Genetic map articles

Agapornis roseicollis (peach-faced lovebird)

Alligator mississippiensis (American alligator)

Amazona vittata (Puerto Rican parrot)

Amblyraja radiata (thorny skate)

Amia calva (bowfin)

Anas platyrhynchos (Mallard)

Andrias davidianus (Chinese giant salamander)

Anser cygnoides (swan goose)

Ara macao (scarlet macaw)

Aratinga solstitialis (sun parakeet)

Archocentrus centrarchus (flier cichlid)

Astatotilapia calliptera (eastern happy)

Astyanax mexicanus (Mexican tetra)

Aythya fuligula (tufted duck)

Bison bison (American bison)

Bos taurus (cattle)

Bubalus bubalis (water buffalo)

Cairina moschata (Muscovy duck)

Callithrix jacchus (white-tufted-ear marmoset)

Calypte anna (Anna's hummingbird)

Camelus bactrianus (Bactrian camel)

Camelus dromedarius (Arabian camel)

Canis lupus (gray wolf)

Canis lupus familiaris (dog)

Capra aegagrus (wild goat)

Capra hircus (goat)

Carassius auratus (goldfish)

Cervidae (deer)

Cervus elaphus (red deer)

Clupea harengus (Atlantic herring)

Cociella crocodila (crocodile flathead)

Colossoma macropomum (tambaqui)

Conuropsis carolinensis (Carolina parakeet)

Cottoperca trigloides (channel bull blenny)

Coturnix japonica (Japanese quail)

Crocodylus porosus (Australian saltwater crocodile)

Cyanistes caeruleus (Blue tit)

Cynomys gunnisoni (Gunnison's prairie dog)

Cyprinus carpio (common carp)

Danio rerio (zebrafish)

Elephantidae (elephants)

Enhydra lutris (sea otter)

Equus asinus (ass)

Equus caballus (horse)

Erythrura gouldiae (Gouldian finch)

Felis catus (domestic cat)

Ficedula

Gadus morhua (Atlantic cod)

Gallus gallus (chicken)

Gavialis gangeticus (Gharial)

Giraffa camelopardalis tippelskirchi

Gopherus evgoodei (Goodes thornscrub tortoise)

Gouania willdenowi (blunt-snouted clingfish)

Ictalurus punctatus (channel catfish)

Labeo rohita (rohu)

Lamprotornis superbus (superb starling)

Lemur catta (Ring-tailed lemur)

Lynx canadensis (Canada lynx)

Macaca mulatta (Rhesus monkey)

Mandrillus sphinx (mandrill)

Mastacembelus armatus (zig-zag eel)

Megalobrama amblycephala (Wuchang bream)

Meleagris gallopavo (turkey)

Melopsittacus undulatus (budgerigar)

Mesocricetus auratus (golden hamster)

Monodelphis domestica (gray short-tailed opossum)

Moschus moschiferus (Siberian musk deer)

Neovison vison (American mink)

Nestor notabilis (Kea)

Numida meleagris (helmeted guineafowl)

Nyctereutes procyonoides (raccoon dog)

Ochotona princeps (American pika)

Odontobutis potamophila

Oncorhynchus mykiss (rainbow trout)

Oncorhynchus nerka (sockeye salmon)

Oplegnathus fasciatus (barred knifejaw)

Oreochromis mossambicus (Mozambique tilapia)

Oreochromis niloticus (Nile tilapia)

Ornithorhynchus anatinus (platypus)

Orycteropus afer (aardvark)

Oryctolagus cuniculus (rabbit)

Oryzias latipes (Japanese medaka)

Oryzias melastigma (Indian medaka)

Ovis aries (sheep)

Ovis orientalis (Asiatic mouflon)

Pangasianodon hypophthalmus (striped catfish)

Panthera tigris (tiger)

Pantherophis guttatus (corn snake)

Paracanthobrama guichenoti

Penaeus monodon (black tiger shrimp)

Perisoreus infaustus

Phascolarctos cinereus (koala)

Phocoena sinus (vaquita)

Phyllostomus discolor (pale spear-nosed bat)

Plecoglossus altivelis (ayu)

Prionailurus bengalensis (leopard cat)

Protosalanx hyalocranius (clearhead icefish)

Pseudocaranx georgianus (silver trevally)

Pteronura brasiliensis (giant otter)

Puma yagouaroundi (jaguarundi)

Puntigrus tetrazona (Sumatra barb)

Rhinatrema bivittatum (two-lined caecilian)

Rhinolophus ferrumequinum (greater horseshoe bat)

Saccostrea glomerata

Salmo salar (Atlantic salmon)

Salmo trutta (brown trout)

Sciurus niger (fox squirrel)

Seriola lalandi (yellowtail amberjack)

Siniperca chuatsi (mandarin fish)

Strigops habroptilus (kakapo)

Struthio camelus (African ostrich)

Sus scrofa (pig)

Tachyglossus aculeatus (Australian echidna)

Tachysurus fulvidraco × Tachysurus vachelli (hybrid yellow catfish)

Taeniopygia guttata (zebra finch)

Thymallus thymallus (grayling)

Tremarctos ornatus (spectacled bear)

Ursus arctos (brown bear)

Varanus komodoensis (Komodo dragon)

Vicugna pacos (alpaca)

Vulpes vulpes (red fox)

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.

Alligator mississippiensis (American alligator) :

2017 Rice, E.S., Kohno, S., John, J.S., Pham, S., Howard, J., Lareau, L.F., O'Connell, B.L., Hickey, G., Armstrong, J., Deran, A., Fiddes, I., Platt, R.N., Gresham, C., McCarthy, F., Kern, C., Haan, D., Phan, T., Schmidt, C., Sanford, J.R., Ray, D.A., Paten, B., Guillette, L.J., Green, R.E. :
Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res :, 2017. Pubmed reference: 28137821. DOI: 10.1101/gr.213595.116.
2014 Green, R.E., Braun, E.L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M.W., St John, J.A., Capella-Gutiérrez, S., Castoe, T.A., Kern, C., Fujita, M.K., Opazo, J.C., Jurka, J., Kojima, K.K., Caballero, J., Hubley, R.M., Smit, A.F., Platt, R.N., Lavoie, C.A., Ramakodi, M.P., Finger, J.W., Suh, A., Isberg, S.R., Miles, L., Chong, A.Y., Jaratlerdsiri, W., Gongora, J., Moran, C., Iriarte, A., McCormack, J., Burgess, S.C., Edwards, S.V., Lyons, E., Williams, C., Breen, M., Howard, J.T., Gresham, C.R., Peterson, D.G., Schmitz, J., Pollock, D.D., Haussler, D., Triplett, E.W., Zhang, G., Irie, N., Jarvis, E.D., Brochu, C.A., Schmidt, C.J., McCarthy, F.M., Faircloth, B.C., Hoffmann, F.G., Glenn, T.C., Gabaldón, T., Paten, B., Ray, D.A. :
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449, 2014. Pubmed reference: 25504731. DOI: 10.1126/science.1254449.

Amazona 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.

Anas platyrhynchos (Mallard) :

2021 Zhu, F., Yin, Z.T., Wang, Z., Smith, J., Zhang, F., Martin, F., Ogeh, D., Hincke, M., Lin, F.B., Burt, D.W., Zhou, Z.K., Hou, S.S., Zhao, Q.S., Li, X.Q., Ding, S.R., Li, G.S., Yang, F.X., Hao, J.P., Zhang, Z., Lu, L.Z., Yang, N., Hou, Z.C. :
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. Nat Commun 12:5932, 2021. Pubmed reference: 34635656. DOI: 10.1038/s41467-021-26272-1.
2013 Huang, Y., Li, Y., Burt, D.W., Chen, H., Zhang, Y., Qian, W., Kim, H., Gan, S., Zhao, Y., Li, J., Yi, K., Feng, H., Zhu, P., Li, B., Liu, Q., Fairley, S., Magor, K.E., Du, Z., Hu, X., Goodman, L., Tafer, H., Vignal, A., Lee, T., Kim, K.W., Sheng, Z., An, Y., Searle, S., Herrero, J., Groenen, M.A., Crooijmans, R.P., Faraut, T., Cai, Q., Webster, R.G., Aldridge, J.R., Warren, W.C., Bartschat, S., Kehr, S., Marz, M., Stadler, P.F., Smith, J., Kraus, R.H., Zhao, Y., Ren, L., Fei, J., Morisson, M., Kaiser, P., Griffin, D.K., Rao, M., Pitel, F., Wang, J., Li, N. :
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet 45:776-83, 2013. Pubmed reference: 23749191. DOI: 10.1038/ng.2657.

Andrias davidianus (Chinese giant salamander) :

2021 Hu, Q., Liu, Y., Liao, X., Tian, H., Ji, X., Zhu, J., Xiao, H. :
A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander. BMC Genomics 22:230, 2021. Pubmed reference: 33794798. DOI: 10.1186/s12864-021-07550-0.

Anser cygnoides (swan goose) :

2015 Lu, L., Chen, Y., Wang, Z., Li, X., Chen, W., Tao, Z., Shen, J., Tian, Y., Wang, D., Li, G., Chen, L., Chen, F., Fang, D., Yu, L., Sun, Y., Ma, Y., Li, J., Wang, J. :
The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver. Genome Biol 16:89, 2015. Pubmed reference: 25943208. DOI: 10.1186/s13059-015-0652-y.

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.

Archocentrus centrarchus (flier cichlid) :

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.

Astatotilapia calliptera (eastern happy) :

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.

Astyanax mexicanus (Mexican tetra) :

2014 McGaugh, S.E., Gross, J.B., Aken, B., Blin, M., Borowsky, R., Chalopin, D., Hinaux, H., Jeffery, W.R., Keene, A., Ma, L., Minx, P., Murphy, D., O'Quin, K.E., Rétaux, S., Rohner, N., Searle, S.M., Stahl, B.A., Tabin, C., Volff, J.N., Yoshizawa, M., Warren, W.C. :
The cavefish genome reveals candidate genes for eye loss. Nat Commun 5:5307, 2014. Pubmed reference: 25329095. DOI: 10.1038/ncomms6307.
2002 Borowsky, R., Wilkens, H. :
Mapping a cave fish genome: polygenic systems and regressive evolution. J Hered 93:19-21, 2002. Pubmed reference: 12011170.

Aythya fuligula (tufted duck) :

2021 Mueller, R.C., Ellström, P., Howe, K., Uliano-Silva, M., Kuo, R.I., Miedzinska, K., Warr, A., Fedrigo, O., Haase, B., Mountcastle, J., Chow, W., Torrance, J., Wood, J.M.D., Järhult, J.D., Naguib, M.M., Olsen, B., Jarvis, E.D., Smith, J., Eöry, L., Kraus, R.H.S. :
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). Gigascience 10:, 2021. Pubmed reference: 34927191. DOI: 10.1093/gigascience/giab081.

Bison bison (American bison) :

2021 Dobson, L.K., Zimin, A., Bayles, D., Fritz-Waters, E., Alt, D., Olsen, S., Blanchong, J., Reecy, J., Smith, T.P.L., Derr, J.N. :
De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification. Anim Genet :, 2021. Pubmed reference: 33780561. DOI: 10.1111/age.13060.
Oppenheimer, J., Rosen, B.D., Heaton, M.P., Vander Ley, B.L., Shafer, W.R., Schuetze, F.T., Stroud, B., Kuehn, L.A., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Bickhart, D.M., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Smith, T.P.L. :
A reference genome assembly of American bison, Bison bison bison. J Hered 112:174-183, 2021. Pubmed reference: 33595645. DOI: 10.1093/jhered/esab003.

Bos taurus (cattle) :

