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 & 155 others 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

    Research output: Contribution to journalArticle

    1830 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

    Fingerprint

    Sequence Analysis
    Vertebrates
    Chickens
    Genome
    Dinosaurs
    Synteny
    Group Processes
    Base Pairing
    Genes
    Birds
    Mammals
    Chromosomes

    Cite this

    Hillier, L. W., Miller, W., Birney, E., Warren, W., Hardison, R. C., Ponting, C. P., ... 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
    Hillier, Ladeana W. ; Miller, Webb ; Birney, Ewan ; Warren, Wesley ; Hardison, Ross C. ; Ponting, Chris P. ; Bork, Peer ; Burt, David W. ; Groenen, Martien A M ; Delany, Mary E. ; Dodgson, Jerry B. ; Chinwalla, Asif T. ; Cliften, Paul F. ; Clifton, Sandra W. ; Delehaunty, Kimberly D. ; Fronick, Catrina ; Fulton, Robert S. ; Graves, Tina A. ; Kremitzki, Colin ; Layman, Dan ; Magrini, Vincent ; McPherson, John D. ; Miner , Tracie L. ; Nash, William E. ; Nhan, Michael N. ; Nelson, Joanne O. ; Oddy, Lachlan G. ; Pohl, Craig S. ; Randall-Maher, Jennifer ; Smith, Scott M. ; Wallis, John W. ; Yang, Shiaw Pyng ; Romanov, Michael N. ; Rondelli, Catherine M. ; Paton, Bob ; Smith, Jacqueline ; Morrice, David ; Daniels, Laura ; Tempest, Helen G. ; Robertson, Lindsay ; Masabanda, Julio S. ; Griffin, Darren K. ; Vignal, Alain ; Fillon, Valerie ; Jacobbson, Lina ; Kerje, Susanne ; Andersson, Leif ; Crooijmans, Richard P. M. ; Aerts, Jan ; Van Der Poel, Jan J. ; Ellegren, Hans ; Caldwell, Randolph B. ; Hubbard, Simon J. ; Grafham, Darren V. ; Kierzek, Andrzej M. ; McLaren, Stuart R. ; Overton, Ian M. ; Arakawa, Hiroshi ; Beattie, Kevin J. ; Bezzubov, Yuri ; Boardman, Paul E. ; Bonfield, James K. ; Croning, Michael D R ; Davies, Robert M. ; Francis, Matthew D. ; Humphray, Sean J. ; Scott, Carol E. ; Taylor, Ruth G. ; Tickle, Cheryll ; Brown, William R A ; Rogers, Jane ; Buerstedde, Jean Marie ; Wilson, Stuart A. ; Stubbs, Lisa ; Ovcharenko, Ivan ; Gordon, Laurie ; Lucas, Susan ; Miller, Marcia M. ; Inoko, Hidetoshi ; Shiina, Takashi ; Kaufman, Jim ; Salomonsen, Jan ; Skjoedt, Karsten ; Wong, Gane Ka Shu ; Wang, Jun ; Liu, Bin ; Wang, Jian ; Yu, Jun ; Yang, Huanming ; Nefedov, Mikhail ; Koriabine, Maxim ; DeJong, Pieter J. ; Goodstadt, Leo ; Webber, Caleb ; Dickens, Nicholas J. ; Letunic, Ivica ; Suyama, Mikita ; Torrents, David ; Von Mering, Christian ; Zdobnov, Evgeny M. ; Makova, Kateryna ; Nekrutenko, Anton ; Elnitski, Laura ; Eswara, Pallavi ; King, David C. ; Yang, Shan ; Tyekucheva, Svitlana ; Radakrishnan, Anusha ; Harris, Robert S. ; Chiaromonte, Francesca ; Taylor, James ; He, Jianbin ; Rijnkels, Monique ; Griffiths-Jones, Sam ; Ureta-Vidal, Abel ; Hoffman, Michael M. ; Severin, Jessica ; