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 Layman; Vincent 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

doi:10.1038/nature03154

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 journal › Article › peer-review

2265 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 language	English
Pages (from-to)	695-716
Number of pages	22
Journal	Nature
Volume	423
Issue number	7018
DOIs	https://doi.org/10.1038/nature03154
Publication status	Published - 9 Dec 2004

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Hillier, L. W., Miller, W., Birney, E., Warren, W., Hardison, R. C., Ponting, C. P., Bork, P., Burt, D. W., Groenen, M. A. M., Delany, M. E., Dodgson, J. B., Chinwalla, A. T., Cliften, P. F., Clifton, S. W., Delehaunty, K. D., Fronick, C., Fulton, R. S., Graves, T. A., Kremitzki, C., ... Minx, P. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 423(7018), 695-716. https://doi.org/10.1038/nature03154

@article{c5823c8f980047719ef22bb4aaeac58d,

title = "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution",

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.",

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

year = "2004",

month = dec,

day = "9",

doi = "10.1038/nature03154",

language = "English",

volume = "423",

pages = "695--716",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7018",

}

Hillier, LW, Miller, W, Birney, E, Warren, W, Hardison, RC, Ponting, CP, Bork, P, Burt, DW, Groenen, MAM, Delany, ME, Dodgson, JB, Chinwalla, AT, Cliften, PF, Clifton, SW, Delehaunty, KD, Fronick, C, Fulton, RS, Graves, TA, Kremitzki, C, Layman, D, Magrini, V, McPherson, JD, Miner , TL, Nash, WE, Nhan, MN, Nelson, JO, Oddy, LG, Pohl, CS, Randall-Maher, J, Smith, SM, Wallis, JW, Yang, SP, 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, 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, JM, Wilson, SA, Stubbs, L, Ovcharenko, I, Gordon, L, Lucas, S, Miller, MM, Inoko, H, Shiina, T, Kaufman, J, Salomonsen, J, Skjoedt, K, Wong, GKS, Wang, J, Liu, B, Wang, J, Yu, J, Yang, H, Nefedov, M, Koriabine, M, DeJong, PJ, 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, Brandstrom, M, Axelsson, E, Backstrom, N, Berlin, S, Webster, MT, Pourquie, O, Reymond, A, Ucla, C, Antonarakis, SE, Long, M, Emerson, JJ, Betran, 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, Fulton, LA, Mardis, ER, Wilson, RK & Minx, P 2004, 'Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution', Nature, vol. 423, no. 7018, pp. 695-716. https://doi.org/10.1038/nature03154

TY - JOUR

T1 - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

AU - Hillier, Ladeana W.

AU - Miller, Webb

AU - Birney, Ewan

AU - Warren, Wesley

AU - Hardison, Ross C.

AU - Ponting, Chris P.

AU - Bork, Peer

AU - Burt, David W.

AU - Groenen, Martien A M

AU - Delany, Mary E.

AU - Dodgson, Jerry B.

AU - Chinwalla, Asif T.

AU - Cliften, Paul F.

AU - Clifton, Sandra W.

AU - Delehaunty, Kimberly D.

AU - Fronick, Catrina

AU - Fulton, Robert S.

AU - Graves, Tina A.

AU - Kremitzki, Colin

AU - Layman, Dan

AU - Magrini, Vincent

AU - McPherson, John D.

AU - Miner , Tracie L.

AU - Nash, William E.

AU - Nhan, Michael N.

AU - Nelson, Joanne O.

AU - Oddy, Lachlan G.

AU - Pohl, Craig S.

AU - Randall-Maher, Jennifer

AU - Smith, Scott M.

AU - Wallis, John W.

AU - Yang, Shiaw Pyng

AU - Romanov, Michael N.

AU - Rondelli, Catherine M.

AU - Paton, Bob

AU - Smith, Jacqueline

AU - Morrice, David

AU - Daniels, Laura

AU - Tempest, Helen G.

AU - Robertson, Lindsay

AU - Masabanda, Julio S.

AU - Griffin, Darren K.

AU - Vignal, Alain

AU - Fillon, Valerie

AU - Jacobbson, Lina

AU - Kerje, Susanne

AU - Andersson, Leif

AU - Crooijmans, Richard P. M.

AU - Aerts, Jan

AU - Van Der Poel, Jan J.

AU - Ellegren, Hans

AU - Caldwell, Randolph B.

AU - Hubbard, Simon J.

AU - Grafham, Darren V.

AU - Kierzek, Andrzej M.