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.
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.
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. :
Erratum to: A reference genome assembly of Simmental cattle, Bos taurus taurus. J Hered :, 2021. Pubmed reference: 34436588. DOI: 10.1093/jhered/esab039.
MacPhillamy, C., Pitchford, W.S., Alinejad-Rokny, H., Low, W.Y. :
Opportunity to improve livestock traits using 3D genomics. Anim Genet :, 2021. Pubmed reference: 34494283. DOI: 10.1111/age.13135.
Neumann, G.B., Korkuć, P., Arends, D., Wolf, M.J., May, K., Reißmann, M., Elzaki, S., König, S., Brockmann, G.A. :
Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN). BMC Genomics 22:905, 2021. Pubmed reference: 34922441. DOI: 10.1186/s12864-021-08237-2.
2020 De Lorenzi, L., Parma, P. :
Identification of Some Errors in the Genome Assembly of Bovidae by FISH. Cytogenet Genome Res :, 2020. Pubmed reference: 32235117. DOI: 10.1159/000506221.
Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M., Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. :
De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience 9:, 2020. Pubmed reference: 32191811. DOI: 10.1093/gigascience/giaa021.
Triant, D.A., Le Tourneau, J.J., Diesh, C.M., Unni, D.R., Shamimuzzaman, M., Walsh, A.T., Gardiner, J., Goldkamp, A.K., Li, Y., Nguyen, H.N., Roberts, C., Zhao, Z., Alexander, L.J., Decker, J.E., Schnabel, R.D., Schroeder, S.G., Sonstegard, T.S., Taylor, J.F., Rivera, R.M., Hagen, D.E., Elsik, C.G. :
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. Anim Genet :, 2020. Pubmed reference: 32537769. DOI: 10.1111/age.12962.
2019 Sasaki, S., Muraki, E., Inoue, Y., Suezawa, R., Nikadori, H., Yoshida, Y., Nariai, S., Hideshima, R., Moriwaki, S., Nakashima, R., Uchiyama, K., Yoshinari, K., Takeda, M., Kojima, T. :
Genotypes and allele frequencies of buried SNPs in a bovine single-nucleotide polymorphism array in Japanese Black cattle. Anim Sci J 90:1503-1509, 2019. Pubmed reference: 31599477. DOI: 10.1111/asj.13293.
Womack, J.E.J. :
Mapping Genes Is Good for You. Annu Rev Anim Biosci 7:1-16, 2019. Pubmed reference: 30296836. DOI: 10.1146/annurev-animal-020518-114902.
2015 Ma, L., O'Connell, J.R., VanRaden, P.M., Shen, B., Padhi, A., Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G.E., Da, Y., Wiggans, G.R. :
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis. PLoS Genet 11:e1005387, 2015. Pubmed reference: 26540184. DOI: 10.1371/journal.pgen.1005387.
2013 Kõks, S., Lilleoja, R., Reimann, E., Salumets, A., Reemann, P., Jaakma, Ü. :
Sequencing and annotated analysis of the Holstein cow genome. Mamm Genome 24:309-21, 2013. Pubmed reference: 23893136. DOI: 10.1007/s00335-013-9464-0.
2012 Boichard, D., Chung, H., Dassonneville, R., David, X., Eggen, A., Fritz, S., Gietzen, K.J., Hayes, B.J., Lawley, C.T., Sonstegard, T.S., Van Tassell, C.P., VanRaden, P.M., Viaud-Martinez, K.A., Wiggans, G.R. :
Design of a bovine low-density SNP array optimized for imputation. PLoS One 7:e34130, 2012. Pubmed reference: 22470530. DOI: 10.1371/journal.pone.0034130.
2011 Stothard, P., Choi, J.W., Basu, U., Sumner-Thomson, J.M., Meng, Y., Liao, X., Moore, S.S. :
Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12:559, 2011. Pubmed reference: 22085807. DOI: 10.1186/1471-2164-12-559.
Rincon, G., Weber, K.L., Eenennaam, A.L., Golden, B.L., Medrano, J.F. :
Hot topic: performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J Dairy Sci 94:6116-21, 2011. Pubmed reference: 22118099. DOI: 10.3168/jds.2011-4764.
2009 Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J.A., Salzberg, S.L. :
A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 10:R42, 2009. Pubmed reference: 19393038. DOI: 10.1186/gb-2009-10-4-r42.
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.
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.
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 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.
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.
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 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.
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.
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.
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.
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.
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.
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.
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.
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 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.
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.
1999 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.
Rexroad, C.E., Womack, J.E. :
Parallel RH mapping of BTA1 with HSA3 and HSA21 Mammalian Genome 10:1095-1097, 1999. Pubmed reference: 10556430.
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.
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.
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.
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.
1997 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.
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.
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.
Barendse, W. :
A medium density genetic linkage map of the bovine genome (vol 8, pg 21, 1997) Mammalian Genome 8:798, 1997.
Kappes, S.M., Keele, J.W., Stone, R.T., Sonstegard, T.S., Smith, T.P.L., Mcgraw, R.A., Lopezcorrales, N.L., Beattie, C.W. :
A second-generation linkage map of the bovine genome Genome Research 7:235-249, 1997. Pubmed reference: 9074927.
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.
Kalm, E. :
Genome mapping by cattle [German] Archiv fur Tierzucht-Archives of Animal Breeding 40:74-79, 1997.
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Mapping of eight human chromosome 1 orthologs to cattle chromosomes 3 and 16 Mammalian Genome 8:533-536, 1997. Pubmed reference: 9196004.
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.
Barendse, W., Vaiman, D., Kemp, S.J., Sugimoto, Y., Armitage, S.M., Williams, J.L., Sun, H.S., Eggen, A., Agaba, M., Aleyasin, S.A., Band, M., Bishop, M.D., Buitkamp, J., Byrne, K., Collins, F., Cooper, L., Coppettiers, W., Denys, B., Drinkwater, R.D., Easterday, K., Elduque, C., Ennis, S., Erhardt, G., Ferretti, L., Flavin, N., et al. :
A medium-density genetic linkage map of the bovine genome Mammalian Genome 8:21-28, 1997. Pubmed reference: 9021143.
1996 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.
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.
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A male linkage map of the cattle (bos taurus) genome Journal of Heredity 87:261-271, 1996. Pubmed reference: 8776874.
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. :
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1994 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.
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1993 Vaiman, D., Bahridarwich, I., Mercier, D., Yerle, M., Eggen, A., Leveziel, H., Guerin, G., Gellin, J., Cribiu, E.P. :
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1989 Fries, R., Beckmann, J.S., Georges, M., Soller, M., Womack, J. :
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Bubalus bubalis (water buffalo) :

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.

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.

Callithrix jacchus (white-tufted-ear marmoset) :

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.

Calypte anna (Anna's hummingbird) :

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.

Camelus bactrianus (Bactrian camel) :

2019 Futas, J., Oppelt, J., Jelinek, A., Elbers, J.P., Wijacki, J., Knoll, A., Burger, P.A., Horin, P. :
Natural killer cell receptor genes in camels: Another mammalian model. Front Genet 10:620, 2019. Pubmed reference: 31312212. DOI: 10.3389/fgene.2019.00620.

Camelus dromedarius (Arabian camel) :

2020 Sabahat, S., Brauning, R., Clarke, S.M., Nadeem, A., Thomson, P.C., Khatkar, M.S. :
SNP discovery and population structure analysis in Lassi and Marecha camel breeds using a genotyping by sequencing method. Anim Genet 51:620-623, 2020. Pubmed reference: 32421863. DOI: 10.1111/age.12953.
2019 Ruvinskiy, D., Larkin, D.M., Farré, M. :
A near chromosome assembly of the dromedary camel genome. Front Genet 10:32, 2019. Pubmed reference: 30804979. DOI: 10.3389/fgene.2019.00032.
Futas, J., Oppelt, J., Jelinek, A., Elbers, J.P., Wijacki, J., Knoll, A., Burger, P.A., Horin, P. :
Natural killer cell receptor genes in camels: Another mammalian model. Front Genet 10:620, 2019. Pubmed reference: 31312212. DOI: 10.3389/fgene.2019.00620.

Canis lupus (gray wolf) :

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 familiaris (dog) :

2021 Wang, C., Wallerman, O., Arendt, M.L., Sundström, E., Karlsson, Å., Nordin, J., Mäkeläinen, S., Pielberg, G.R., Hanson, J., Ohlsson, Å., Saellström, S., Rönnberg, H., Ljungvall, I., Häggström, J., Bergström, T.F., Hedhammar, Å., Meadows, J.R.S., Lindblad-Toh, K. :
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Commun Biol 4:185, 2021. Pubmed reference: 33568770. DOI: 10.1038/s42003-021-01698-x.
Edwards, R.J., Field, M.A., Ferguson, J.M., Dudchenko, O., Keilwagen, J., Rosen, B.D., Johnson, G.S., Rice, E.S., Hillier, D., Hammond, J.M., Towarnicki, S.G., Omer, A., Khan, R., Skvortsova, K., Bogdanovic, O., Zammit, R.A., Aiden, E.L., Warren, W.C., Ballard, J.W.O. :
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 22:188, 2021. Pubmed reference: 33726677. DOI: 10.1186/s12864-021-07493-6.
Jagannathan, V., Hitte, C., Kidd, J.M., Masterson, P., Murphy, T.D., Emery, S., Davis, B., Buckley, R.M., Liu, Y.H., Zhang, X.Q., Leeb, T., Zhang, Y.P., Ostrander, E.A., Wang, G.D. :
Dog10K_Boxer_Tasha_1.0: A long-read assembly of the dog reference genome. Genes (Basel) 12:847, 2021. Pubmed reference: 34070911. DOI: 10.3390/genes12060847.
Serres-Armero, A., Davis, B.W., Povolotskaya, I.S., Morcillo-Suarez, C., Plassais, J., Juan, D., Ostrander, E.A., Marques-Bonet, T. :
Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 31:762-774, 2021. Pubmed reference: 33863806. DOI: 10.1101/gr.266049.120.
2020 Field, M.A., Rosen, B.D., Dudchenko, O., Chan, E.K.F., Minoche, A.E., Edwards, R.J., Barton, K., Lyons, R.J., Tuipulotu, D.E., Hayes, V.M., D Omer, A., Colaric, Z., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Smith, M.A., Aiden, E.L., Smith, T.P.L., Zammit, R.A., Ballard, J.W.O. :
Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Gigascience 9:, 2020. Pubmed reference: 32236524. DOI: 10.1093/gigascience/giaa027.
2019 Hayward, J.J., White, M.E., Boyle, M., Shannon, L.M., Casal, M.L., Castelhano, M.G., Center, S.A., Meyers-Wallen, V.N., Simpson, K.W., Sutter, N.B., Todhunter, R.J., Boyko, A.R. :
Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genet 15:e1008003, 2019. Pubmed reference: 31525180. DOI: 10.1371/journal.pgen.1008003.
Ostrander, E.A., Wang, G.D., Larson, G., vonHoldt, B.M., Davis, B.W., Jagannathan, V., Hitte, C., Wayne, R.K., Zhang, Y.P. :
Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. Natl Sci Rev 6:810-824, 2019. Pubmed reference: 31598383. DOI: 10.1093/nsr/nwz049.
Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., Zhai, S., Xiao, J., Zhang, Z., Bao, Y., Zhang, Y.P., Wang, G.D., Zhao, W. :
iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Res 47:D793-D800, 2019. Pubmed reference: 30371881. DOI: 10.1093/nar/gky1041.
2018 Holden, L.A., Arumilli, M., Hytönen, M.K., Hundi, S., Salojärvi, J., Brown, K.H., Lohi, H. :
Assembly and analysis of unmapped genome sequence reads reveal novel sequence and variation in dogs. Sci Rep 8:10862, 2018. Pubmed reference: 30022108. DOI: 10.1038/s41598-018-29190-3.
2014 Hoeppner, M.P., Lundquist, A., Pirun, M., Meadows, J.R., Zamani, N., Johnson, J., Sundström, G., Cook, A., Fitzgerald, M.G., Swofford, R., Mauceli, E., Moghadam, B.T., Greka, A., Alföldi, J., Abouelleil, A., Aftuck, L., Bessette, D., Berlin, A., Brown, A., Gearin, G., Lui, A., Macdonald, J.P., Priest, M., Shea, T., Turner-Maier, J., Zimmer, A., Lander, E.S., di Palma, F., Lindblad-Toh, K., Grabherr, M.G. :
An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS One 9:e91172, 2014. Pubmed reference: 24625832. DOI: 10.1371/journal.pone.0091172.
2010 Wong, A.K., Ruhe, A.L., Dumont, B.L., Robertson, K.R., Guerrero, G., Shull, S.M., Ziegle, J.S., Millon, L.V., Broman, K.W., Payseur, B.A., Neff, M.W. :
A comprehensive linkage map of the dog genome. Genetics 184:595-605, 2010. Pubmed reference: 19966068. DOI: 10.1534/genetics.109.106831.
2008 Thomas, R., Duke, S.E., Karlsson, E.K., Evans, A., Ellis, P., Lindblad-Toh, K., Langford, C.F., Breen, M. :
A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis. Cytogenet Genome Res 122:110-21, 2008. Pubmed reference: 19096206. DOI: 10.1159/000163088.
2007 Thomas, R., Duke, S.E., Bloom, S.K., Breen, T.E., Young, A.C., Feiste, E., Seiser, E.L., Tsai, P.C., Langford, C.F., Ellis, P., Karlsson, E.K., Lindblad-Toh, K., Breen, M. :
A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog. J Hered 98:474-84, 2007. Pubmed reference: 17702974. DOI: 10.1093/jhered/esm053.
Sargan, D.R., Aguirre-Hernandez, J., Galibert, F., Ostrander, E.A. :
An extended microsatellite set for linkage mapping in the domestic dog. J Hered 98:221-31, 2007. Pubmed reference: 17406025. DOI: 10.1093/jhered/esm006.
2005 Lindblad-Toh, K., Wade, C.M., Mikkelsen, T.S., Karlsson, E.K., Jaffe, D.B., Kamal, M., Clamp, M., Chang, J.L., Kulbokas, E.J., Zody, M.C., Mauceli, E., Xie, X., Breen, M., Wayne, R.K., Ostrander, E.A., Ponting, C.P., Galibert, F., Smith, D.R., DeJong, P.J., Kirkness, E., Alvarez, P., Biagi, T., Brockman, W., Butler, J., Chin, C.W., Cook, A., Cuff, J., Daly, M.J., DeCaprio, D., Gnerre, S., Grabherr, M., Kellis, M., Kleber, M., Bardeleben, C., Goodstadt, L., Heger, A., Hitte, C., Kim, L., Koepfli, K.P., Parker, H.G., Pollinger, J.P., Searle, S.M., Sutter, N.B., Thomas, R., Webber, C., Baldwin, J., Abebe, A., Abouelleil, A., Aftuck, L., Ait-Zahra, M., Aldredge, T., Allen, N., An, P., Anderson, S., Antoine, C., Arachchi, H., Aslam, A., Ayotte, L., Bachantsang, P., Barry, A., Bayul, T., Benamara, M., Berlin, A., Bessette, D., Blitshteyn, B., Bloom, T., Blye, J., Boguslavskiy, L., Bonnet, C., Boukhgalter, B., Brown, A., Cahill, P., Calixte, N., Camarata, J., Cheshatsang, Y., Chu, J., Citroen, M., Collymore, A., Cooke, P., Dawoe, T., Daza, R., Decktor, K., DeGray, S., Dhargay, N., Dooley, K., Dooley, K., Dorje, P., Dorjee, K., Dorris, L., Duffey, N., Dupes, A., Egbiremolen, O., Elong, R., Falk, J., Farina, A., Faro, S., Ferguson, D., Ferreira, P., Fisher, S., FitzGerald, M., Foley, K., Foley, C., Franke, A., Friedrich, D., Gage, D., Garber, M., Gearin, G., Giannoukos, G., Goode, T., Goyette, A., Graham, J., Grandbois, E., Gyaltsen, K., Hafez, N., Hagopian, D., Hagos, B., Hall, J., Healy, C., Hegarty, R., Honan, T., Horn, A., Houde, N., Hughes, L., Hunnicutt, L., Husby, M., Jester, B., Jones, C., Kamat, A., Kanga, B., Kells, C., Khazanovich, D., Kieu, A.C., Kisner, P., Kumar, M., Lance, K., Landers, T., Lara, M., Lee, W., Leger, J.P., Lennon, N., Leuper, L., LeVine, S., Liu, J., Liu, X., Lokyitsang, Y., Lokyitsang, T., Lui, A., Macdonald, J., Major, J., Marabella, R., Maru, K., Matthews, C., McDonough, S., Mehta, T., Meldrim, J., Melnikov, A., Meneus, L., Mihalev, A., Mihova, T., Miller, K., Mittelman, R., Mlenga, V., Mulrain, L., Munson, G., Navidi, A., Naylor, J., Nguyen, T., Nguyen, N., Nguyen, C., Nguyen, T., Nicol, R., Norbu, N., Norbu, C., Novod, N., Nyima, T., Olandt, P., O'Neill, B., O'Neill, K., Osman, S., Oyono, L., Patti, C., Perrin, D., Phunkhang, P., Pierre, F., Priest, M., Rachupka, A., Raghuraman, S., Rameau, R., Ray, V., Raymond, C., Rege, F., Rise, C., Rogers, J., Rogov, P., Sahalie, J., Settipalli, S., Sharpe, T., Shea, T., Sheehan, M., Sherpa, N., Shi, J., Shih, D., Sloan, J., Smith, C., Sparrow, T., Stalker, J., Stange-Thomann, N., Stavropoulos, S., Stone, C., Stone, S., Sykes, S., Tchuinga, P., Tenzing, P., Tesfaye, S., Thoulutsang, D., Thoulutsang, Y., Topham, K., Topping, I., Tsamla, T., Vassiliev, H., Venkataraman, V., Vo, A., Wangchuk, T., Wangdi, T., Weiand, M., Wilkinson, J., Wilson, A., Yadav, S., Yang, S., Yang, X., Young, G., Yu, Q., Zainoun, J., Zembek, L., Zimmer, A., Lander, E.S. :
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-19, 2005. Pubmed reference: 16341006. DOI: 10.1038/nature04338.
2004 Switonski, M., Szczerbal, I., Nowacka, J. :
The dog genome map and its use in mammalian comparative genomics. J Appl Genet 45:195-214, 2004. Pubmed reference: 15131351.
2003 Guyon, R., Lorentzen, T.D., Hitte, C., Kim, L., Cadieu, E., Parker, H.G., Quignon, P., Lowe, J.K., Renier, C., Gelfenbeyn, B., Vignaux, F., DeFrance, H.B., Gloux, S., Mahairas, G.G., Andre, C., Galibert, F., Ostrander, E.A. :
A 1-Mb resolution radiation hybrid map of the canine genome Proceedings of the National Academy of Sciences of the United States of America 100:5296-301, 2003. Pubmed reference: 12700351. DOI: 10.1073/pnas.0831002100.
Spriggs, H.F., Holmes, N.G., Breen, M.G., Deloukas, P.G., Langford, C.F., Ross, M.T., Carter, N.P., Davis, M.E., Knights, C.E., Smith, A.E., Farr, C.J., McCarthy, L.C., Binns, M.M. :
Construction and integration of radiation-hybrid and cytogenetic maps of dog Chromosome X Mammalian Genome 14:214-21, 2003. Pubmed reference: 12647244. DOI: 10.1007/s00335-002-3051-0.
Roberts, M.C., Hitte, C.C., Hendrickson, J.A., Hoffmann, D.E., Flickinger, G.H., Rutherford, M.S., Guyon, R.S., Galibert, F.S., Mickelson, J.R. :
Characterization and radiation hybrid mapping of expressed sequence tags from the canine brain Mammalian Genome 14:203-13, 2003. Pubmed reference: 12647243. DOI: 10.1007/s00335-002-2207-2.
2002 Dukes-McEwan, J., Jackson, I.J. :
The promises and problems of linkage analysis by using the current canine genome map Mammalian Genome 13:667-672, 2002. Pubmed reference: 12461654. DOI: 10.1007/s00335-002-4004-3.
2001 Breen, M., Jouquand, S., Renier, C., Mellersh, C.S., Hitte, C., Holmes, N.G., Cheron, A., Suter, N., Vignaux, F., Bristow, A.E., Priat, C., McCann, E., Andre, C., Boundy, S., Gitsham, P., Thomas, R., Bridge, W.L., Spriggs, H.F., Ryder, E.J., Curson, A., Sampson, J., Ostrander, E.A., Binns, M.M., Galibert, F. :
Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes Genome Research 11:1784-1795, 2001. Pubmed reference: 11591656. DOI: 10.1101/gr.189401.
2000 Mellersh, C.S., Hitte, C., Richman, M., Vignaux, F., Priat, C., Jouquand, S., Werner, P., Andre, C., DeRose, S., Patterson, D.F., Ostrander, E.A., Galibert, F. :
An integrated linkage-radiation hybrid map of the canine genome Mammalian Genome 11:120-130, 2000. Pubmed reference: 10656926.
1999 Vignaux, F., Priat, C., Jouquand, S., Hitte, C., Jiang, Z., Cheron, A., Renier, C., Andre, C., Galibert, F. :
Toward a dog radiation hybrid map Journal of Heredity 90:62-67, 1999. Pubmed reference: 9987906.
Langston, A.A., Mellersh, C.S., Wiegand, N.A., Acland, G.M., Ray, K., Aguirre, G.D., Ostrander, E.A. :
Toward a framework linkage map of the canine genome Journal of Heredity 90:7-14, 1999. Pubmed reference: 9987896.
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.
Dolf, G., Batt, R., Baumle, E., Binns, M., Brenig, B., Bull, B., Dunner, S., Fredholm, M., Gaillard, C., Gerlach, J., Giger, U., Goldspink, G., Graphodatsky, A.S., Holmes, N., Judd, S., Juneja, K., Kelly, E.P., Kent, M.G., King, W.A., Lingaas, F., Long, S.E., Lubas, G., Mariat, D., Marki, U., Matthews, M., et al. :
DogMap: An international collaboration toward a low-resolution canine genetic marker map Journal of Heredity 90:3-6, 1999. Pubmed reference: 9987895.
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.

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) :

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

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.

Cervidae (deer) :

2002 Slate, J., Van Stijn, T.C., Anderson, R.M., McEwan, K.M., Maqbool, N.J., Mathias, H.C., Bixley, M.J., Stevens, D.R., Molenaar, A.J., Beever, J.E., Galloway, S.M., Tate, M.L. :
A deer (subfamily cervinae) genetic linkage map and the evolution of ruminant Genomes Genetics 160:1587-1597, 2002. Pubmed reference: 11973312.
1995 Tate, M.L., Mathias, H.C., Fennessy, P.F., Dodds, K.G., Penty, J.M., Hill, D.F. :
A new gene mapping resource: Interspecies hybrids between Pere David's deer (Elaphurus davidianus) and red deer (Cervus elaphus) Genetics 139:1383-1391, 1995. Pubmed reference: 7768446.

Cervus elaphus (red deer) :

2021 Vozdova, M., Kubickova, S., Cernohorska, H., Fröhlich, J., Rubes, J. :
Anchoring the CerEla1.0 genome assembly to red deer (Cervus elaphus) and cattle (Bos taurus) chromosomes and specification of evolutionary chromosome rearrangements in cervidae. Animals (Basel) 11:, 2021. Pubmed reference: 34573579. DOI: 10.3390/ani11092614.
2018 Bana, N.Á., Nyiri, A., Nagy, J., Frank, K., Nagy, T., Stéger, V., Schiller, M., Lakatos, P., Sugár, L., Horn, P., Barta, E., Orosz, L. :
The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes. Mol Genet Genomics 293:665-684, 2018. Pubmed reference: 29294181. DOI: 10.1007/s00438-017-1412-3.
2017 Johnston, S.E., Huisman, J., Ellis, P.A., Pemberton, J.M. :
A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer (<i>Cervus elaphus</i>). G3 (Bethesda) 7:2859-2870, 2017. Pubmed reference: 28667018. DOI: 10.1534/g3.117.044198.

Clupea harengus (Atlantic herring) :

2019 Pettersson, M.E., Rochus, C.M., Han, F., Chen, J., Hill, J., Wallerman, O., Fan, G., Hong, X., Xu, Q., Zhang, H., Liu, S., Liu, X., Haggerty, L., Hunt, T., Martin, F.J., Flicek, P., Bunikis, I., Folkvord, A., Andersson, L. :
A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection. Genome Res 29:1919-1928, 2019. Pubmed reference: 31649060. DOI: 10.1101/gr.253435.119.
2016 Martinez Barrio, A., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M., Zhang, H., Dainat, J., Ekman, D., Höppner, M., Jern, P., Martin, M., Nystedt, B., Liu, X., Chen, W., Liang, X., Shi, C., Fu, Y., Ma, K., Zhan, X., Feng, C., Gustafson, U., Rubin, C.J., Sällman Almén, M., Blass, M., Casini, M., Folkvord, A., Laikre, L., Ryman, N., Ming-Yuen Lee, S., Xu, X., Andersson, L. :
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. Elife 5:, 2016. Pubmed reference: 27138043. DOI: 10.7554/eLife.12081.

Cociella crocodila (crocodile flathead) :

2021 Zhao, R., Lu, Z., Cai, S., Gao, T., Xu, S. :
Whole genome survey and genetic markers development of crocodile flathead Cociella crocodilus. Anim Genet 52:891-895, 2021. Pubmed reference: 34486145. DOI: 10.1111/age.13136.

Colossoma macropomum (tambaqui) :

2021 Varela, E.S., Bekaert, M., Ganeco-Kirschnik, L.N., Torati, L.S., Shiotsuki, L., de Almeida, F.L., Villela, L.C.V., Rezende, F.P., da Silva Barroso, A., de Freitas, L.E.L., Taggart, J.B., Migaud, H. :
A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum. BMC Genomics 22:709, 2021. Pubmed reference: 34598670. DOI: 10.1186/s12864-021-08037-8.

Conuropsis carolinensis (Carolina 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.

Cottoperca trigloides (channel bull blenny) :

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.

Coturnix japonica (Japanese quail) :

2020 Morris, K.M., Hindle, M.M., Boitard, S., Burt, D.W., Danner, A.F., Eory, L., Forrest, H.L., Gourichon, D., Gros, J., Hillier, L.W., Jaffredo, T., Khoury, H., Lansford, R., Leterrier, C., Loudon, A., Mason, A.S., Meddle, S.L., Minvielle, F., Minx, P., Pitel, F., Seiler, J.P., Shimmura, T., Tomlinson, C., Vignal, A., Webster, R.G., Yoshimura, T., Warren, W.C., Smith, J. :
The quail genome: insights into social behaviour, seasonal biology and infectious disease response. BMC Biol 18:14, 2020. Pubmed reference: 32050986. DOI: 10.1186/s12915-020-0743-4.

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 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.

Cyanistes caeruleus (Blue tit) :

2010 Hansson, B., Ljungqvist, M., Dawson, DA., Mueller, JC., Olano-Marin, J., Ellegren, H., Nilsson, JA. :
Avian genome evolution: insights from a linkage map of the blue tit (Cyanistes caeruleus). Heredity 104:67-78, 2010. Pubmed reference: 19707235. DOI: 10.1038/hdy.2009.107.

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. :
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.
2014 Xu, P., Zhang, X., Wang, X., Li, J., Liu, G., Kuang, Y., Xu, J., Zheng, X., Ren, L., Wang, G., Zhang, Y., Huo, L., Zhao, Z., Cao, D., Lu, C., Li, C., Zhou, Y., Liu, Z., Fan, Z., Shan, G., Li, X., Wu, S., Song, L., Hou, G., Jiang, Y., Jeney, Z., Yu, D., Wang, L., Shao, C., Song, L., Sun, J., Ji, P., Wang, J., Li, Q., Xu, L., Sun, F., Feng, J., Wang, C., Wang, S., Wang, B., Li, Y., Zhu, Y., Xue, W., Zhao, L., Wang, J., Gu, Y., Lv, W., Wu, K., Xiao, J., Wu, J., Zhang, Z., Yu, J., Sun, X. :
Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet 46:1212-9, 2014. Pubmed reference: 25240282. DOI: 10.1038/ng.3098.
2013 Zhao, L., Zhang, Y., Ji, P., Zhang, X., Zhao, Z., Hou, G., Huo, L., Liu, G., Li, C., Xu, P., Sun, X. :
A dense genetic linkage map for common carp and its integration with a BAC-based physical map. PLoS One 8:e63928, 2013. Pubmed reference: 23704958. DOI: 10.1371/journal.pone.0063928.

Danio rerio (zebrafish) :

1999 Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., Talbot, W.S. :
A genetic linkage map for zebrafish: Comparative analysis and localization of genes and expressed sequences Genome Research 9:334-347, 1999. Pubmed reference: 10207156.
1998 Knapik, E.W., Goodman, A., Ekker, M., Chevrette, M., Delgado, J., Neuhauss, S., Shimoda, N., Driever, W., Fishman, M.C., Jacob, H.J. :
A microsatellite genetic linkage map for zebrafish (danio rerio) Nature Genetics 18:338-343, 1998. Pubmed reference: 9537415. DOI: 10.1038/ng0498-338.
Postlethwait, J.H., Yan, Y.L., Gates, M.A., Horne, S., Amores, A., Brownlie, A., Donovan, A., Egan, E.S., Force, A., Gong, Z.Y., Goutel, C., Fritz, A., Kelsh, R., Knapik, E., Liao, E., Paw, B., Ransom, D., Singer, A., Thomson, M., Abduljabbar, T.S., Yelick, P., Beier, D., Joly, J.S., Larhammar, D., Rosa, F., et al. :
Vertebrate genome evolution and the zebrafish gene map Nature Genetics 18:345-349, 1998. Pubmed reference: 9537416. DOI: 10.1038/ng0498-345.
1996 Johnson, S.L., Gates, M.A., Johnson, M., Talbot, W.S., Horne, S., Baik, K., Rude, S., Wong, J.R., Postlethwait, J.H. :
Centromere-linkage analysis and consolidation of the zebrafish genetic map Genetics 142:1277-1288, 1996. Pubmed reference: 8846904.

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.

Enhydra lutris (sea otter) :

2019 Beichman, A.C., Koepfli, K.P., Li, G., Murphy, W., Dobrynin, P., Kliver, S., Tinker, M.T., Murray, M.J., Johnson, J., Lindblad-Toh, K., Karlsson, E.K., Lohmueller, K.E., Wayne, R.K. :
Aquatic adaptation and depleted diversity: A deep dive into the genomes of the sea otter and giant otter. Mol Biol Evol 36:2631-2655, 2019. Pubmed reference: 31212313. DOI: 10.1093/molbev/msz101.
2017 Jones, S.J., Haulena, M., Taylor, G.A., Chan, S., Bilobram, S., Warren, R.L., Hammond, S.A., Mungall, K.L., Choo, C., Kirk, H., Pandoh, P., Ally, A., Dhalla, N., Tam, A.K.Y., Troussard, A., Paulino, D., Coope, R.J.N., Mungall, A.J., Moore, R., Zhao, Y., Birol, I., Ma, Y., Marra, M., Jones, S.J.M. :
The genome of the Northern sea otter (Enhydra lutris kenyoni). Genes (Basel) 8:, 2017. Pubmed reference: 29232880. DOI: 10.3390/genes8120379.

Equus asinus (ass) :

2020 Wang, C., Li, H., Guo, Y., Huang, J., Sun, Y., Min, J., Wang, J., Fang, X., Zhao, Z., Wang, S., Zhang, Y., Liu, Q., Jiang, Q., Wang, X., Guo, Y., Yang, C., Wang, Y., Tian, F., Zhuang, G., Fan, Y., Gao, Q., Li, Y., Ju, Z., Li, J., Li, R., Hou, M., Yang, G., Liu, G., Liu, W., Guo, J., Pan, S., Fan, G., Zhang, W., Zhang, R., Yu, J., Zhang, X., Yin, Q., Ji, C., Jin, Y., Yue, G., Liu, M., Xu, J., Liu, S., Jordana, J., Noce, A., Amills, M., Wu, D.D., Li, S., Zhou, X., Zhong, J. :
Donkey genomes provide new insights into domestication and selection for coat color. Nat Commun 11:6014, 2020. Pubmed reference: 33293529. DOI: 10.1038/s41467-020-19813-7.

Equus caballus (horse) :

2021 Peng, S., Petersen, J.L., Bellone, R.R., Kalbfleisch, T., Kingsley, N.B., Barber, A.M., Cappelletti, E., Giulotto, E., Finno, C.J. :
Decoding the equine genome: Lessons from ENCODE. Genes (Basel) 12:1707, 2021. Pubmed reference: 34828313. DOI: 10.3390/genes12111707.
Durward-Akhurst, S.A., Schaefer, R.J., Grantham, B., Carey, W.K., Mickelson, J.R., McCue, M.E. :
Genetic variation and the distribution of variant types in the horse. Front Genet 12:758366, 2021. Pubmed reference: 34925451. DOI: 10.3389/fgene.2021.758366.
2020 Beeson, S.K., Mickelson, J.R., McCue, M.E. :
Equine recombination map updated to EquCab3.0. Anim Genet 51:341-2, 2020. Pubmed reference: 31887785. DOI: 10.1111/age.12898.
Schaefer, R.J., McCue, M.E. :
Equine genotyping arrays. Vet Clin North Am Equine Pract 36:183-93, 2020. Pubmed reference: 32534852. DOI: 10.1016/j.cveq.2020.03.001.
2018 Janečka, J.E., Davis, B.W., Ghosh, S., Paria, N., Das, P.J., Orlando, L., Schubert, M., Nielsen, M.K., Stout, T.A.E., Brashear, W., Li, G., Johnson, C.D., Metz, R.P., Zadjali, A.M.A., Love, C.C., Varner, D.D., Bellott, D.W., Murphy, W.J., Chowdhary, B.P., Raudsepp, T. :
Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nat Commun 9:2945, 2018. Pubmed reference: 30054462. DOI: 10.1038/s41467-018-05290-6.
Kalbfleisch, T.S., Rice, E.S., DePriest, M.S., Walenz, B.P., Hestand, M.S., Vermeesch, J.R., O Connell, B.L., Fiddes, I.T., Vershinina, A.O., Saremi, N.F., Petersen, J.L., Finno, C.J., Bellone, R.R., McCue, M.E., Brooks, S.A., Bailey, E., Orlando, L., Green, R.E., Miller, D.C., Antczak, D.F., MacLeod, J.N. :
Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol 1:197, 2018. Pubmed reference: 30456315. DOI: 10.1038/s42003-018-0199-z.
2017 Schaefer, R.J., Schubert, M., Bailey, E., Bannasch, D.L., Barrey, E., Bar-Gal, G.K., Brem, G., Brooks, S.A., Distl, O., Fries, R., Finno, C.J., Gerber, V., Haase, B., Jagannathan, V., Kalbfleisch, T., Leeb, T., Lindgren, G., Lopes, M.S., Mach, N., da Câmara Machado, A., MacLeod, J.N., McCoy, A., Metzger, J., Penedo, C., Polani, S., Rieder, S., Tammen, I., Tetens, J., Thaller, G., Verini-Supplizi, A., Wade, C.M., Wallner, B., Orlando, L., Mickelson, J.R., McCue, M.E. :
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 18:565, 2017. Pubmed reference: 28750625. DOI: 10.1186/s12864-017-3943-8.
2012 McCue, M.E., Bannasch, D.L., Petersen, J.L., Gurr, J., Bailey, E., Binns, M.M., Distl, O., Guérin, G., Hasegawa, T., Hill, E.W., Leeb, T., Lindgren, G., Penedo, M.C., Røed, K.H., Ryder, O.A., Swinburne, J.E., Tozaki, T., Valberg, S.J., Vaudin, M., Lindblad-Toh, K., Wade, C.M., Mickelson, J.R. :
A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet 8:e1002451, 2012. Pubmed reference: 22253606. DOI: 10.1371/journal.pgen.1002451.
2010 Mittmann, E.H., Wrede, J., Pook, J., Distl, O. :
Identification of 21 781 equine microsatellites on the horse genome assembly 2.0. Anim Genet 41:222, 2010. Pubmed reference: 19793266. DOI: 10.1111/j.1365-2052.2009.01970.x.
2009 Wade, C.M., Giulotto, E., Sigurdsson, S., Zoli, M., Gnerre, S., Imsland, F., Lear, T.L., Adelson, D.L., Bailey, E., Bellone, R.R., Blöcker, H., Distl, O., Edgar, R.C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J.N., Penedo, M.C., Raison, J.M., Sharpe, T., Vogel, J., Andersson, L., Antczak, D.F., Biagi, T., Binns, M.M., Chowdhary, B.P., Coleman, S.J., Della Valle, G., Fryc, S., Guérin, G., Hasegawa, T., Hill, E.W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J.R., Murray, J., Nergadze, S.G., Onofrio, R., Pedroni, S., Piras, M.F., Raudsepp, T., Rocchi, M., Røed, K.H., Ryder, O.A., Searle, S., Skow, L., Swinburne, J.E., Syvänen, A.C., Tozaki, T., Valberg, S.J., Vaudin, M., White, J.R., Zody, M.C. :
Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326:865-7, 2009. Pubmed reference: 19892987. DOI: 10.1126/science.1178158.
2008 Raudsepp, T., Gustafson-Seabury, A., Durkin, K., Wagner, M.L., Goh, G., Seabury, C.M., Brinkmeyer-Langford, C., Lee, E.J., Agarwala, R., Stallknecht-Rice, E., Schäffer, A.A., Skow, L.C., Tozaki, T., Yasue, H., Penedo, M.C., Lyons, L.A., Khazanehdari, K.A., Binns, M.M., MacLeod, J.N., Distl, O., Guérin, G., Leeb, T., Mickelson, J.R., Chowdhary, B.P. :
A 4,103 marker integrated physical and comparative map of the horse genome. Cytogenet Genome Res 122:28-36, 2008. Pubmed reference: 18931483. DOI: 10.1159/000151313.
Chowdhary, B.P., Raudsepp, T. :
The horse genome derby: racing from map to whole genome sequence. Chromosome Res 16:109-27, 2008. Pubmed reference: 18274866. DOI: 10.1007/s10577-008-1204-z.
Brinkmeyer-Langford, C., Raudsepp, T., Gustafson-Seabury, A., Chowdhary, B.P. :
A BAC contig map over the proximal approximately 3.3 Mb region of horse chromosome 21. Cytogenet Genome Res 120:164-72, 2008. Pubmed reference: 18467843. DOI: 10.1159/000118758.
2007 Tozaki, T., Swinburne, J., Hirota, K., Hasegawa, T., Ishida, N., Tobe, T. :
Improved resolution of the comparative horse-human map: investigating markers with in silico and linkage mapping approaches. Gene 392:181-6, 2007. Pubmed reference: 17306472. DOI: 10.1016/j.gene.2006.12.018.
Goh, G., Raudsepp, T., Durkin, K., Wagner, M.L., Schäffer, A.A., Agarwala, R., Tozaki, T., Mickelson, J.R., Chowdhary, B.P. :
High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals. Genomics 89:89-112, 2007. Pubmed reference: 16916595. DOI: 10.1016/j.ygeno.2006.06.012.
2006 Chowdhary, B.P., Raudsepp, T. :
The horse genome. Genome Dyn 2:97-110, 2006. Pubmed reference: 18753773. DOI: 10.1159/000095098.
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.
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.
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.
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.
2004 Wagner, M.L., Goh, G., Wu, J.T., Morrison, L.Y., Alexander, L.J., Raudsepp, T., Skow, L.C., Chowdhary, B.P., Mickelson, J.R. :
Sixty-seven new equine microsatellite loci assigned to the equine radiation hybrid map. Anim Genet 35:484-6, 2004. Pubmed reference: 15566483. DOI: 10.1111/j.1365-2052.2004.01205.x.
Mickelson, J.R., Wagner, M.L., Goh, G., Wu, J.T., Morrison, L.Y., Alexander, L.J., Raudsepp, T., Skow, L.C., Chowdhary, B.P., Swinburne, J.E., Binns, M.M. :
Thirty-five new equine microsatellite loci assigned to genetic linkage and radiation hybrid maps. Anim Genet 35:481-4, 2004. Pubmed reference: 15566482. DOI: 10.1111/j.1365-2052.2004.01206.x.
Raudsepp, T., Santani, A., Wallner, B., Kata, S.R., Ren, C., Zhang, H.B., Womack, J.E., Skow, L.C., Chowdhary, B.P. :
A detailed physical map of the horse Y chromosome. Proc Natl Acad Sci U S A 101:9321-6, 2004. Pubmed reference: 15197257. DOI: 10.1073/pnas.0403011101.
Yang, F., Fu, B., O'Brien, P.C., Nie, W., Ryder, O.A., Ferguson-Smith, M.A. :
Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules. Chromosome Res 12:65-76, 2004. Pubmed reference: 14984103.
Lee, E.J., Raudsepp, T., Kata, S.R., Adelson, D., Womack, J.E., Skow, L.C., Chowdhary, B.P. :
A 1.4-Mb interval RH map of horse chromosome 17 provides detailed comparison with human and mouse homologues. Genomics 83:203-15, 2004. Pubmed reference: 14706449.
2003 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.
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.
2002 O'Rourke, K. :
And coming around the track, looking promising ... the horse genome map. J Am Vet Med Assoc 221:15, 20, 2002. Pubmed reference: 12420810.
Chowdhary, B.P., Raudsepp, T., Honeycutt, D., Owens, E.K., Piumi, F., Guérin, G., Matise, T.C., Kata, S.R., Womack, J.E., Skow, L.C. :
Construction of a 5000(rad) whole-genome radiation hybrid panel in the horse and generation of a comprehensive and comparative map for ECA11. Mamm Genome 13:89-94, 2002. Pubmed reference: 11889556. DOI: 10.1007/s00335-001-2089-8.
2001 Lear, T.L., Brandon, R., Piumi, F., Terry, R.R., Guérin, G., Thomas, S., Bailey, E. :
Mapping of 31 horse genes in BACs by FISH. Chromosome Res 9:261-2, 2001. Pubmed reference: 11330401.
2000 Kiguwa, S.L., Hextall, P., Smith, A.L., Critcher, R., Swinburne, J., Millon, L., Binns, M.M., Goodfellow, P.N., McCarthy, L.C., Farr, C.J., Oakenfull, E.A. :
A horse whole-genome-radiation hybrid panel: chromosome 1 and 10 preliminary maps. Mamm Genome 11:803-5, 2000. Pubmed reference: 10967144.
Swinburne, J., Gerstenberg, C., Breen, M., Aldridge, V., Lockhart, L., Marti, E., Antczak, D., Eggleston-Stott, M., Bailey, E., Mickelson, J., Røed, K., Lindgren, G., von Haeringen, W., Guérin, G., Bjarnason, J., Allen, T., Binns, M. :
First comprehensive low-density horse linkage map based on two 3-generation, full-sibling, cross-bred horse reference families. Genomics 66:123-34, 2000. Pubmed reference: 10860657. DOI: 10.1006/geno.2000.6207.
1999 Caetano, A.R., Shiue, Y.L., Lyons, L.A., O'Brien, S.J., Laughlin, T.F., Bowling, A.T., Murray, J.D. :
A comparative gene map of the horse (Equus caballus). Genome Res 9:1239-49, 1999. Pubmed reference: 10613847.
Guérin, G., Bailey, E., Bernoco, D., Anderson, I., Antczak, D.F., Bell, K., Binns, M.M., Bowling, A.T., Brandon, R., Cholewinski, G., Cothran, E.G., Ellegren, H., Förster, M., Godard, S., Horin, P., Ketchum, M., Lindgren, G., McPartlan, H., Mériaux, J.C., Mickelson, J.R., Millon, L.V., Murray, J., Neau, A., Røed, K., Ziegle, J. :
Report of the International Equine Gene Mapping Workshop: male linkage map. Anim Genet 30:341-54, 1999. Pubmed reference: 10582279.
Shiue, Y.L., Bickel, L.A., Caetano, A.R., Millon, L.V., Clark, R.S., Eggleston, M.L., Michelmore, R., Bailey, E., Guérin, G., Godard, S., Mickelson, J.R., Valberg, S.J., Murray, J.D., Bowling, A.T. :
A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers. Anim Genet 30:1-9, 1999. Pubmed reference: 10050277.
1998 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.
Bailey, E., Binns, M.M. :
The Horse Gene Map. ILAR J 39:171-176, 1998. Pubmed reference: 11528075.

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.

