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Avian Genomics in Animal Breeding and the End of the Model Organism

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Avian Genomics in Ecology and Evolution

Abstract

Avian genomics have long benefited from chicken being not only an important agricultural species but also a model organism for various fields of research including genetics, immunology, embryology and more recently vertebrate genome organisation and function. Thanks to this, chicken was in 2004 amongst the first vertebrates sequenced, and its genome annotation still benefits from a large community of users. Hundreds of quantitative trait loci (QTLs) have been mapped in chicken, and genome-wide information is now used in breeding programmes in agriculture. The chicken genome sequence was soon followed by the zebra finch sequencing, a model for the biology of learned vocalisation. Shortly after, the advent of new sequencing technologies, reducing cost and increasing speed of sequencing, allowed the turkey and duck genomes to follow. Now, close to 50 bird genomes are published, and with the ever-decreasing cost of sequencing and most recent genome assembly techniques, many more are expected soon. In the new era of genomics technologies, will model organisms remain essential?

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References

  • Abasht B, Dekkers JCM, Lamont SJ (2006) Review of quantitative trait loci identified in the chicken. Poult Sci 85:2079–2096

    Article  CAS  PubMed  Google Scholar 

  • Abzhanov A, Protas M, Grant BR, Grant PR, Tabin CJ (2004) Bmp4 and morphological variation of beaks in Darwin’s finches. Science 305:1462–1465. https://doi.org/10.1126/science.1098095

    Article  CAS  PubMed  Google Scholar 

  • Agnvall B, Bélteky J, Jensen P (2017) Brain size is reduced by selection for tameness in Red Junglefowl? Correlated effects in vital organs. Sci Rep 7:645. https://doi.org/10.1016/j.applanim.2008.04.003

    Article  Google Scholar 

  • Anderson TM, Vonholdt BM, Candille SI, Musiani M, Greco C, Stahler DR, Smith DW, Padhukasahasram B, Randi E, Leonard JA, Bustamante CD, Ostrander EA, Tang H, Wayne RK, Barsh GS (2009) Molecular and evolutionary history of melanism in North American gray wolves. Science 323:1339–1343. https://doi.org/10.1126/science.1165448

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, Mccarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H, FAANG Consortium (2015) Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol 16:57

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Aparicio S, Chapman J, Stupka E, Putnam N, Chia J-M, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MDS, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJK, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310

    Article  CAS  PubMed  Google Scholar 

  • Auer H, Mayr B, Lambrou M, Schleger W (1987) An extended chicken karyotype, including the NOR chromosome. Cytogenet Cell Genet 45:218–221

    Article  CAS  PubMed  Google Scholar 

  • Augui S, Nora EP, Heard E (2011) Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet 12:429–442. https://doi.org/10.1038/nrg2987

    Article  CAS  PubMed  Google Scholar 

  • Avery OT (1944) Studies on the chemical nature of the substance inducing chemical transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 79:137–158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Axelsson E, Webster MT, Smith NGC, Burt DW, Ellegren H (2005) Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res 15:120–125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baker Z, Schumer M, Haba Y, Bashkirova L, Holland C, Rosenthal GG, Przeworski M (2017) Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. eLife 6:e24133. https://doi.org/10.7554/eLife.24133

    Article  PubMed  PubMed Central  Google Scholar 

  • Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338:1587–1593. https://doi.org/10.1126/science.1230612

    Article  CAS  PubMed  Google Scholar 

  • Bay RA, Harrigan RJ, Underwood VL, Gibbs HL, Smith TB, Ruegg K (2018) Genomic signals of selection predict climate-driven population declines in a migratory bird. Science 359:83–86. https://doi.org/10.1126/science.aan4380

    Article  CAS  PubMed  Google Scholar 

  • Bed’hom B, Vaez M, Coville J-L, Gourichon D, Chastel O, Follett S, Burke T, Minvielle F (2012) The lavender plumage colour in Japanese quail is associated with a complex mutation in the region of MLPH that is related to differences in growth, feed consumption and body temperature. BMC Genomics 13:442

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bellott DW, Skaletsky H, Pyntikova T, Mardis ER, Graves T, Kremitzki C, Brown LG, Rozen S, Warren WC, Wilson RK, Page DC (2010) Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature 466:612–616

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bellott DW, Skaletsky H, Cho T-J, Brown L, Locke D, Chen N, Galkina S, Pyntikova T, Koutseva N, Graves T, Kremitzki C, Warren WC, Clark AG, Gaginskaya E, Wilson RK, Page DC (2017) Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nat Genet 49:387–394. https://doi.org/10.1038/ng.3778

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bitgood JJ (1993) Manipulation of the avian genome, Chapter 5. CRC Press, Guelph, ON

    Google Scholar 

  • Blanchette M, Green ED, Miller W, Haussler D (2004) Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res 14(12):2412–2423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boardman PE, Sanz-Ezquerro J, Overton IM, Burt DW, Bosch E, Fong WT, Tickle C, Brown WRA, Wilson SA, Hubbard SJ (2002) A comprehensive collection of chicken cDNAs. Curr Biol 12:1965–1969