AU - McLaren, Stuart R.

AU - Overton, Ian M.

AU - Arakawa, Hiroshi

AU - Beattie, Kevin J.

AU - Bezzubov, Yuri

AU - Boardman, Paul E.

AU - Bonfield, James K.

AU - Croning, Michael D R

AU - Davies, Robert M.

AU - Francis, Matthew D.

AU - Humphray, Sean J.

AU - Scott, Carol E.

AU - Taylor, Ruth G.

AU - Tickle, Cheryll

AU - Brown, William R A

AU - Rogers, Jane

AU - Buerstedde, Jean Marie

AU - Wilson, Stuart A.

AU - Stubbs, Lisa

AU - Ovcharenko, Ivan

AU - Gordon, Laurie

AU - Lucas, Susan

AU - Miller, Marcia M.

AU - Inoko, Hidetoshi

AU - Shiina, Takashi

AU - Kaufman, Jim

AU - Salomonsen, Jan

AU - Skjoedt, Karsten

AU - Wong, Gane Ka Shu

AU - Wang, Jun

AU - Liu, Bin

AU - Wang, Jian

AU - Yu, Jun

AU - Yang, Huanming

AU - Nefedov, Mikhail

AU - Koriabine, Maxim

AU - DeJong, Pieter J.

AU - Goodstadt, Leo

AU - Webber, Caleb

AU - Dickens, Nicholas J.

AU - Letunic, Ivica

AU - Suyama, Mikita

AU - Torrents, David

AU - Von Mering, Christian

AU - Zdobnov, Evgeny M.

AU - Makova, Kateryna

AU - Nekrutenko, Anton

AU - Elnitski, Laura

AU - Eswara, Pallavi

AU - King, David C.

AU - Yang, Shan

AU - Tyekucheva, Svitlana

AU - Radakrishnan, Anusha

AU - Harris, Robert S.

AU - Chiaromonte, Francesca

AU - Taylor, James

AU - He, Jianbin

AU - Rijnkels, Monique

AU - Griffiths-Jones, Sam

AU - Ureta-Vidal, Abel

AU - Hoffman, Michael M.

AU - Severin, Jessica

AU - Searle, Stephen M J

AU - Law, Andy S.

AU - Speed, David

AU - Waddington, Dave

AU - Cheng, Ze

AU - Tuzun, Eray

AU - Eichler, Evan

AU - Bao, Zhirong

AU - Flicek, Paul

AU - Shteynberg, David D.

AU - Brent, Michael R.

AU - Bye, Jacqueline M.

AU - Huckle, Elizabeth J.

AU - Chatterji, Sourav

AU - Dewey, Colin

AU - Pachter, Lior

AU - Kouranov, Andrei

AU - Mourelatos, Zissimos

AU - Hatzigeorgiou, Artemis G.

AU - Paterson, Andrew H.

AU - Ivarie, Robert

AU - Brandstrom, Mikael

AU - Axelsson, Erik

AU - Backstrom, Niclas

AU - Berlin, Sofia

AU - Webster, Matthew T.

AU - Pourquie, Olivier

AU - Reymond, Alexandre

AU - Ucla, Catherine

AU - Antonarakis, Stylianos E.

AU - Long, Manyuan

AU - Emerson, J. J.

AU - Betran, Esther

AU - Dupanloup, Isabelle

AU - Kaessmann, Henrik

AU - Hinrichs, Angie S.

AU - Bejerano, Gill

AU - Furey, Terrence S.

AU - Harte, Rachel A.

AU - Raney, Brian

AU - Siepel, Adam

AU - Kent, W. James

AU - Haussler, David

AU - Eyras, Eduardo

AU - Castelo, Robert

AU - Abril, Josep F.

AU - Castellano, Sergi

AU - Camara, Francisco

AU - Parra, Genis

AU - Guigo, Roderic

AU - Bourque, Guillaume

AU - Tesler, Glenn

AU - Pevzner, Pavel A.

AU - Smit, Arian

AU - Fulton, Lucinda A.

AU - Mardis, Elaine R.

AU - Wilson, Richard K.

AU - Minx, Patrick

PY - 2004/12/9

Y1 - 2004/12/9

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84915750377&partnerID=8YFLogxK

U2 - 10.1038/nature03154

DO - 10.1038/nature03154

M3 - Article

C2 - 15592404

SN - 0028-0836

VL - 423

SP - 695

EP - 716

JO - Nature

JF - Nature

IS - 7018

ER -

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

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