Felis catus (domestic cat) :

2021 de Groot, M., Anderson, H., Bauer, H., Bauguil, C., Bellone, R.R., Brugidou, R., Buckley, R.M., Dovč, P., Forman, O., Grahn, R.A., Kock, L., Longeri, M., Mouysset-Geniez, S., Qiu, J., Sofronidis, G., van der Goor, L.H.P., Lyons, L.A. :
Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus). Anim Genet :, 2021. Pubmed reference: 34143521. DOI: 10.1111/age.13100.
2020 Zhang, W., Schoenebeck, J.J. :
The ninth life of the cat reference genome, Felis_catus. PLoS Genet 16:e1009045, 2020. Pubmed reference: 33091014. DOI: 10.1371/journal.pgen.1009045.
Buckley, R.M., Davis, B.W., Brashear, W.A., Farias, F.H.G., Kuroki, K., Graves, T., Hillier, L.W., Kremitzki, M., Li, G., Middleton, R.P., Minx, P., Tomlinson, C., Lyons, L.A., Murphy, W.J., Warren, W.C. :
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 16:e1008926, 2020. Pubmed reference: 33090996. DOI: 10.1371/journal.pgen.1008926.
Bredemeyer, K.R., Harris, A.J., Li, G., Zhao, L., Foley, N.M., Roelke-Parker, M., O'Brien, S.J., Lyons, L.A., Warren, W.C., Murphy, W.J. :
Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis). J Hered 112:165-73, 2020. Pubmed reference: 33305796. DOI: 10.1093/jhered/esaa057.
2019 Gandolfi, B., Alhaddad, H., Abdi, M., Bach, L.H., Creighton, E.K., Davis, B.W., Decker, J.E., Dodman, N.H., Ginns, E.I., Grahn, J.C., Grahn, R.A., Haase, B., Haggstrom, J., Hamilton, M.J., Helps, C.R., Kurushima, J.D., Lohi, H., Longeri, M., Malik, R., Meurs, K.M., Montague, M.J., Mullikin, J.C., Murphy, W.J., Nilson, S.M., Pedersen, N.C., Peterson, C.B., Rusbridge, C., Saif, R., Shelton, G.D., Warren, W.C., Wasim, M., Lyons, L.A. :
Author Correction: Applications and efficiencies of the first cat 63 K DNA array. Sci Rep 9:4664, 2019. Pubmed reference: 30858384. DOI: 10.1038/s41598-018-38073-6.
2018 Gandolfi, B., Alhaddad, H., Abdi, M., Bach, L.H., Creighton, E.K., Davis, B.W., Decker, J.E., Dodman, N.H., Grahn, J.C., Grahn, R.A., Haase, B., Haggstrom, J., Hamilton, M.J., Helps, C.R., Kurushima, J.D., Lohi, H., Longeri, M., Malik, R., Meurs, K.M., Montague, M.J., Mullikin, J.C., Murphy, W.J., Nilson, S.M., Pedersen, N.C., Peterson, C.B., Rusbridge, C., Saif, R., Shelton, G.D., Warren, W.C., Wasim, M., Lyons, L.A. :
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.
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.
2016 Li, G., Hillier, L.W., Grahn, R., Zimin, A.V., David, V.A., Menotti-Raymond, M., Middleton, R., Hannah, S., Hendrickson, S., Makunin, A., O'Brien, S.J., Minx, P., Wilson, R.K., Lyons, L.A., Warren, W.C., Murphy, W.J. :
A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (Bethesda) :, 2016. Pubmed reference: 27172201. DOI: 10.1534/g3.116.028746.
2014 Willet, C.E., Haase, B. :
An updated felCat5 SNP manifest for the Illumina Feline 63k SNP genotyping array. Anim Genet :, 2014. Pubmed reference: 24804964. DOI: 10.1111/age.12169.
Tamazian, G., Simonov, S., Dobrynin, P., Makunin, A., Logachev, A., Komissarov, A., Shevchenko, A., Brukhin, V., Cherkasov, N., Svitin, A., Koepfli, K.P., Pontius, J., Driscoll, C.A., Blackistone, K., Barr, C., Goldman, D., Antunes, A., Quilez, J., Lorente-Galdos, B., Alkan, C., Marques-Bonet, T., Menotti-Raymond, M., David, V.A., Narfström, K., O'Brien, S.J. :
Annotated features of domestic cat - Felis catus genome. Gigascience 3:13, 2014. Pubmed reference: 25143822. DOI: 10.1186/2047-217X-3-13.
Montague, M.J., Li, G., Gandolfi, B., Khan, R., Aken, B.L., Searle, S.M., Minx, P., Hillier, L.W., Koboldt, D.C., Davis, B.W., Driscoll, C.A., Barr, C.S., Blackistone, K., Quilez, J., Lorente-Galdos, B., Marques-Bonet, T., Alkan, C., Thomas, G.W., Hahn, M.W., Menotti-Raymond, M., O'Brien, S.J., Wilson, R.K., Lyons, L.A., Murphy, W.J., Warren, W.C. :
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc Natl Acad Sci U S A 111:17230-5, 2014. Pubmed reference: 25385592. DOI: 10.1073/pnas.1410083111.
2012 Bach, L.H., Gandolfi, B., Grahn, J.C., Millon, L.V., Kent, M.S., Narfstrom, K., Cole, S.A., Mullikin, J.C., Grahn, R.A., Lyons, L.A. :
A high-resolution 15,000(Rad) radiation hybrid panel for the domestic cat. Cytogenet Genome Res 137:7-14, 2012. Pubmed reference: 22777158. DOI: 10.1159/000339416.
2010 Mullikin, J.C., Hansen, N.F., Shen, L., Ebling, H., Donahue, W.F., Tao, W., Saranga, D.J., Brand, A., Rubenfield, M.J., Young, A.C., Cruz, P. :
Light whole genome sequence for SNP discovery across domestic cat breeds. BMC Genomics 11:406, 2010. Pubmed reference: 20576142. DOI: 10.1186/1471-2164-11-406.
2009 Menotti-Raymond, M., David, V.A., Schäffer, A.A., Tomlin, J.F., Eizirik, E., Phillip, C., Wells, D., Pontius, J.U., Hannah, S.S., O'Brien, S.J. :
An autosomal genetic linkage map of the domestic cat, Felis silvestris catus. Genomics 93:305-13, 2009. Pubmed reference: 19059333. DOI: 10.1016/j.ygeno.2008.11.004.
2008 Borodin, P.M., Karamysheva, T.V., Rubtsov, N.B. :
[Immunofluorescent analysis of meiotic recombination and interference in the domestic cat]. Tsitologiia 50:62-6, 2008. Pubmed reference: 18409370.
O'Brien, S.J., Johnson, W., Driscoll, C., Pontius, J., Pecon-Slattery, J., Menotti-Raymond, M. :
State of cat genomics. Trends Genet 24:268-79, 2008. Pubmed reference: 18471926. DOI: 10.1016/j.tig.2008.03.004.
2007 Pontius, J.U., Mullikin, J.C., Smith, D.R., Agencourt Sequencing Team et al. :
Initial sequence and comparative analysis of the cat genome. Genome Res 17:1675-89, 2007. Pubmed reference: 17975172. DOI: 10.1101/gr.6380007.
2006 Murphy, W.J. :
The feline genome. Genome Dyn 2:60-8, 2006. Pubmed reference: 18753769. DOI: 10.1159/000095093.
2003 Menotti-Raymond, M., David, V.A., Roelke, M.E., Chen, Z.Q., Menotti, K.A., Sun, S., Schäffer, A.A., Tomlin, J.F., Agarwala, R., O'Brien, S.J., Murphy, W.J. :
Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus). J Hered 94:95-106, 2003. Pubmed reference: 12692169.
2002 O'Brien, S.J., Menotti-Raymond, M., Murphy, W.J., Yuhki, N. :
The Feline Genome Project. Annu Rev Genet 36:657-86, 2002. Pubmed reference: 12359739. DOI: 10.1146/annurev.genet.36.060602.145553.
2001 Sun, S., Murphy, W.J., Menotti-Raymond, M., O'Brien, S.J. :
Integration of the feline radiation hybrid and linkage maps. Mamm Genome 12:436-41, 2001. Pubmed reference: 11353390. DOI: 10.1007/s003350010289.
2000 Murphy, W.J., Sun, S., Chen, Z.Q., Yuhki, N., Hirschmann, D., Menotti-Raymond, M., O'Brien, S.J. :
A radiation hybrid map of the cat genome: Implications for comparative mapping Genome Research 10:691-702, 2000. Pubmed reference: 10810092.
1999 Menotti-Raymond, M., David, V.A., Lyons, L.A., Schäffer, A.A., Tomlin, J.F., Hutton, M.K., O'Brien, S.J. :
A genetic linkage map of microsatellites in the domestic cat (Felis catus). Genomics 57:9-23, 1999. Pubmed reference: 10191079. DOI: 10.1006/geno.1999.5743.
1997 Obrien, S.J., Cevario, S.J., Martenson, J.S., Thompson, M.A., Nash, W.G., Chang, E., Graves, J.A.M., Spencer, J.A., Cho, K.W., Tsujimoto, H., Lyons, L.A. :
Comparative gene mapping in the domestic cat (felis catus) Journal of Heredity 88:408-414, 1997. Pubmed reference: 9378918.
Obrien, S.J., Wienberg, J., Lyons, L.A. :
Comparative genomics - lessons from cats [Review] Trends in Genetics 13:393-399, 1997. Pubmed reference: 9351340.
1995 Rettenberger, G., Klett, C., Zechner, U., Bruch, J., Just, W., Vogel, W., Hameister, H. :
ZOO-FISH analysis - cat and human karyotypes closely resemble the putative ancestral mammalian karyotype Chromosome Research 3:479-486, 1995. Pubmed reference: 8581300.
1982 O'Brien, S.J., Nash, W.G. :
Genetic mapping in mammals: chromosome map of domestic cat. Science 216:257-65, 1982. Pubmed reference: 7063884.

Ficedula :

2014 Kawakami, T., Backström, N., Burri, R., Husby, A., Olason, P., Rice, A.M., Alund, M., Qvarnström, A., Ellegren, H. :
Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k SNP array. Mol Ecol Resour :, 2014. Pubmed reference: 24784959. DOI: 10.1111/1755-0998.12270.

Gadus morhua (Atlantic cod) :

2012 Ghigliotti, L., Fevolden, S.E., Cheng, C.H., Babiak, I., Dettai, A., Pisano, E. :
Karyotyping and cytogenetic mapping of Atlantic cod (Gadus morhua Linnaeus, 1758). Anim Genet 43:746-52, 2012. Pubmed reference: 22497346. DOI: 10.1111/j.1365-2052.2012.02343.x.
2009 Higgins, B., Hubert, S., Simpson, G., Stone, C., Bowman, S. :
Characterization of 155 EST-derived microsatellites from Atlantic cod (Gadus morhua) and validation for linkage mapping. Mol Ecol Resour 9:733-7, 2009. Pubmed reference: 21564732. DOI: 10.1111/j.1755-0998.2008.02475.x.

Gallus gallus (chicken) :