    Article  PubMed  Google Scholar 

  • Boije H, Harun-Or-Rashid M, Lee Y-J, Imsland F, Bruneau N, Vieaud A, Gourichon D, Tixier-Boichard M, Bed’hom B, Andersson L, Hallböök F (2012) Sonic hedgehog-signalling patterns the developing chicken comb as revealed by exploration of the pea-comb mutation. PLoS One 7:e50890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bornelöv S, Seroussi E, Yosefi S, Pendavis K, Burgess SC, Grabherr M, Friedman-Einat M, Andersson L (2017) Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost. Genome Biol 18:112. https://doi.org/10.1186/s13059-017-1231-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G (2005) Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res 15:98–110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10:1213–1218. https://doi.org/10.1073/pnas.95.25.14863

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bumstead N, Palyga J (1992) A preliminary linkage map of the chicken genome. Genomics 13:690–697

    Article  CAS  PubMed  Google Scholar 

  • Burt DW (2007) Emergence of the chicken as a model organism: implications for agriculture and biology. Poult Sci 86(7):1460–1471

    Article  CAS  PubMed  Google Scholar 

  • Burt DW, Bruley C, Dunn IC, Jones CT, Ramage A, Law AS, Morrice DR, Paton IR, Smith J, Windsor D, Sazanov A, Fries R, Waddington D (1999) The dynamics of chromosome evolution in birds and mammals. Nature 402:411–413

    Article  CAS  PubMed  Google Scholar 

  • Cao W, Edery I (2017) Mid-day siesta in natural populations of D. melanogaster from Africa exhibits an altitudinal cline and is regulated by splicing of a thermosensitive intron in the period clock gene. BMC Evol Biol:1–17. https://doi.org/10.1186/s12862-017-0880-8

  • Chang C-M, Coville J-L, Coquerelle G, Gourichon D, Oulmouden A, Tixier-Boichard M (2006) Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens. BMC Genomics 7:19. https://doi.org/10.1186/1471-2164-7-19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Christidis L (1990) Animal cytogenetics. Chordata 3. B. Aves. Gebruder Borntraeger Verlagsbuchhandlung, Berlin

    Google Scholar 

  • Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen H-C, Agarwala R, McLaren WM, Ritchie GRS, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T (2011) Modernizing reference genome assemblies. PLoS Biol 9:e1001091

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Claussnitzer M, Dankel SN, Kim K-H, Quon G, Meuleman W, Haugen C, Glunk V, Sousa IS, Beaudry JL, Puviindran V, Abdennur NA, Liu J, Svensson P-A, Hsu Y-H, Drucker DJ, Mellgren G, Hui C-C, Hauner H, Kellis M (2015) FTO obesity variant circuitry and adipocyte browning in humans. N Engl J Med 373:895–907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Consortium MGS, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O’Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang S-P, Zdobnov EM, Zody MC, Lander ES (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562

    Article  CAS  Google Scholar 

  • Cooper MD, Peterson RDA, Good RA (1965) Delineation of the thymic and bursal lymphoid systems in the chicken. Nature 205:143–146

    Article  CAS  PubMed  Google Scholar 

  • Crooijmans RP, Vrebalov J, Dijkhof RJ, Van Der Poel JJ, Groenen MA (2000) Two-dimensional screening of the Wageningen chicken BAC library. Mamm Genome 11:360–363

    Article  CAS  PubMed  Google Scholar 

  • Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg LA, Bouffard P, Burt DW, Crasta O, Crooijmans RPMA, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MAM, Harkins TT, 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, Marçais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SMJ, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang H-B, Zhang X, Zhang Y, Reed KM (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 8:e1000475

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Davies B, Hatton E, Altemose N, Hussin JG, Pratto F, Zhang G, Hinch AG, Moralli D, Biggs D, Diaz R, Preece C, Li R, Bitoun E, Brick K, Green CM, Camerini-Otero RD, Myers SR, Donnelly P (2016) Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice. Nature 530(7589):171–176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S (2010) Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 6:e1001025. https://doi.org/10.1371/journal.pcbi.1001025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Magalhaes JP (2015) The big, the bad and the ugly: extreme animals as inspiration for biomedical research. EMBO Rep 16:771–776. https://doi.org/10.15252/embr.201540606

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delany ME (2004) Genetic variants for chick biology research: from breeds to mutants. Mech Dev 121:1169–1177. https://doi.org/10.1016/j.mod.2004.05.018

    Article  CAS  PubMed  Google Scholar 

  • 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 (2013) Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 31:135–141

    Article  CAS  PubMed  Google Scholar 

  • Donis-Keller H, Green P, Helms C, Cartinhour S, Weiffenbach B, Stephens K, Keith TP, Bowden DW, Smith DR, Lander ES (1987) A genetic linkage map of the human genome. Cell 51:319–337

    Article  CAS  PubMed  Google Scholar 

  • Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, Rubin C-J, Ashwell C, Gourichon D, Tixier-Boichard M, Hallböök F, Andersson L (2015) A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes. PLoS Genet 11:e1004947. https://doi.org/10.1371/journal.pgen.1004947

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Douaud M, Feve K, Gerus M, Fillon V, Bardes S, Gourichon D, Dawson DA, Hanotte O, Burke T, Vignoles F, Morisson M, Tixier-Boichard M, Vignal A, Pitel F (2008) Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping. BMC Genomics 9:129

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dunn IC, Paton IR, Clelland AK, Sebastian S, Johnson EJ, McTeir L, Windsor D, Sherman A, Sang H, Burt DW, Tickle C, Davey MG (2011) The chicken polydactyly (Po) locus causes allelic imbalance and ectopic expression of Shh during limb development. Dev Dyn 240:1163–1172. https://doi.org/10.1002/dvdy.22623

    Article  CAS  PubMed  Google Scholar 

  • Dunn IC, Meddle SL, Wilson PW, Wardle CA, Law AS, Bishop VR, Hindar C, Robertson GW, Burt DW, Ellison SJH, Morrice DM, Hocking PM (2013) Decreased expression of the satiety signal receptor CCKAR is responsible for increased growth and body weight during the domestication of chickens. Am J Physiol Endocrinol Metab 304:E909–E921

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eory L, Halligan DL, Keightley PD (2010) Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol 27(1):177–192

    Article  CAS  PubMed  Google Scholar 

  • ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee B-K, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassman T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SCJ, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LAL, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigo R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Starnatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See L-H, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigo R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent WJ, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL et al (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74

    Article  CAS  Google Scholar 

  • Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigo R, Bertone P, RGASP Consortium (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods 10:1185–1191. https://doi.org/10.1038/nmeth.2722

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eriksson J, Larson G, Gunnarsson U, Bed’hom B, Tixier-Boichard M, Strömstedt L, Wright D, Jungerius A, Vereijken A, Randi E, Jensen P, Andersson L (2008) Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet 4:e1000010. https://doi.org/10.1371/journal.pgen.1000010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ernst J, Kellis M (2012) ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9:215–216. https://doi.org/10.1101/gr.229102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feng C, Gao Y, Dorshorst B, Song C, Gu X, Li Q, Li J, Liu T, Rubin C-J, Zhao Y, Wang Y, Fei J, Li H, Chen K, Qu H, Shu D, Ashwell C, Da Y, Andersson L, Hu X, Li N (2014) A cis-regulatory mutation of PDSS2 causes silky-feather in chickens. PLoS Genet 10:e1004576

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fillon V, Zoorob R, Yerle M, Auffray C, Vignal A (1996) Mapping of the genetically independent chicken major histocompatibility complexes B@ and RFP-Y@ to the same microchromosome by two-color fluorescent in situ hybridization. Cytogenet Cell Genet 75:7–9

    Article  CAS  PubMed  Google Scholar 

  • Fillon V, Morisson M, Zoorob R, Auffray C, Douaire M, Gellin J, Vignal A (1998) Identification of 16 chicken microchromosomes by molecular markers using two-colour fluorescence in situ hybridization (FISH). Chromosom Res 6:307–313

    Article  CAS  Google Scholar 

  • Flink LG, Allen R, Barnett R, Malmström H, Peters J, Eriksson J, Andersson L, Dobney K, Larson G (2014) Establishing the validity of domestication genes using DNA from ancient chickens. Proc Natl Acad Sci USA 111:6184–6189. https://doi.org/10.1073/pnas.1308939110

    Article  CAS  Google Scholar 

  • Fresard L, Leroux S, Servin B, Gourichon D, Dehais P, Cristobal MS, Marsaud N, Vignoles F, Bed’hom B, Coville J-L, Hormozdiari F, Beaumont C, Zerjal T, Vignal A, Morisson M, Lagarrigue S, Pitel F (2014) Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Res 42:3768–3782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Galkina S, Fillon V, Saifitdinova A, Daks A, Kulak M, Dyomin A, Koshel E, Gaginskaya ER (2017) Chicken microchromosomes in the lampbrush phase: a cytogenetic description. Cytogenet Genome Res 152(1):46–54. https://doi.org/10.1159/000475563

    Article  CAS  PubMed  Google Scholar 

  • Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee H-M, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song X-Z, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D’Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee Y-A, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Consortium RGSP (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493–521

    Article  CAS  PubMed  Google Scholar 

  • Goddard ME, Hayes BJ (2007) Genomic selection. J Anim Breed Genet 124:323–330. https://doi.org/10.1111/j.1439-0388.2007.00702.x

    Article  CAS  PubMed  Google Scholar 

  • Groenen MA, Cheng HH, Bumstead N, Benkel BF, Briles WE, Burke T, Burt DW, Crittenden LB, Dodgson J, Hillel J, Lamont S, de Leon AP, Soller M, Takahashi H, Vignal A (2000) A consensus linkage map of the chicken genome. Genome Res 10:137–147

    CAS  PubMed  PubMed Central  Google Scholar 

  • Groenen MAM, Wahlberg P, Foglio M, Cheng HH, Megens H-J, Crooijmans RPMA, Besnier F, Lathrop M, Muir WM, Wong GK-S, Andersson L (2009) A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res 19:510–519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gross JB, Borowsky R, Tabin CJ (2009) A novel role for Mc1r in the parallel evolution of depigmentation in independent populations of the cavefish Astyanax mexicanus. PLoS Genet 5:e1000326. https://doi.org/10.1371/journal.pgen.1000326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gunnarsson U, Hellström AR, Tixier-Boichard M, Minvielle F, Bed’hom B, Ito S, Jensen P, Rattink A, Vereijken A, Andersson L (2007) Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail. Genetics 175:867–877

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gunnarsson U, Kerje S, Bed’hom B, Sahlqvist A-S, Ekwall O, Tixier-Boichard M, Kämpe O, Andersson L (2011) The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10. Pigment Cell Melanoma Res 24:268–274. https://doi.org/10.1111/j.1755-148X.2011.00825.x

    Article  CAS  PubMed  Google Scholar 

  • Haig D (2014) Coadaptation and conflict, misconception and muddle, in the evolution of genomic imprinting. Heredity 113:96–103. https://doi.org/10.1038/hdy.2013.97

    Article  CAS  PubMed  Google Scholar 

  • Halaas JL, Gajiwala KS, Maffei M, Cohen SL, Chait BT, Rabinowitz D, Lallone RL, Burley SK, Friedman JM (1995) Weight-reducing effects of the plasma protein encoded by the obese gene. Science 269:543–546

    Article  CAS  PubMed  Google Scholar 

  • Hamburger V, Hamilton HL (1992) A series of normal stages in the development of the chick embryo. 1951. Dev Dyn 195(4):231–272. Department of Zoology, Washington University, St. Louis, Missouri

    Article  CAS  PubMed  Google Scholar 

  • Hickey G, Paten B, Earl D, Zerbino D, Haussler D (2013) HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics 29:1341–1342. https://doi.org/10.1093/bioinformatics/btt128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME, Dodgson JB, Genome Fingerprint Map Sequence, Assembly, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang S-P, Mapping, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RPM, Aerts J, van der Poel JJ, Ellegren H, sequencing cDNA, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MDR, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WRA, Rogers J, Buerstedde J-M, Wilson SA, sequencing O, libraries, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GK-S, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Analysis, annotation, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SMJ, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandström M, Axelsson E, Backström N, Berlin S, Webster MT, Pourquié O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betrán E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, management P, Fulton LA, Mardis ER, Wilson RK (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716

    Article  CAS  Google Scholar 

  • Huang Y, Li Y, Burt DW, 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 KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim K-W, Sheng Z, An Y, Searle S, Herrero J, Groenen MAM, Crooijmans RPMA, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RHS, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N (2013) The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet 45:776–783. https://doi.org/10.1038/ng.2657

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huss D, Lansford R (2017) Fluorescent quail: a transgenic model system for the dynamic study of avian development. Methods Mol Biol 1650:125–147. https://doi.org/10.1007/978-1-4939-7216-6_8

    Article  CAS  PubMed  Google Scholar 

  • Hutt FB (1933) Genetics of the fowl. II. A four-gene autosomal linkage group. Genetics 18:82–94

    CAS  PubMed  PubMed Central  Google Scholar 

  • Imsland F, Feng C, Boije H, Bed’hom B, Fillon V, Dorshorst B, Rubin C-J, Liu R, Gao Y, Gu X, Wang Y, Gourichon D, Zody MC, Zecchin W, Vieaud A, Tixier-Boichard M, Hu X, Hallböök F, Li N, Andersson L (2012) The rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility. PLoS Genet 8:e1002775. https://doi.org/10.1371/journal.pgen.1002775

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Itoh Y, Melamed E, Yang X, Kampf K, Wang S, Yehya N, Van Nas A, Replogle K, Band MR, Clayton DF, Schadt EE, Lusis AJ, Arnold AP (2007) Dosage compensation is less effective in birds than in mammals. J Biol 6:2. https://doi.org/10.1186/jbiol53

    Article  PubMed  PubMed Central  Google Scholar 

  • Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldså J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli K-P, O’Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320–1331

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jax E, Wink M, Kraus RHS (2018) Avian transcriptomics: opportunities and challenges. J Ornithol 159(3):599–629

    Article  Google Scholar 

  • Kain KH, Miller JWI, Jones-Paris CR, Thomason RT, Lewis JD, Bader DM, Barnett JV, Zijlstra A (2014) The chick embryo as an expanding experimental model for cancer and cardiovascular research. Dev Dyn 243:216–228. https://doi.org/10.1002/dvdy.24093

    Article  PubMed  Google Scholar 

  • Karlsson A-C, Svemer F, Eriksson J, Darras VM, Andersson L, Jensen P (2015) The effect of a mutation in the thyroid stimulating hormone receptor (TSHR) on development, behaviour and TH levels in domesticated chickens. PLoS One 10:e0129040. https://doi.org/10.1371/journal.pone.0129040

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karlsson A-C, Fallahshahroudi A, Johnsen H, Hagenblad J, Wright D, Andersson L, Jensen P (2016) A domestication related mutation in the thyroid stimulating hormone receptor gene (TSHR) modulates photoperiodic response and reproduction in chickens. Gen Comp Endocrinol 228:69–78

    Article  CAS  PubMed  Google Scholar 

  • Kerje S, Lind J, Schütz K, Jensen P, Andersson L (2003) Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken. Anim Genet 34:241–248

    Article  CAS  PubMed  Google Scholar 

  • Kerje S, Sharma P, Gunnarsson U, Kim H, Bagchi S, Fredriksson R, Schütz K, Jensen P, von Heijne G, Okimoto R, Andersson L (2004) The dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics 168:1507–1518. https://doi.org/10.1534/genetics.104.027995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Korlach J, Gedman G, Kingan SB, Chin C-S, Howard JT, Audet J-N, Cantin L, Jarvis ED (2017) De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Gigascience 6:1–16. https://doi.org/10.1093/gigascience/gix085

    Article  PubMed  PubMed Central  Google Scholar 

  • Kranis A, Gheyas AA, Boschiero C, Turner F, Yu L, Smith S, Talbot R, Pirani A, Brew F, Kaiser P, Hocking PM, Fife M, Salmon N, Fulton J, Strom TM, Haberer G, Weigend S, Preisinger R, Gholami M, Qanbari S, Simianer H, Watson KA, Woolliams JA, Burt DW (2013) Development of a high density 600K SNP genotyping array for chicken. BMC Genomics 14:59

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kraus RHS, Wink M (2015) Avian genomics: fledging into the wild! J Ornithol 156:851–865. https://doi.org/10.1007/s10336-015-1253-y

