Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Ladeana W. Hillier, Webb Miller, Ewan Birney, Wesley Warren, Ross C. Hardison, Chris P. Ponting, Peer Bork, David W. Burt, Martien A M Groenen, Mary E. Delany, Jerry B. Dodgson, Asif T. Chinwalla, Paul F. Cliften, Sandra W. Clifton, Kimberly D. Delehaunty, Catrina Fronick, Robert S. Fulton, Tina A. Graves, Colin Kremitzki, Dan LaymanVincent Magrini, John D. McPherson, Tracie L. Miner , William E. Nash, Michael N. Nhan, Joanne O. Nelson, Lachlan G. Oddy, Craig S. Pohl, Jennifer Randall-Maher, Scott M. Smith, John W. Wallis, Shiaw Pyng Yang, Michael N. Romanov, Catherine M. Rondelli, Bob Paton, Jacqueline Smith, David Morrice, Laura Daniels, Helen G. Tempest, Lindsay Robertson, Julio S. Masabanda, Darren K. Griffin, Alain Vignal, Valerie Fillon, Lina Jacobbson, Susanne Kerje, Leif Andersson, Richard P. M. Crooijmans, Jan Aerts, Jan J. Van Der Poel, Hans Ellegren, Randolph B. Caldwell, Simon J. Hubbard, Darren V. Grafham, Andrzej M. Kierzek, Stuart R. McLaren, Ian M. Overton, Hiroshi Arakawa, Kevin J. Beattie, Yuri Bezzubov, Paul E. Boardman, James K. Bonfield, Michael D R Croning, Robert M. Davies, Matthew D. Francis, Sean J. Humphray, Carol E. Scott, Ruth G. Taylor, Cheryll Tickle, William R A Brown, Jane Rogers, Jean Marie Buerstedde, Stuart A. Wilson, Lisa Stubbs, Ivan Ovcharenko, Laurie Gordon, Susan Lucas, Marcia M. Miller, Hidetoshi Inoko, Takashi Shiina, Jim Kaufman, Jan Salomonsen, Karsten Skjoedt, Gane Ka Shu Wong, Jun Wang, Bin Liu, Jian Wang, Jun Yu, Huanming Yang, Mikhail Nefedov, Maxim Koriabine, Pieter J. DeJong, Leo Goodstadt, Caleb Webber, Nicholas J. Dickens, Ivica Letunic, Mikita Suyama, David Torrents, Christian Von Mering, Evgeny M. Zdobnov, Kateryna Makova, Anton Nekrutenko, Laura Elnitski, Pallavi Eswara, David C. King, Shan Yang, Svitlana Tyekucheva, Anusha Radakrishnan, Robert S. Harris, Francesca Chiaromonte, James Taylor, Jianbin He, Monique Rijnkels, Sam Griffiths-Jones, Abel Ureta-Vidal, Michael M. Hoffman, Jessica Severin, Stephen M J Searle, Andy S. Law, David Speed, Dave Waddington, Ze Cheng, Eray Tuzun, Evan Eichler, Zhirong Bao, Paul Flicek, David D. Shteynberg, Michael R. Brent, Jacqueline M. Bye, Elizabeth J. Huckle, Sourav Chatterji, Colin Dewey, Lior Pachter, Andrei Kouranov, Zissimos Mourelatos, Artemis G. Hatzigeorgiou, Andrew H. Paterson, Robert Ivarie, Mikael Brandstrom, Erik Axelsson, Niclas Backstrom, Sofia Berlin, Matthew T. Webster, Olivier Pourquie, Alexandre Reymond, Catherine Ucla, Stylianos E. Antonarakis, Manyuan Long, J. J. Emerson, Esther Betran, Isabelle Dupanloup, Henrik Kaessmann, Angie S. Hinrichs, Gill Bejerano, Terrence S. Furey, Rachel A. Harte, Brian Raney, Adam Siepel, W. James Kent, David Haussler, Eduardo Eyras, Robert Castelo, Josep F. Abril, Sergi Castellano, Francisco Camara, Genis Parra, Roderic Guigo, Guillaume Bourque, Glenn Tesler, Pavel A. Pevzner, Arian Smit, Lucinda A. Fulton, Elaine R. Mardis, Richard K. Wilson, Patrick Minx

    Research output: Contribution to journalArticlepeer-review

    1925 Citations (Scopus)

    Abstract

    We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome-composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes-provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

    Original languageEnglish
    Pages (from-to)695-716
    Number of pages22
    JournalNature
    Volume423
    Issue number7018
    DOIs
    Publication statusPublished - 9 Dec 2004

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