2019 Liu, R., Xing, S., Wang, J., Zheng, M., Cui, H., Crooijmans, R.P.M.A., Li, Q., Zhao, G., Wen, J. :
A new chicken 55K SNP genotyping array. BMC Genomics 20:410, 2019. Pubmed reference: 31117951. DOI: 10.1186/s12864-019-5736-8.
2018 Piégu, B., Arensburger, P., Guillou, F., Bigot, Y. :
But where did the centromeres go in the chicken genome models? Chromosome Res 26:297-306, 2018. Pubmed reference: 30225548. DOI: 10.1007/s10577-018-9585-0.
2014 Griffin, D., Burt, D.W. :
All chromosomes great and small: 10 years on. Chromosome Res :, 2014. Pubmed reference: 24700106. DOI: 10.1007/s10577-014-9413-0.
2013 Gheyas, A.A., Burt, D.W. :
Microarray resources for genetic and genomic studies in chicken: A review. Genesis :, 2013. Pubmed reference: 23468091. DOI: 10.1002/dvg.22387.
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.
2011 Groenen, M.A., Megens, H.J., Zare, Y., Warren, W.C., Hillier, L.W., Crooijmans, R.P., Vereijken, A., Okimoto, R., Muir, W.M., Cheng, H.H. :
The development and characterization of a 60K SNP chip for chicken. BMC Genomics 12:274, 2011. Pubmed reference: 21627800. DOI: 10.1186/1471-2164-12-274.
2008 Muir, W.M., Wong, G.K., Zhang, Y., Wang, J., Groenen, M.A.M., Crooijmans, R.P.M.A., Megens, H.-J., Zhang, H.M., McKay, J.C., McLeod, S., Okimoto, R., Fulton, J.E., Settar, P., O'Sullivan, N.P., Vereijken, A., Jungerius-Rattink, A., Albers, G.A.A., Taylor Lawley, C., Delaney, M.E., Cheng, H.H. :
Review of the initial validation and characterization of a chicken 3K SNP array. Worlds Poultry Science Journal 64:219-226, 2008.
2007 Burt, D.W., White, S.J. :
Avian genomics in the 21st century. Cytogenet Genome Res 117:6-13, 2007. Pubmed reference: 17675839. DOI: 10.1159/000103159.
2006 Burt, D.W. :
The chicken genome. Genome Dyn 2:123-37, 2006. Pubmed reference: 18753775. DOI: 10.1159/000095100.
Mu, Y.S., Li, H. :
[Latest progress on the chicken genome project]. Yi Chuan 28:617-22, 2006. Pubmed reference: 16735245.
2005 Burt, D.W. :
Chicken genome: current status and future opportunities. Genome Res 15:1692-8, 2005. Pubmed reference: 16339367. DOI: 10.1101/gr.4141805.
Schmid, M., Nanda, I., Hoehn, H., Schartl, M., Haaf, T., Buerstedde, J.M., Arakawa, H., Caldwell, R.B., Weigend, S., Burt, D.W., Smith, J., Griffin, D.K., Masabanda, J.S., Groenen, M.A., Crooijmans, R.P., Vignal, A., Fillon, V., Morisson, M., Pitel, F., Vignoles, M., Garrigues, A., Gellin, J., Rodionov, A.V., Galkina, S.A., Lukina, N.A., Ben-Ari, G., Blum, S., Hillel, J., Twito, T., Lavi, U., David, L., Feldman, M.W., Delany, M.E., Conley, C.A., Fowler, V.M., Hedges, S.B., Godbout, R., Katyal, S., Smith, C., Hudson, Q., Sinclair, A., Mizuno, S. :
Second report on chicken genes and chromosomes 2005. Cytogenet Genome Res 109:415-79, 2005. Pubmed reference: 15905640. DOI: 10.1159/000084205.
2004 Wong, G.K., Liu, B., Wang, J., Zhang, Y., Yang, X., Zhang, Z., Meng, Q., Zhou, J., Li, D., Zhang, J., Ni, P., Li, S., Ran, L., Li, H., Zhang, J., Li, R., Li, S., Zheng, H., Lin, W., Li, G., Wang, X., Zhao, W., Li, J., Ye, C., Dai, M., Ruan, J., Zhou, Y., Li, Y., He, X., Zhang, Y., Wang, J., Huang, X., Tong, W., Chen, J., Ye, J., Chen, C., Wei, N., Li, G., Dong, L., Lan, F., Sun, Y., Zhang, Z., Yang, Z., Yu, Y., Huang, Y., He, D., Xi, Y., Wei, D., Qi, Q., Li, W., Shi, J., Wang, M., Xie, F., Wang, J., Zhang, X., Wang, P., Zhao, Y., Li, N., Yang, N., Dong, W., Hu, S., Zeng, C., Zheng, W., Hao, B., Hillier, L.W., Yang, S.P., Warren, W.C., Wilson, R.K., Brandström, M., Ellegren, H., Crooijmans, R.P., van der Poel, J.J., Bovenhuis, H., Groenen, M.A., Ovcharenko, I., Gordon, L., Stubbs, L., Lucas, S., Glavina, T., Aerts, A., Kaiser, P., Rothwell, L., Young, J.R., Rogers, S., Walker, B.A., van Hateren, A., Kaufman, J., Bumstead, N., Lamont, S.J., Zhou, H., Hocking, P.M., Morrice, D., de Koning, D.J., Law, A., Bartley, N., Burt, D.W., Hunt, H., Cheng, H.H., Gunnarsson, U., Wahlberg, P., Andersson, L., Kindlund, E., Tammi, M.T., Andersson, B., Webber, C., Ponting, C.P., Overton, I.M., Boardman, P.E., Tang, H., Hubbard, S.J., Wilson, S.A., Yu, J., Wang, J., Yang, H. :
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432:717-22, 2004. Pubmed reference: 15592405. DOI: 10.1038/nature03156.
Burt, D.W. :
Chicken genomics charts a path to the genome sequence. Brief Funct Genomic Proteomic 3:60-7, 2004. Pubmed reference: 15163360.
International Chicken Genome Sequencing Consortium :
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716, 2004. Pubmed reference: 15592404. DOI: 10.1038/nature03154.
Wallis, J.W., Aerts, J., Groenen, M.A., Crooijmans, R.P., Layman, D., Graves, T.A., Scheer, D.E., Kremitzki, C., Fedele, M.J., Mudd, N.K., Cardenas, M., Higginbotham, J., Carter, J., McGrane, R., Gaige, T., Mead, K., Walker, J., Albracht, D., Davito, J., Yang, S.P., Leong, S., Chinwalla, A., Sekhon, M., Wylie, K., Dodgson, J., Romanov, M.N., Cheng, H., de Jong, P.J., Osoegawa, K., Nefedov, M., Zhang, H., McPherson, J.D., Krzywinski, M., Schein, J., Hillier, L., Mardis, E.R., Wilson, R.K., Warren, W.C. :
A physical map of the chicken genome. Nature 432:761-4, 2004. Pubmed reference: 15592415. DOI: 10.1038/nature03030.
2003 Dodgson, J.B. :
Chicken genome sequence: a centennial gift to poultry genetics. Cytogenet Genome Res 102:291-6, 2003. Pubmed reference: 14970719. DOI: 75765.
2002 Smith, J., Paton, I.R., Murray, F., Crooijmans, R.P.M.A., Groenen, M.A.M., Burt, D.W. :
Comparative mapping of human Chromosome 19 with the chicken shows conserved synteny and gives an insight into chromosomal evolution Mammalian Genome 13:310-315, 2002. Pubmed reference: 12115034. DOI: 10.1007/s00335-001-3071-1.
2000 Smith, J., Paton, I.R., Bruley, C.K., Windsor, D., Burke, D., de, Leon, F.A.P., Burt, D.W. :
Integration of the genetic and physical maps of the chicken macrochromosomes Animal Genetics 31:20-27, 2000. Pubmed reference: 10690357.
Groenen, M.A.M., Cheng, H.H., Bumstead, N., Benkel, B.F., Briles, W.E., Burke, T., Burt, D.W., Crittenden, L.B., Dodgson, J., Hillel, J., Lamont, S., de, Leon, A.P., Soller, M., Takahashi, H., Vignal, A. :
A consensus linkage map of the chicken genome Genome Research 10:137-147, 2000. Pubmed reference: 10645958.
1998 Groenen, M.A.M., Crooijmans, R.P.M.A., Veenendaal, A., Cheng, H.H., Siwek, M., Vanderpoel, J.J. :
A comprehensive microsatellite linkage map of the chicken genome Genomics 49:265-274, 1998. Pubmed reference: 9598314. DOI: 10.1006/geno.1998.5225.
Burt, D.W., Cheng, H.H. :
The Chicken Gene Map. ILAR J 39:229-236, 1998. Pubmed reference: 11528082.
1997 Koi, M., Lamb, P.W., Filatov, L., Feinberg, A.P., Barrett, J.C. :
Construction of chicken x human microcell hybrids for human gene targeting Cytogenetics & Cell Genetics 76:72-76, 1997.
1996 Crooijmans, R.P.M.A., Vanoers, P.A.M., Strijk, J.A., Vanderpoel, J.J., Groenen, M.A.M. :
Preliminary linkage map of the chicken (gallus domesticus) genome based on microsatellite markers - 77 new markers mapped Poultry Science 75:746-754, 1996. Pubmed reference: 8737840.
Crittenden, L.B., Bitgood, J.J., Burt, D.W., Deleon, F.A.P., Tixierboichard, M. :
Nomenclature for naming loci, alleles, linkage groups and chromosomes to be used in poultry genome publications and databases Genetics Selection Evolution 28:289-297, 1996.
1995 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.
Burt, D.W., Bumstead, N., Bitgood, J.J., Deleon, F.A.P., Crittenden, L.B. :
Chicken genome mapping: A new era in avian genetics Trends in Genetics 11:190-194, 1995. Pubmed reference: 7785078.
1994 Levin, I., Santangelo, L., Cheng, H., Crittenden, L.B., Dodgson, J.B. :
An Autosomal Genetic Linkage Map of the Chicken Journal of Heredity 85:79-85, 1994. Pubmed reference: 7910177.
Beattie, C.W. :
Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.
1992 Bumstead, N., Palyga, J. :
A Preliminary Linkage Map of the Chicken Genome Genomics 13:690-697, 1992. Pubmed reference: 1353476.
1990 Bitgood, J.J., Somes, R.G. Jr :
Linkage relationships and gene mapping. In "Poultry Breeding and Genetics" (ed. R.D. Crawford), Elsevier, Amsterdam; Chapter 21 :469-495, 1990.
1949 Warren, DC. :
Linkage relations of autosomal factors in the fowl. Genetics 34:333-50, 1949. Pubmed reference: 17247319.
1933 Hutt, F.B. :
Genetics of the fowl. II. a four-gene autosomal linkage group. Genetics 18:82-94, 1933. Pubmed reference: 17246679.
Warren, D.C. :
Nine independently inherited autosomal factors in the domestic fowl. Genetics 18:68-81, 1933. Pubmed reference: 17246678.
1928 Serebrovsky, A.S., Petrov, S.G. :
A case of close autosomal linkage in the fowl Journal of Heredity 19:305-306, 1928.
1921 Haldane, J.B.S. :
Linkage in poultry. Science 54:663 only, 1921. Pubmed reference: 17816160. DOI: 10.1126/science.54.1409.663.

Gavialis gangeticus (Gharial) :

2014 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.

Giraffa camelopardalis tippelskirchi :

2019 Farré, M., Li, Q., Darolti, I., Zhou, Y., Damas, J., Proskuryakova, A.A., Kulemzina, A.I., Chemnick, L.G., Kim, J., Ryder, O.A., Ma, J., Graphodatsky, A.S., Zhang, G., Larkin, D.M., Lewin, H.A. :
An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). Gigascience 8:, 2019. Pubmed reference: 31367745. DOI: 10.1093/gigascience/giz090.

Gopherus evgoodei (Goodes thornscrub tortoise) :

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.

Gouania willdenowi (blunt-snouted clingfish) :

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.

Ictalurus punctatus (channel catfish) :

2019 Zhang, S., Zhang, X., Chen, X., Xu, T., Wang, M., Qin, Q., Zhong, L., Jiang, H., Zhu, X., Liu, H., Shao, J., Zhu, Z., Shi, Q., Bian, W., You, X. :
Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (<i>Ictalurus punctatus</i>). Front Genet 10:251, 2019. Pubmed reference: 30984241. DOI: 10.3389/fgene.2019.00251.

Labeo rohita (rohu) :

2020 Das, P., Sahoo, L., Das, S.P., Bit, A., Joshi, C.G., Kushwaha, B., Kumar, D., Shah, T.M., Hinsu, A.T., Patel, N., Patnaik, S., Agarwal, S., Pandey, M., Srivastava, S., Meher, P.K., Jayasankar, P., Koringa, P.G., Nagpure, N.S., Kumar, R., Singh, M., Iquebal, M.A., Jaiswal, S., Kumar, N., Raza, M., Das Mahapatra, K., Jena, J. :
De novo assembly and genome-wide SNP discovery in rohu carp, Labeo rohita. Front Genet 11:386, 2020. Pubmed reference: 32373166. DOI: 10.3389/fgene.2020.00386.

Lamprotornis superbus (superb starling) :

2021 Rubenstein, D.R., Corvelo, A., MacManes, M.D., Maia, R., Narzisi, G., Rousaki, A., Vandenabeele, P., Shawkey, M.D., Solomon, J. :
Feather gene expression elucidates the developmental basis of plumage iridescence in African starlings. J Hered 112:417-429, 2021. Pubmed reference: 33885791. DOI: 10.1093/jhered/esab014.

Lemur catta (Ring-tailed lemur) :

2022 Palmada-Flores, M., Orkin, J.D., Haase, B., Mountcastle, J., Bertelsen, M.F., Fedrigo, O., Kuderna, L.F.K., Jarvis, E.D., Marques-Bonet, T. :
A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). Gigascience 11:, 2022. Pubmed reference: 35365833. DOI: 10.1093/gigascience/giac026.

Lynx canadensis (Canada lynx) :

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.

Macaca mulatta (Rhesus monkey) :

2022 Rogers, J. :
Genomic resources for rhesus macaques (Macaca mulatta). Mamm Genome :, 2022. Pubmed reference: 34999909. DOI: 10.1007/s00335-021-09922-z.

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.

Mastacembelus armatus (zig-zag eel) :

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.

Megalobrama amblycephala (Wuchang bream) :

2021 Liu, H., Chen, C., Lv, M., Liu, N., Hu, Y., Zhang, H., Enbody, E.D., Gao, Z., Andersson, L., Wang, W. :
A Chromosome-Level Assembly of Blunt Snout Bream (Megalobrama amblycephala) Genome Reveals an Expansion of Olfactory Receptor Genes in Freshwater Fish. Mol Biol Evol 38:4238-4251, 2021. Pubmed reference: 34003267. DOI: 10.1093/molbev/msab152.

Meleagris gallopavo (turkey) :

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.

Mesocricetus auratus (golden hamster) :

1997 Okuizumi, H., Ohsumi, T., Sasaki, N., Imoto, H., Mizuno, Y., Hanami, T., Yamashita, H., Kamiya, M., Takada, S., Kitamura, A., Muramatsu, M., Nishimura, M., Mori, M., Matsuda, Y., Tagaya, O., Okazaki, Y., Hayashizaki, Y. :
Linkage map of syrian hamster with restriction landmark genomic scanning Mammalian Genome 8:121-128, 1997. Pubmed reference: 9060411.

Monodelphis domestica (gray short-tailed opossum) :

2007 Mikkelsen, T.S., Wakefield, M.J., Aken, B., Amemiya, C.T., Chang, J.L., Duke, S., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S.M., Sharpe, T., Baker, M.L., Batzer, M.A., Benos, P.V., Belov, K., Clamp, M., Cook, A., Cuff, J., Das, R., Davidow, L., Deakin, J.E., Fazzari, M.J., Glass, J.L., Grabherr, M., Greally, J.M., Gu, W., Hore, T.A., Huttley, G.A., Kleber, M., Jirtle, R.L., Koina, E., Lee, J.T., Mahony, S., Marra, M.A., Miller, R.D., Nicholls, R.D., Oda, M., Papenfuss, A.T., Parra, Z.E., Pollock, D.D., Ray, D.A., Schein, J.E., Speed, T.P., Thompson, K., VandeBerg, J.L., Wade, C.M., Walker, J.A., Waters, P.D., Webber, C., Weidman, J.R., Xie, X., Zody, M.C. :
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167-77, 2007. Pubmed reference: 17495919. DOI: 10.1038/nature05805.

Moschus moschiferus (Siberian musk deer) :

2020 Yi, L., Dalai, M., Su, R., Lin, W., Erdenedalai, M., Luvsantseren, B., Chimedtseren, C., Wang, Z., Hasi, S. :
Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features. BMC Genomics 21:108, 2020. Pubmed reference: 32005147. DOI: 10.1186/s12864-020-6495-2.

Neovison vison (American mink) :

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.

Numida meleagris (helmeted guineafowl) :

2019 Vignal, A., Boitard, S., Thebault, N., Dayo, G.K., Yapi-Gnaore, V., Youssao, I., Berthouly-Salazar, C., Pálinkás-Bodzsár, N., Guémené, D., Thibaud-Nissen, F., Warren, W.C., Tixier-Boichard, M., Rognon, X. :
A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour :, 2019. Pubmed reference: 30945415. DOI: 10.1111/1755-0998.13017.

Nyctereutes procyonoides (raccoon dog) :

2021 Chueca, L.J., Kochmann, J., Schell, T., Greve, C., Janke, A., Pfenninger, M., Klimpel, S. :
De novo genome assembly of the raccoon dog (Nyctereutes procyonoides). Front Genet 12:658256, 2021. Pubmed reference: 33995489. DOI: 10.3389/fgene.2021.658256.

