J.F. :

Chromosome-level genome assembly of Huai pig (Sus scrofa). Sci Data 11:1072, 2024. Pubmed reference: 39358406. DOI: 10.1038/s41597-024-03921-w.

Du, H., Zhuo, Y., Lu, S., Li, W., Zhou, L., Sun, F., Liu, G., Liu, J.F. :

Pangenome reveals gene content variations and structural variants contributing to pig characteristics. Genomics Proteomics Bioinformatics :qzae081, 2024. Pubmed reference: 39535885. DOI: 10.1093/gpbjnl/qzae081.

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 34:418-436, 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 34:520-530, 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 33:1833-1847, 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.

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:giad042, 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 J Hered 88:380-3, 1997. Pubmed reference: 9378913. DOI: 10.1093/oxfordjournals.jhered.a023122.

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. DOI: 10.1111/j.1365-2052.1996.tb00487.x.

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] :

J Genet Genomics 51:394-406, None. Pubmed reference: 38056526. DOI: 10.1016/j.jgg.2023.11.005.

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.

Symphalangus syndactylus (siamang) :

2024

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

Syncerus caffer (African buffalo) :

2024

Talenti, A., Wilkinson, T., Cook, E.A., Hemmink, J.D., Paxton, E., Mutinda, M., Ngulu, S.D., Jayaraman, S., Bishop, R.P., Obara, I., Hourlier, T., Garcia Giron, C., Martin, F.J., Labuschagne, M., Atimnedi, P., Nanteza, A., Keyyu, J.D., Mramba, F., Caron, A., Cornelis, D., Chardonnet, P., Fyumagwa, R., Lembo, T., Auty, H.K., Michaux, J., Smitz, N., Toye, P., Robert, C., Prendergast, J.G.D., Morrison, L.J. :

Continent-wide genomic analysis of the African buffalo (Syncerus caffer). Commun Biol 7:792, 2024. Pubmed reference: 38951693. DOI: 10.1038/s42003-024-06481-2.

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) :

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) 9:1283-1294, 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 65:1-17, 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

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) 12:291, 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) 11:522, 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 7:1267-1286, 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. :

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. :

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) 10:409, 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 2:1514, 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. :

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 186:2959-2976.e22, 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 33:557-571, 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 30:dsad021, 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.

Nam, S.E., Rhee, J.S. :

Chromosomal-level genome assembly data from the pale chub, Zacco platypus (Jordan & Evermann, 1902). Data Brief 55:110596, 2024. Pubmed reference: 39022690. DOI: 10.1016/j.dib.2024.110596.

Zoarces viviparus (viviparous blenny) :

2024

Fuhrmann, N., Brasseur, M.V., Bakowski, C.E., Podsiadlowski, L., Prost, S., Krehenwinkel, H., Mayer, C. :

Chromosome-level genome assembly of the viviparous eelpout Zoarces viviparus. Genome Biol Evol 16:evae155, 2024. Pubmed reference: 39018026. DOI: 10.1093/gbe/evae155.

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) :

Alectoris rufa (red-legged partridge) :

Allactaga sibirica (Mongolian five-toed jerboa) :

Alligator mississippiensis (American alligator) :

Amazona aestiva (blue-fronted amazon) :

Amazona vittata (Puerto Rican parrot) :

Amblyraja radiata (thorny skate) :

Amia calva (bowfin) :

Amphibia (amphibians) :

Amphilophus citrinellus (Midas cichlid) :

Amphiprion bicinctus (twoband anemonefish) :

Amphiprion percula (orange clownfish) :

Anas platyrhynchos (Mallard) :

Anas platyrhynchos x Cairina moschata (domestic duck x muscovy duck) :

Anatidae (waterfowl) :

Andrias davidianus (Chinese giant salamander) :

Anguilla bicolor (Indonesian shortfin eel) :

Anolis apletophallus (slender anole) :

Anomalopteryx didiformis (little bush moa) :

Anoplopoma fimbria (sablefish) :

Anser anser (domestic goose) :

Anser cygnoides (swan goose) :

Antennarius striatus (striated frogfish) :

Apareiodon sp. 'Rio Verde' :

Aphelocoma californica (Western scrub-jay) :

Aphelocoma coerulescens (scrub jay) :

Apis mellifera (honey bee) :

Ara macao (scarlet macaw) :

Aratinga solstitialis (sun parakeet) :

Archilochus colubris :

Archocentrus centrarchus (flier cichlid) :

Arctocephalus gazella (antarctic fur seal) :

Argyrosomus japonicus (mulloway) :

Ariidae (sea catfishes) :

Arizona elegans occidentalis :

Asaccus caudivolvulus :

Aselliscus stoliczkanus (Stoliczka's Asian trident bat) :

Astatotilapia calliptera (eastern happy) :

Astyanax mexicanus (Mexican tetra) :

Atelerix albiventris (middle-African hedgehog) :

Ateles fusciceps (brown-headed spider monkey) :

Aythya baeri (Baer's pochard) :

Aythya ferina (common 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 primigenius (aurochs) :

Bos taurus (taurine cattle) :

Bovichtus diacanthus :

Bovichtus variegatus (thornfish) :

Brachyistius frenatus (kelp perch) :

Bradypodion pumilum :

Bradypodion ventrale (Southern dwarf chameleon) :