    Article  Google Scholar 

  • Kuo RI, Tseng E, Eory L, Paton IR, Archibald AL, Burt DW (2017) Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human. BMC Genomics 18:323. https://doi.org/10.1186/s12864-017-3691-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ladjali K, Tixier-Boichard M, Cribiu EP (1995) High-resolution chromosome preparations for G-and R-banding in Gallus domesticus. J Hered 86:136–139

    Article  Google Scholar 

  • Laine VN, Gossmann TI, Schachtschneider KM, Garroway CJ, Madsen O, Verhoeven KJF, de Jager V, Megens H-J, Warren WC, Minx P, Crooijmans RPMA, Corcoran P, Great Tit HapMap Consortium, Sheldon BC, Slate J, Zeng K, van Oers K, Visser ME, Groenen MAM (2016) Evolutionary signals of selection on cognition from the great tit genome and methylome. Nat Commun 7:10474. https://doi.org/10.1038/ncomms10474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N, Xiao M, Kwok P-Y (2012) Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol 30:771–776

    Article  CAS  PubMed  Google Scholar 

  • Lamichhaney S, Fan G, Widemo F, Gunnarsson U, Thalmann DS, Hoeppner MP, Kerje S, Gustafson U, Shi C, Zhang H, Chen W, Liang X, Huang L, Wang J, Liang E, Wu Q, Lee SM-Y, Xu X, Höglund J, Liu X, Andersson L (2016) Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nat Genet 48:84–88

    Article  CAS  PubMed  Google Scholar 

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang S-P, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    Article  CAS  PubMed  Google Scholar 

  • Laun K, Coggill P, Palmer S, Sims S, Ning Z, Ragoussis J, Volpi E, Wilson N, Beck S, Ziegler A, Volz A (2006) The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like loci. PLoS Genet 2:e73

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Laver T, Harrison J, O’Neill PA, Moore K, Farbos A, Paszkiewicz K, Studholme DJ (2015) Assessing the performance of the Oxford nanopore technologies MinION. Biomol Detect Quantif 3:1–8. https://doi.org/10.1016/j.bdq.2015.02.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Le Bihan-Duval E, Nadaf J, Berri C, Pitel F, Graulet B, Godet E, Leroux SY, Demeure O, Lagarrigue S, Duby C, Cogburn LA, Beaumont CM, Duclos MJ (2011) Detection of a cis eQTL controlling BMCO1 gene expression leads to the identification of a QTG for chicken breast meat color. PLoS One 6:e14825

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Le Douarin NM, Teillet MA (1974) Experimental analysis of the migration and differentiation of neuroblasts of the autonomic nervous system and of neurectodermal mesenchymal derivatives, using a biological cell marking technique. Dev Biol 41:162–184

    Article  PubMed  Google Scholar 

  • Lennox J (2017) Aristotle’s biology, Spring 2017 Edition. The Stanford Encyclopedia of Philosophy

    Google Scholar 

  • Levin I, Santangelo L, Cheng H, Crittenden LB, Dodgson JB (1994) An autosomal genetic linkage map of the chicken. J Hered 85:79–85

    Article  CAS  PubMed  Google Scholar 

  • Lin MF, Jungreis I, Kellis M (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27:i275–i282. https://doi.org/10.1093/bioinformatics/btr209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478:476–482. https://doi.org/10.1038/nature10530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401

    CAS  PubMed  PubMed Central  Google Scholar 

  • Loog L, Thomas MG, Barnett R, Allen R, Sykes N, Paxinos PD, Lebrasseur O, Dobney K, Peters J, Manica A, Larson G, Eriksson A (2017) Inferring allele frequency trajectories from ancient DNA indicates that selection on a chicken gene coincided with changes in medieval husbandry practices. Mol Biol Evol 34(8):1981–1990. https://doi.org/10.1093/molbev/msx142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lovell PV, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, Warren WC, Mello CV (2014) Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol 15(12):565

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lowe CB, Clarke JA, Baker AJ, Haussler D, Edwards SV (2015) Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol 32:23–28. https://doi.org/10.1093/molbev/msu309

    Article  CAS  PubMed  Google Scholar 

  • Mack KL, Nachman MW (2017) Gene regulation and speciation. Trends Genet 33:68–80. https://doi.org/10.1016/j.tig.2016.11.003

    Article  CAS  PubMed  Google Scholar 

  • Margulies EH (2003) Identification and characterization of multi-species conserved sequences. Genome Res 13:2507–2518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mariani P, Barrow PA, Cheng HH, Groenen MM, Negrini R, Bumstead N (2001) Localization to chicken chromosome 5 of a novel locus determining salmonellosis resistance. Immunogenetics 53:786–791

    Article  CAS  PubMed  Google Scholar 

  • Masabanda JS, Burt DW, O’Brien PCM, Vignal A, Fillon V, Walsh PS, Cox H, Tempest HG, Smith J, Habermann F, Schmid M, Matsuda Y, Ferguson-Smith MA, Crooijmans RPMA, Groenen MAM, Griffin DK (2004) Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype. Genetics 166:1367–1373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McQueen HA, Fantes J, Cross SH, Clark VH, Archibald AL, Bird AP (1996) CpG islands of chicken are concentrated on microchromosomes. Nat Genet 12:321–324. https://doi.org/10.1038/ng0396-321