Ochotona princeps (American pika) :

2021 Sjodin, B.M.F., Galbreath, K.E., Lanier, H.C., Russello, M.A. :
Chromosome-level reference genome assembly for the American pika (Ochotona princeps). J Hered 112:549-557, 2021. Pubmed reference: 34036348. DOI: 10.1093/jhered/esab031.
2016 Fontanesi, L., Di Palma, F., Flicek, P., Smith, A.T., Thulin, C.G., Alves, P.C. :
LaGomiCs-Lagomorph Genomics Consortium: An international collaborative effort for sequencing the genomes of an entire mammalian order. J Hered 107:295-308, 2016. Pubmed reference: 26921276. DOI: 10.1093/jhered/esw010.

Odontobutis potamophila :

2017 Zhang, H., Huang, L., Yin, S., Zhang, G., Ding, Y., Zang, X. :
High-density SNP-based genetic map for Odontobutis potamophila. Anim Genet 48:126-127, 2017. Pubmed reference: 27476504. DOI: 10.1111/age.12471.

Oncorhynchus mykiss (rainbow trout) :

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.

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 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.
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.
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. :
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.

Oryctolagus cuniculus (rabbit) :

2021 Yang, N., Zhao, B., Chen, Y., D'Alessandro, E., Chen, C., Ji, T., Wu, X., Song, C. :
Distinct retrotransposon evolution profile in the genome of rabbit (Oryctolagus cuniculus). Genome Biol Evol 13:, 2021. Pubmed reference: 34270728. DOI: 10.1093/gbe/evab168.
2018 Zhou, L., Xiao, Q., Bi, J., Wang, Z., Li, Y. :
RabGTD: a comprehensive database of rabbit genome and transcriptome. Database (Oxford) 2018:, 2018. Pubmed reference: 30010730. DOI: 10.1093/database/bay075.
2016 Fontanesi, L., Di Palma, F., Flicek, P., Smith, A.T., Thulin, C.G., Alves, P.C. :
LaGomiCs-Lagomorph Genomics Consortium: An international collaborative effort for sequencing the genomes of an entire mammalian order. J Hered 107:295-308, 2016. Pubmed reference: 26921276. DOI: 10.1093/jhered/esw010.
2015 Sternstein, I., Reissmann, M., Maj, D., Bieniek, J., Brockmann, G.A. :
A comprehensive linkage map and QTL map for carcass traits in a cross between Giant Grey and New Zealand White rabbits. BMC Genet 16:16, 2015. Pubmed reference: 25887754. DOI: 10.1186/s12863-015-0168-1.
2014 Carneiro, M., Rubin, C.J., Di Palma, F., Albert, F.W., Alföldi, J., Martinez Barrio, A., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., Younis, S., Afonso, S., Aken, B., Alves, J.M., Barrell, D., Bolet, G., Boucher, S., Burbano, H.A., Campos, R., Chang, J.L., Duranthon, V., Fontanesi, L., Garreau, H., Heiman, D., Johnson, J., Mage, R.G., Peng, Z., Queney, G., Rogel-Gaillard, C., Ruffier, M., Searle, S., Villafuerte, R., Xiong, A., Young, S., Forsberg-Nilsson, K., Good, J.M., Lander, E.S., Ferrand, N., Lindblad-Toh, K., Andersson, L. :
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345:1074-1079, 2014. Pubmed reference: 25170157. DOI: 10.1126/science.1253714.
Lohmueller, K.E. :
Evolution. On the origin of Peter Rabbit. Science 345:1000-1, 2014. Pubmed reference: 25170135. DOI: 10.1126/science.1258775.
2012 Fontanesi, L., Martelli, P.L., Scotti, E., Russo, V., Rogel-Gaillard, C., Casadio, R., Vernesi, C. :
Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization. Genomics 100:245-51, 2012. Pubmed reference: 22800765. DOI: 10.1016/j.ygeno.2012.07.001.
1983 Soulié, J., de Grouchy, J. :
New gene assignments in the rabbit (Oryctolagus cuniculus). Comparison with other species. Hum Genet 63:48-52, 1983. Pubmed reference: 6572613. DOI: 10.1007/BF00285397.
1941 Castle, W.E., Sawin, P.B. :
Genetic linkage in the rabbit. Proc Natl Acad Sci U S A 27:519-23, 1941. Pubmed reference: 16588495.
1936 Castle, W.E. :
Further Data on Linkage in Rabbits. Proc Natl Acad Sci U S A 22:222-5, 1936. Pubmed reference: 16577699.

Oryzias latipes (Japanese medaka) :

1999 Ohtsuka, M., Makino, S., Yoda, K., Wada, H., Naruse, K., Mitani, H., Shima, A., Ozato, K., Kimura, M., Inoko, H. :
Construction of a linkage map of the medaka (Oryzias latipes) and mapping of the Da mutant locus defective in dorsoventral patterning Genome Research 9:1277-1287, 1999. Pubmed reference: 10613850.

Oryzias melastigma (Indian medaka) :

2020 Liang, P., Saqib, H.S.A., Ni, X., Shen, Y. :
Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). BMC Genomics 21:640, 2020. Pubmed reference: 32938378. DOI: 10.1186/s12864-020-07042-7.

Ovis aries (sheep) :

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 (<i>Oar rambouillet v1.0</i>). 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.
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 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 orientalis (Asiatic mouflon) :

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.

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 tigris (tiger) :

2013 Cho, Y.S., Hu, L., Hou, H., Lee, H., Xu, J., Kwon, S., Oh, S., Kim, H.M., Jho, S., Kim, S., Shin, Y.A., Kim, B.C., Kim, H., Kim, C.U., Luo, S.J., Johnson, W.E., Koepfli, K.P., Schmidt-Küntzel, A., Turner, J.A., Marker, L., Harper, C., Miller, S.M., Jacobs, W., Bertola, L.D., Kim, T.H., Lee, S., Zhou, Q., Jung, H.J., Xu, X., Gadhvi, P., Xu, P., Xiong, Y., Luo, Y., Pan, S., Gou, C., Chu, X., Zhang, J., Liu, S., He, J., Chen, Y., Yang, L., Yang, Y., He, J., Liu, S., Wang, J., Kim, C.H., Kwak, H., Kim, J.S., Hwang, S., Ko, J., Kim, C.B., Kim, S., Bayarlkhagva, D., Paek, W.K., Kim, S.J., O'Brien, S.J., Wang, J., Bhak, J. :
The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun 4:2433, 2013. Pubmed reference: 24045858. DOI: 10.1038/ncomms3433.

Pantherophis guttatus (corn snake) :

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.

Paracanthobrama guichenoti :

2021 Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :
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.

Penaeus monodon (black tiger shrimp) :

2018 Huerlimann, R., Wade, N.M., Gordon, L., Montenegro, J.D., Goodall, J., McWilliam, S., Tinning, M., Siemering, K., Giardina, E., Donovan, D., Sellars, M.J., Cowley, J.A., Condon, K., Coman, G.J., Khatkar, M.S., Raadsma, H.W., Maes, G.E., Zenger, K.R., Jerry, D.R. :
De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. Sci Rep 8:13553, 2018. Pubmed reference: 30202061. DOI: 10.1038/s41598-018-31148-4.

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.

Phascolarctos cinereus (koala) :

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.

Phyllostomus discolor (pale spear-nosed bat) :

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.

Plecoglossus altivelis (ayu) :

2021 Nakamoto, M., Uchino, T., Koshimizu, E., Kuchiishi, Y., Sekiguchi, R., Wang, L., Sudo, R., Endo, M., Guiguen, Y., Schartl, M., Postlethwait, J.H., Sakamoto, T. :
A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis. PLoS Genet 17:e1009705, 2021. Pubmed reference: 34437539. DOI: 10.1371/journal.pgen.1009705.

Prionailurus bengalensis (leopard cat) :

2020 Bredemeyer, K.R., Harris, A.J., Li, G., Zhao, L., Foley, N.M., Roelke-Parker, M., O'Brien, S.J., Lyons, L.A., Warren, W.C., Murphy, W.J. :
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.

Protosalanx hyalocranius (clearhead icefish) :

2017 Liu, K., Xu, D., Li, J., Bian, C., Duan, J., Zhou, Y., Zhang, M., You, X., You, Y., Chen, J., Yu, H., Xu, G., Fang, D.A., Qiang, J., Jiang, S., He, J., Xu, J., Shi, Q., Zhang, Z., Xu, P. :
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. Gigascience 6:1-6, 2017. Pubmed reference: 28327943. DOI: 10.1093/gigascience/giw012.

Pseudocaranx georgianus (silver trevally) :

2021 Catanach, A., Ruigrok, M., Bowatte, D., Davy, M., Storey, R., Valenza-Troubat, N., López-Girona, E., Hilario, E., Wylie, M.J., Chagné, D., Wellenreuther, M. :
The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus. BMC Genomics 22:785, 2021. Pubmed reference: 34727894. DOI: 10.1186/s12864-021-08102-2.

Pteronura brasiliensis (giant otter) :

2019 Beichman, A.C., Koepfli, K.P., Li, G., Murphy, W., Dobrynin, P., Kliver, S., Tinker, M.T., Murray, M.J., Johnson, J., Lindblad-Toh, K., Karlsson, E.K., Lohmueller, K.E., Wayne, R.K. :
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.

Puma yagouaroundi (jaguarundi) :

2021 Tamazian, G., Dobrynin, P., Zhuk, A., Zhernakova, D.V., Perelman, P.L., Serdyukova, N.A., Graphodatsky, A.S., Komissarov, A., Kliver, S., Cherkasov, N., Scott, A.F., Mohr, D.W., Koepfli, K.P., O'Brien, S.J., Krasheninnikova, K. :
Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi. J Hered 112:540-548, 2021. Pubmed reference: 34146095. DOI: 10.1093/jhered/esab036.

Puntigrus tetrazona (Sumatra barb) :

2021 Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :
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.

Rhinatrema bivittatum (two-lined caecilian) :

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.

Rhinolophus ferrumequinum (greater horseshoe bat) :

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.

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.

Salmo salar (Atlantic salmon) :

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 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.
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.

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.

Sciurus niger (fox squirrel) :

2021 Kang, L., Michalak, P., Hallerman, E., Moncrief, N.D. :
A draft genome assembly for the Eastern fox squirrel, Sciurus niger. G3 (Bethesda) :jkab315, 2021. Pubmed reference: 34550334. DOI: 10.1093/g3journal/jkab315.

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 (<i>Seriola lalandi</i>). Front Genet 12:825742, 2021. Pubmed reference: 35126476. DOI: 10.3389/fgene.2021.825742.

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.

Strigops habroptilus (kakapo) :

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.
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.

Struthio camelus (African ostrich) :

2018 Papoli Yazdi, H., Ellegren, H. :
A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution. Genome Biol Evol :, 2018. Pubmed reference: 30099482. DOI: 10.1093/gbe/evy163.

Sus scrofa (pig) :

2021 Pan, Z., Yao, Y., Yin, H., Cai, Z., Wang, Y., Bai, L., Kern, C., Halstead, M., Chanthavixay, G., Trakooljul, N., Wimmers, K., Sahana, G., Su, G., Lund, M.S., Fredholm, M., Karlskov-Mortensen, P., Ernst, C.W., Ross, P., Tuggle, C.K., Fang, L., Zhou, H. :
Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat Commun 12:5848, 2021. Pubmed reference: 34615879. DOI: 10.1038/s41467-021-26153-7.
Wang, D., Yang, L., Ning, C., Liu, J.F., Zhao, X. :
Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs. BMC Genomics 22:736, 2021. Pubmed reference: 34641784. DOI: 10.1186/s12864-021-08030-1.
Zhang, Y., Fan, G., Liu, X., Skovgaard, K., Sturek, M., Heegaard, P.M.H. :
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. iScience 24:103081, 2021. Pubmed reference: 34585119. DOI: 10.1016/j.isci.2021.103081.
2020 Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Girón, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Schwartz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P.L., Archibald, A.L. :
An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience 9:giaa051, 2020. Pubmed reference: 32543654. DOI: 10.1093/gigascience/giaa051.
2018 Keel, B.N., Nonneman, D.J., Lindholm-Perry, A.K., Oliver, W.T., Rohrer, G.A. :
Porcine single nucleotide polymorphisms and their functional effect: an update. BMC Res Notes 11:860, 2018. Pubmed reference: 30514360. DOI: 10.1186/s13104-018-3973-6.
2014 Fernández, A.I., Muñoz, M., Alves, E., Folch, J.M., Noguera, J.L., Enciso, M.P., Rodríguez, M.d.e.l. .C., Silió, L. :
Recombination of the porcine X chromosome: a high density linkage map. BMC Genet 15:148, 2014. Pubmed reference: 25526890. DOI: 10.1186/s12863-014-0148-x.
2012 Freeman, T.C., Ivens, A., Baillie, J.K., Beraldi, D., Barnett, M.W., Dorward, D., Downing, A., Fairbairn, L., Kapetanovic, R., Raza, S., Tomoiu, A., Alberio, R., Wu, C., Su, A.I., Summers, K.M., Tuggle, C.K., Archibald, A.L., Hume, D.A. :
A gene expression atlas of the domestic pig. BMC Biol 10:90, 2012. Pubmed reference: 23153189. DOI: 10.1186/1741-7007-10-90.
Tortereau, F., Servin, B., Frantz, L., Megens, H.J., Milan, D., Rohrer, G., Wiedmann, R., Beever, J., Archibald, A.L., Schook, L.B., Groenen, M.A. :
A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics 13:586, 2012. Pubmed reference: 23152986. DOI: 10.1186/1471-2164-13-586.
Groenen, M.A., Archibald, A.L., Uenishi, H., Tuggle, C.K., Takeuchi, Y., Rothschild, M.F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H.J., Li, S., Larkin, D.M., Kim, H., Frantz, L.A., Caccamo, M., Ahn, H., Aken, B.L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C.W., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S.H., Chow, W., Clark, R.C., Clee, C., Crooijmans, R.P., Dawson, H.D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z.Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G.J., Fowler, K.E., Fredholm, M., Fritz, E., Gilbert, J.G., Giuffra, E., Gorodkin, J., Griffin, D.K., Harrow, J.L., Hayward, A., Howe, K., Hu, Z.L., Humphray, S.J., Hunt, T., Hornshøj, H., Jeon, J.T., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J.H., Kim, K.W., Kim, T.H., Larson, G., Lee, K., Lee, K.T., Leggett, R., Lewin, H.A., Li, Y., Liu, W., Loveland, J.E., Lu, Y., Lunney, J.K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M.P., Narayan, J., Nguyen, D.T., Ni, P., Oh, S.J., Onteru, S., Panitz, F., Park, E.W., Park, H.S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J.M., Rodriguez-Zas, S., Rohrer, G.A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J.G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B.R., Sperber, G., Stadler, P., Sweedler, J.V., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C., Schook, L.B. :
Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393-8, 2012. Pubmed reference: 23151582. DOI: 10.1038/nature11622.
2010 Archibald, A.L., Bolund, L., Churcher, C., Fredholm, M., Groenen, M.A., Harlizius, B., Lee, K.T., Milan, D., Rogers, J., Rothschild, M.F., Uenishi, H., Wang, J., Schook, L.B. :
Pig genome sequence--analysis and publication strategy. BMC Genomics 11:438, 2010. Pubmed reference: 20642822. DOI: 10.1186/1471-2164-11-438.
2009 Ramos, A.M., Crooijmans, R.P., Affara, N.A., Amaral, A.J., Archibald, A.L., Beever, J.E., Bendixen, C., Churcher, C., Clark, R., Dehais, P., Hansen, M.S., Hedegaard, J., Hu, Z.L., Kerstens, H.H., Law, A.S., Megens, H.J., Milan, D., Nonneman, D.J., Rohrer, G.A., Rothschild, M.F., Smith, T.P., Schnabel, R.D., Van Tassell, C.P., Taylor, J.F., Wiedmann, R.T., Schook, L.B., Groenen, M.A. :
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4:e6524, 2009. Pubmed reference: 19654876. DOI: 10.1371/journal.pone.0006524.
Amaral, A.J., Megens, H.J., Kerstens, H.H., Heuven, H.C., Dibbits, B., Crooijmans, R.P., den Dunnen, J.T., Groenen, M.A. :
Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics 10:374, 2009. Pubmed reference: 19674453. DOI: 10.1186/1471-2164-10-374.
2007 Humphray, S.J., Scott, C.E., Clark, R., Marron, B., Bender, C., Camm, N., Davis, J., Jenks, A., Noon, A., Patel, M., Sehra, H., Yang, F., Rogatcheva, M.B., Milan, D., Chardon, P., Rohrer, G., Nonneman, D., de Jong, P., Meyers, S.N., Archibald, A., Beever, J.E., Schook, L.B., Rogers, J. :
A high utility integrated map of the pig genome. Genome Biol 8:R139, 2007. Pubmed reference: 17625002. DOI: 10.1186/gb-2007-8-7-r139.
2005 Schook, L.B., Beever, J.E., Rogers, J., Humphray, S., Archibald, A., Chardon, P., Milan, D., Rohrer, G., Eversole, K. :
Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome. Comp Funct Genomics 6:251-5, 2005. Pubmed reference: 18629187. DOI: 10.1002/cfg.479.
2003 Karsenty, E., Barillot, E., Tosser-Klopp, G., Lahbib-Mansais, Y., Milan, D., Hatey, F., Cirera, S., Sawera, M., Jorgensen, C.B., Chowdhary, B., Fredholm, M., Wimmers, K., Ponsuksili, S., Davoli, R., Fontanesi, L., Braglia, S., Zambonelli, P., Bigi, D., Neuenschwander, S., Gellin, J. :
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa) Nucleic Acids Research 31:138-41, 2003. Pubmed reference: 12519967.
Martins-Wess, F., Milan, D., Drogemuller, C., Vobeta-Nemitz, R., Brenig, B., Robic, A., Yerle, M., Leeb, T. :
A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1 BMC Genomics 4:20, 2003. Pubmed reference: 12744726. DOI: 10.1186/1471-2164-4-20.
Rothschild, M.F. :
From a sow's ear to a silk purse: real progress in porcine genomics. Cytogenet Genome Res 102:95-9, 2003. Pubmed reference: 14970686. DOI: 75732.
2002 Jiang, Z.H., Melville, J.S., Cao, H.H., Kumar, S., Filipski, A., Gibbins, A.M.V. :
Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome Genome 45:769-776, 2002. Pubmed reference: 12175081.
Yerle, M., Pinton, P., Delcros, C., Arnal, N., Milan, D., Robic, A. :
Generation and characterization of a 12,,000-rad radiation hybrid panel for fine mapping in pig Cytogenetic & Genome Research 97:219-228, 2002.
Rink, A., Santschi, E.M., Eyer, K.M., Roelofs, B., Hess, M., Godfrey, M., Karajusuf, E.K., Yerle, M., Milan, D., Beattie, C.W. :
A first-generation EST RH comparative map of the porcine and human genome Mammalian Genome 13:578-87, 2002. Pubmed reference: 12420136. DOI: 10.1007/s00335-002-2192-5.
1999 Hawken, R.J., Murtaugh, J., Flickinger, G.H., Yerle, M., Robic, A., Milan, D., Gellin, J., Beattie, C.W., Schook, L.B., Alexander, L.J. :
A first-generation porcine whole-genome radiation hybrid map Mammalian Genome 10:824-830, 1999. Pubmed reference: 10430669.
Mikawa, S., Akita, T., Hisamatsu, N., Inage, Y., Ito, Y., Kobayashi, E., Kusumoto, H., Matsumoto, T., Mikami, H., Minezawa, M., Miyake, M., Shimanuki, S., Sugiyama, C., Uchida, Y., Wada, Y., Yanai, S., Yasue, H. :
A linkage map of 243 DNA markers in an intercross of Gottingen miniature and Meishan pigs Animal Genetics 30:407-417, 1999. Pubmed reference: 10612229.
1998 Yerle, M., Pinton, P., Robic, A., Alfonso, A., Palvadeau, Y., Delcros, C., Hawken, R., Alexander, L., Beattie, C., Schook, L., Milan, D., Gellin, J. :
Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs Cytogenetics & Cell Genetics 82:182-188, 1998.
1997 Ambady, S., Mendiola, J.R., Louis, C.F., Janzen, M.A., Schook, L.B., Buoen, L., Lunney, J.K., Grimm, D.R., Deleon, F.A.P. :
Development and use of a microdissected swine chromosome 6 dna library Cytogenetics & Cell Genetics 76:27-33, 1997.
Rohrer, G.A., Alexander, L.J., Beattie, C.W., Wilkie, P., Flickinger, G.H., Schook, L.B., Paszek, A.A., Andersson, L., Mariani, P., Marklund, L., Fredholm, M., Hoyheim, B., Archibald, A.L., Nielsen, V.H., Milan, D., Groenen, M.A.M. :
A consensus linkage map for swine chromosome 7 Animal Genetics 28:223-229, 1997.
Yerle, M., Lahbibmansais, Y., Pinton, P., Robic, A., Goureau, A., Milan, D., Gellin, J. :
The cytogenetic map of the domestic pig (sus scrofa domestica) [Review] Mammalian Genome 8:592-607, 1997. Pubmed reference: 9250869.
Andersson, L. :
The use of a wild pig x domestic pig intercross to map phenotypic trait loci Journal of Heredity 88:380-383, 1997. Pubmed reference: 9378913.
1996 Fronicke, L., Chowdhary, B.P., Scherthan, H., Gustavsson, I. :
A comparative map of the porcine and human genomes demonstrates zoo-FISH and gene mapping-based chromosomal homologies Mammalian Genome 7:285-290, 1996. Pubmed reference: 8661700.
Rohrer, G.A., Alexander, L.J., Hu, Z.L., Smith, T.P.L., Keele, J.W., Beattie, C.W. :
A comprehensive map of the porcine genome Genome Research 6:371-391, 1996. Pubmed reference: 8743988.
Marklund, L., Johansson Moller, M., Høyheim, B., Davies, W., Fredholm, M., Juneja, R.K., Mariani, P., Coppieters, W., Ellegren, H., Andersson, L. :
A comprehensive linkage map of the pig based on a wild pig-Large White intercross. Anim Genet 27:255-69, 1996. Pubmed reference: 8856923.
Rettenberger, G., Bruch, J., Hameister, H. :
A comparative mapping approach to the pig genome Journal of Animal Breeding & Genetics-Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 113:331-338, 1996.
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 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.

Tachyglossus aculeatus (Australian echidna) :

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.

Tachysurus fulvidraco × Tachysurus vachelli (hybrid yellow catfish) :

2021 Zhou, H., Duan, G., Jiang, H., Ling, J., Hu, Y., Zhang, Y., Wang, H., Pan, T., Chen, X. :
High-density genetic map and QTL mapping for body color of the yellow catfish (Tachysurus fulvidraco♀ × T. vachellii♂). Anim Genet :, 2021. Pubmed reference: 33503316. DOI: 10.1111/age.13042.

Taeniopygia guttata (zebra finch) :

2021 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.
2008 Stapley, J., Birkhead, TR., Burke, T., Slate, J. :
A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution. Genetics 179:651-67, 2008. Pubmed reference: 10506561.

Thymallus thymallus (grayling) :

2019 Sävilammi, T., Primmer, C.R., Varadharajan, S., Guyomard, R., Guiguen, Y., Sandve, S.R., Vøllestad, L.A., Papakostas, S., Lien, S. :
The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids. G3 (Bethesda) :, 2019. Pubmed reference: 30833292. DOI: 10.1534/g3.118.200919.

Tremarctos ornatus (spectacled bear) :

2021 Saremi, N.F., Oppenheimer, J., Vollmers, C., O'Connell, B., Milne, S.A., Byrne, A., Yu, L., Ryder, O.A., Green, R.E., Shapiro, B. :
An annotated draft genome for the Andean bear, Tremarctos ornatus. J Hered 112:377-384, 2021. Pubmed reference: 33882130. DOI: 10.1093/jhered/esab021.

Ursus arctos (brown bear) :

2021 Scarpulla, E., Boattini, A., Cozzo, M., Giangregorio, P., Ciucci, P., Mucci, N., Randi, E., Davoli, F. :
First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach. BMC Genomics 22:623, 2021. Pubmed reference: 34407764. DOI: 10.1186/s12864-021-07915-5.

Varanus komodoensis (Komodo dragon) :

2019 van Hoek, M.L., Prickett, M.D., Settlage, R.E., Kang, L., Michalak, P., Vliet, K.A., Bishop, B.M. :
The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters. BMC Genomics 20:684, 2019. Pubmed reference: 31470795. DOI: 10.1186/s12864-019-6029-y.

Vicugna pacos (alpaca) :

2021 Calderon, M., More, M.J., Gutierrez, G.A., Ponce de León, F.A. :
Development of a 76k alpaca (Vicugna pacos) single nucleotide polymorphisms (SNPs) microarray. Genes (Basel) 12:, 2021. Pubmed reference: 33669871. DOI: 10.3390/genes12020291.
2020 Mendoza, M.N., Raudsepp, T., More, M.J., Gutiérrez, G.A., Ponce de León, F.A. :
Cytogenetic mapping of 35 new markers in the alpaca (Vicugna pacos). Genes (Basel) 11:, 2020. Pubmed reference: 32397072. DOI: 10.3390/genes11050522.
2019 Richardson, M.F., Munyard, K., Croft, L.J., Allnutt, T.R., Jackling, F., Alshanbari, F., Jevit, M., Wright, G.A., Cransberg, R., Tibary, A., Perelman, P., Appleton, B., Raudsepp, T. :
Chromosome-level alpaca reference genome VicPac3.1 improves genomic insight into the biology of new world camelids. Front Genet 10:586, 2019. Pubmed reference: 31293619. DOI: 10.3389/fgene.2019.00586.
Mendoza, M.N., Raudsepp, T., Alshanbari, F., Gutiérrez, G., Ponce de León, F.A. :
Chromosomal localization of candidate genes for fiber growth and color in alpaca (Vicugna pacos). Front Genet 10:583, 2019. Pubmed reference: 31275359. DOI: 10.3389/fgene.2019.00583.

Vulpes vulpes (red fox) :

2019 Rando, H.M., Wadlington, W.H., Johnson, J.L., Stutchman, J.T., Trut, L.N., Farré, M., Kukekova, A.V. :
The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 10:, 2019. Pubmed reference: 31142040. DOI: 10.3390/genes10060409.
2018 Kukekova, A.V., Johnson, J.L., Xiang, X., Feng, S., Liu, S., Rando, H.M., Kharlamova, A.V., Herbeck, Y., Serdyukova, N.A., Xiong, Z., Beklemischeva, V., Koepfli, K.P., Gulevich, R.G., Vladimirova, A.V., Hekman, J.P., Perelman, P.L., Graphodatsky, A.S., O'Brien, S.J., Wang, X., Clark, A.G., Acland, G.M., Trut, L.N., Zhang, G. :
Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol 2:1479-1491, 2018. Pubmed reference: 30082739. DOI: 10.1038/s41559-018-0611-6.
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. :
Author Correction: Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol :, 2018. Pubmed reference: 30104754. DOI: 10.1038/s41559-018-0664-6.
2011 Kukekova, A.V., Trut, L.N., Chase, K., Kharlamova, A.V., Johnson, J.L., Temnykh, S.V., Oskina, I.N., Gulevich, R.G., Vladimirova, A.V., Klebanov, S., Shepeleva, D.V., Shikhevich, S.G., Acland, G.M., Lark, K.G. :
Mapping Loci for fox domestication: deconstruction/reconstruction of a behavioral phenotype. Behav Genet 41:593-606, 2011. Pubmed reference: 21153916. DOI: 10.1007/s10519-010-9418-1.
2007 Kukekova, A.V., Trut, L.N., Oskina, I.N., Johnson, J.L., Temnykh, S.V., Kharlamova, A.V., Shepeleva, D.V., Gulievich, R.G., Shikhevich, S.G., Graphodatsky, A.S., Aguirre, G.D., Acland, G.M. :
A meiotic linkage map of the silver fox, aligned and compared to the canine genome. Genome Res 17:387-99, 2007. Pubmed reference: 17284676. DOI: 10.1101/gr.5893307.
1998 Rubtsov, N.B. :
The Fox Gene Map. ILAR J 39:182-188, 1998. Pubmed reference: 11528077.