    Article  CAS  PubMed  Google Scholar 

  • McQueen HA, Siriaco G, Bird AP (1998) Chicken microchromosomes are hyperacetylated, early replicating, and gene rich. Genome Res 8:621–630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Melamed E, Arnold AP (2007) Regional differences in dosage compensation on the chicken Z chromosome. Genome Biol 8:R202

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mello CV (2014) The zebra finch, Taeniopygia guttata: an avian model for investigating the neurobiological basis of vocal learning. Cold Spring Harb Protoc 2014:1237–1242

    Article  PubMed  PubMed Central  Google Scholar 

  • Mihola O, Trachtulec Z, Vlcek C, Schimenti JC, Forejt J (2009) A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 323:373–375

    Article  CAS  PubMed  Google Scholar 

  • Miller MM, Taylor RL (2016) Brief review of the chicken major histocompatibility complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance. Poult Sci 95:375–392. https://doi.org/10.3382/ps/pev379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Minvielle F, Bed’hom B, Coville J-L, Ito S, Inoue-Murayama M, Gourichon D (2010) The “silver” Japanese quail and the MITF gene: causal mutation, associated traits and homology with the “blue” chicken plumage. BMC Genet 11:15

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Morisson M, Denis M, Milan D, Klopp C, Leroux S, Bardes S, Pitel F, Vignoles F, Gérus M, Fillon V, Douaud M, Vignal A (2007) The chicken RH map: current state of progress and microchromosome mapping. Cytogenet Genome Res 117:14–21. https://doi.org/10.1159/000103160

    Article  CAS  PubMed  Google Scholar 

  • Morris K, Hindle M, Boitard S et al (2019) The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response. bioRxiv. doi: http://dx.doi.org/10.1101/575332

    Google Scholar 

  • Mou C, Pitel F, Gourichon D, Vignoles F, Tzika A, Tato P, Yu L, Burt DW, Bed’hom B, Tixier-Boichard M, Painter KJ, Headon DJ (2011) Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering. PLoS Biol 9:e1001028. https://doi.org/10.1371/journal.pbio.1001028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mullikin JC, McMurray AA (1999) DNA sequencing – sequencing the genome, fast. Science 283:1867–1868

    Article  CAS  PubMed  Google Scholar 

  • Muret K, Klopp C, Wucher V, Esquerré D, Legeai F, Lecerf F, Désert C, Boutin M, Jehl F, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Lagarrigue S (2017) Long noncoding RNA repertoire in chicken liver and adipose tissue. Genet Sel Evol 49:6. https://doi.org/10.1186/s12711-016-0275-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nadaf J, Gilbert H, Pitel F, Berri CM, Feve K, Beaumont C, Duclos MJ, Vignal A, Porter TE, Simon J, Aggrey SE, Cogburn LA, Le Bihan-Duval E (2007) Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate. BMC Genomics 8:155

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • NCBI Resource Coordinators (2017) Database resources of the national center for biotechnology information. Nucleic Acids Res 45:D12–D17. https://doi.org/10.1093/nar/gkw1071

    Article  CAS  Google Scholar 

  • Ng CS, Wu P, Foley J, Foley A, McDonald M-L, Juan W-T, Huang C-J, Lai Y-T, Lo W-S, Chen C-F, Leal SM, Zhang H, Widelitz RB, Patel PI, Li W-H, Chuong C-M (2012) The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet 8:e1002748. https://doi.org/10.1371/journal.pgen.1002748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B (2014) Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics 30:3293–3301. https://doi.org/10.1093/bioinformatics/btu534

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ohta T (1995) Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol 40:56–63

    Article  CAS  PubMed  Google Scholar 

  • Oliva R, Dixon GH (1989) Chicken protamine genes are intronless. The complete genomic sequence and organization of the two loci. J Biol Chem 264:12472–12481

    CAS  PubMed  Google Scholar 

  • Ottenburghs J (2019) Avian species concepts in the light of genomics. In: Kraus RHS (ed) Avian genomics in ecology and evolution. Springer, Cham

    Google Scholar 

  • Ovcharenko I (2005) Evolution and functional classification of vertebrate gene deserts. Genome Res 15:137–145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680. https://doi.org/10.1038/nbt717

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D (2011) Cactus: algorithms for genome multiple sequence alignment. Genome Res 21:1512–1528. https://doi.org/10.1101/gr.123356.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pertea M, Shumate A, Pertea G, Varabyou A, Chang Y-C, Madugundu AK, Pandey A, Salzberg S (2018) Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise. BioRxiv:332825. https://doi.org/10.1101/332825

  • Pichugin AM, Galkina SA, Potekhin AA, Punina EO, Rautian MS, Rodionov AV (2001) Determination of the minimum size of Gallus gallus domesticus chicken microchromosome by a pulse electrophoresis method. Genetika 37:657–660

    CAS  PubMed  Google Scholar 

  • Pitel F, Bergé R, Coquerelle G, Crooijmans RP, Groenen MA, Vignal A, Tixier-Boichard M (2000) Mapping the naked neck (NA) and polydactyly (PO) mutants of the chicken with microsatellite molecular markers. Genet Sel Evol 32:73–86

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pitel F, Faraut T, Bruneau G, Monget P (2010) Is there a leptin gene in the chicken genome? Lessons from phylogenetics, bioinformatics and genomics. Gen Comp Endocrinol 167:1–5

    Article  CAS  PubMed  Google Scholar 

  • Putnam NH, O’Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE (2016) Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 26:342–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ren C, Lee M-K, Yan B, Ding K, Cox B, Romanov MN, Price JA, Dodgson JB, Zhang H-B (2003) A BAC-based physical map of the chicken genome. Genome Res 13:2754–2758

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu Y-C, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh K-H, Feizi S, Karlic R, Kim A-R, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJM, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai L-H, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317–330

    Article  PubMed Central  CAS  Google Scholar 

  • Roberts RJ, Carneiro MO, Schatz MC (2013) The advantages of SMRT sequencing. Genome Biol 14:405. https://doi.org/10.1186/gb-2013-14-6-405

    Article  PubMed  PubMed Central  Google Scholar 

  • Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, Fischer C, Fizames C, Wincker P, Brottier P, Quétier F, Saurin W, Weissenbach J (2000) Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet 25:235–238

    Article  CAS  PubMed  Google Scholar 

  • Romanov MN, Price JA, Dodgson JB (2003) Integration of animal linkage and BAC contig maps using overgo hybridization. Cytogenet Genome Res 102:277–281

    Article  CAS  PubMed  Google Scholar 

  • Romé H, Varenne A, Hérault F, Chapuis H, Alleno C, Dehais P, Vignal A, Burlot T, Le Roy P (2015) GWAS analyses reveal QTL in egg layers that differ in response to diet differences. Genet Sel Evol 47:83

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rous P (1911) A sarcoma of the fowl transmissible by an agent separable from the tumor cells. J Exp Med 13:397–411

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rubin C-J, Zody MC, Eriksson J, Meadows JRS, Sherwood E, Webster MT, Jiang L, Ingman M, Sharpe T, Ka S, Hallböök F, Besnier F, Carlborg O, Bed’hom B, Tixier-Boichard M, Jensen P, Siegel P, Lindblad-Toh K, Andersson L (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464(7288):587–591

    Article  CAS  PubMed  Google Scholar 

  • Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT (2010) Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328:1036–1040. https://doi.org/10.1126/science.1186176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmutz J, Grimwood J (2004) Fowl sequence. Nature 432:679–680. https://doi.org/10.1038/432679a

    Article  CAS  PubMed  Google Scholar 

  • Schoffner A, Kristan WB (1965) Karyotype of Gallus Domesticus with evidence for a W chromosome. Genetics 52:474

    Google Scholar 

  • Schwochow Thalmann D, Ring H, Sundström E, Cao X, Larsson M, Kerje S, Höglund A, Fogelholm J, Wright D, Jemth P, Hallböök F, Bed’hom B, Dorshorst B, Tixier-Boichard M, Andersson L (2017) The evolution of sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A. PLoS Genet 13:e1006665. https://doi.org/10.1371/journal.pgen.1006665

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Seroussi E, Pitel F, Leroux S, Morisson M, Bornelöv S, Miyara S, Yosefi S, Cogburn LA, Burt DW, Anderson L, Friedman-Einat M (2017) Mapping of leptin and its syntenic genes to chicken chromosome 1p. BMC Genet 18:77. https://doi.org/10.1186/s12863-017-0543-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH (2017) DNA sequencing at 40: past, present and future. Nature 550:345–353. https://doi.org/10.1038/nature24286

    Article  CAS  PubMed  Google Scholar 

  • Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN, Griffith SC, McVean G, Przeworski M (2015) Stable recombination hotspots in birds. Science 350:928–932. https://doi.org/10.1126/science.aad0843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soller M, Beckmann JS (1986) Restriction-fragment-length-polymorphisms in poultry breeding. Poult Sci 65:1474–1488

    Article  CAS  Google Scholar 

  • Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigo R, Harrow J, Bertone P (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10:1177–1184. https://doi.org/10.1038/nmeth.2714

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD (2016) The time scale of recombination rate evolution in great apes. Mol Biol Evol 33:928–945. https://doi.org/10.1093/molbev/msv331

    Article  CAS  PubMed  Google Scholar 

  • Théveneau E, Mayor R (2012) Neural crest delamination and migration: from epithelium-to-mesenchyme transition to collective cell migration. Dev Biol 366:34–54. https://doi.org/10.1016/j.ydbio.2011.12.041

    Article  CAS  PubMed  Google Scholar 

  • Tixier-Boichard M (2007) From phenotype to genotype: major genes in chickens. Worlds Poult Sci J 58:65–75. https://doi.org/10.1079/WPS20020008

    Article  Google Scholar 

  • Tixier-Boichard M, Bed’hom B, Rognon X (2011) Chicken domestication: from archeology to genomics. C R Biol 334:197–204. https://doi.org/10.1016/j.crvi.2010.12.012

    Article  PubMed  Google Scholar 

  • Tobita-Teramoto T, Jang GY, Kino K, Salter DW, Brumbaugh J, Akiyama T (2000) Autosomal albino chicken mutation (ca/ca) deletes hexanucleotide (-deltaGACTGG817) at a copper-binding site of the tyrosinase gene. Poult Sci 79:46–50

    Article  CAS  PubMed  Google Scholar 

  • Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46. https://doi.org/10.1016/j.cell.2013.06.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vaez M, Follett SA, Bed’hom B, Gourichon D, Tixier-Boichard M, Burke T (2008) A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken. BMC Genet 9:7

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (2001) The sequence of the human genome. Science 291:1304–1351

    Article  CAS  PubMed  Google Scholar 

  • 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 WC, Tixier-Boichard M, Rognon X (2019) A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour [Internet]. [cited 2019 Apr 17];0(ja). Available from: https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13017

  • Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JMA, Bertelsen MF, Murchison EP, Flicek P, Odom DT (2015) Enhancer evolution across 20 mammalian species. Cell 160:554–566. https://doi.org/10.1016/j.cell.2015.01.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wallis JW, Aerts J, Groenen MAM, Crooijmans RPMA, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, 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 MN, Cheng H, De Jong PJ, Osoegawa K, Nefedov M, Zhang H, McPherson JD, Krzywinski M, Schein J, Hillier L, Mardis ER, Wilson RK, Warren WC (2004) A physical map of the chicken genome. Nature 432:761–764

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63. https://doi.org/10.1038/nrg2484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Gao Y, Imsland F, Gu X, Feng C, Liu R, Song C, Tixier-Boichard M, Gourichon D, Li Q, Chen K, Li H, Andersson L, Hu X, Li N (2012) The crest phenotype in chicken is associated with ectopic expression of HOXC8 in cranial skin. PLoS One 7:e34012. https://doi.org/10.1371/journal.pone.0034012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Qu L, Yao J, Yang X, Li G, Zhang Y, Li J, Wang X, Bai J, Xu G, Deng X, Yang N, Wu C (2013) An EAV-HP insertion in 5′ flanking region of SLCO1B3 causes blue eggshell in the chicken. PLoS Genet 9:e1003183. https://doi.org/10.1371/journal.pgen.1003183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Q, Li K, Zhang D, Li J, Xu G, Zheng J, Yang N, Qu L (2015) Next-generation sequencing techniques reveal that genomic imprinting is absent in day-old Gallus gallus domesticus brains. PLoS One 10:e0132345. https://doi.org/10.1371/journal.pone.0132345

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Q, Mank JE, Li J, Yang N, Qu L (2017) Allele-specific expression analysis does not support sex chromosome inactivation on the chicken Z chromosome. Genome Biol Evol 9:619–626. https://doi.org/10.1093/gbe/evx031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TAF, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin Y-C, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, López-Otín C, Puente XS, Olender T, Lancet D, Smit AFA, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang S-P, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK (2010) The genome of a songbird. Nature 464:757–762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH (2017) A new chicken genome assembly provides insight into avian genome structure. G3 (Bethesda) 7:109–117. https://doi.org/10.1534/g3.116.035923

    Article  CAS  Google Scholar 

  • Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396

    CAS  PubMed  PubMed Central  Google Scholar 

  • Weissensteiner M, Suh A, Repetitive DNA (2019) The dark matter of avian genomics. In: Kraus RHS (ed) Avian genomics in ecology and evolution. Springer, Cham

    Google Scholar 

  • Wilkins AS, Wrangham RW, Fitch WT (2014) The “domestication syndrome” in mammals: a unified explanation based on neural crest cell behavior and genetics. Genetics 197:795–808. https://doi.org/10.1534/genetics.114.165423

    Article  PubMed  PubMed Central  Google Scholar 

  • Wragg D, Mwacharo JM, Alcalde JA, Wang C, Han J-L, Gongora J, Gourichon D, Tixier-Boichard M, Hanotte O (2013) Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl. PLoS One 8:e71393

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wright D, Boije H, Meadows JRS, Bed’hom B, Gourichon D, Vieaud A, Tixier-Boichard M, Rubin C-J, Imsland F, Hallböök F, Andersson L (2009) Copy number variation in intron 1 of SOX5 causes the pea-comb phenotype in chickens. PLoS Genet 5:e1000512. https://doi.org/10.1371/journal.pgen.1000512

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiang H, Gao J, Yu B, Zhou H, Cai D, Zhang Y, Chen X, Wang X, Hofreiter M, Zhao X (2014) Early Holocene chicken domestication in Northern China. Proc Natl Acad Sci USA 111:17564–17569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiang H, Gao J, Yu B, Hofreiter M, Zhao X (2015) Reply to Peters et al.: further discussions confirm early Holocene chicken domestication in Northern China. Proc Natl Acad Sci USA 112:E2416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yandell M, Ence D (2012) A beginner’s guide to eukaryotic genome annotation. Nat Rev Genet 13:329–342

    Article  CAS  PubMed  Google Scholar 

  • Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P (2016) Ensembl 2016. Nucleic Acids Res 44:D710–D716

    Article  CAS  PubMed  Google Scholar 

  • Zhang F, Wen Y, Guo X (2014a) CRISPR/Cas9 for genome editing: progress, implications and challenges. Hum Mol Genet 23:R40–R46. https://doi.org/10.1093/hmg/ddu125

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Jarvis ED, Gilbert MTP (2014b) A flock of genomes. Science 346(6215):1308–1309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, 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 RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim K-W, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O’Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Avian Genome Consortium, Jarvis ED, Gilbert MTP, Wang J (2014c) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311–1320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang T, Zhang X, Han K, Zhang G, Wang J, Xie K, Xue Q, Fan X (2017) Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken. PLoS One 12:e0172389. https://doi.org/10.1371/journal.pone.0172389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France

    Alain Vignal

  2. Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK

    Lel Eory

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  1. Alain Vignal
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  2. Lel Eory
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Correspondence to Alain Vignal .

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  1. Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany and Department of Biology, University of Konstanz, Konstanz, Germany

    Robert H. S. Kraus

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Vignal, A., Eory, L. (2019). Avian Genomics in Animal Breeding and the End of the Model Organism. In: Kraus, R. (eds) Avian Genomics in Ecology and Evolution. Springer, Cham. https://doi.org/10.1007/978-3-030-16477-5_3

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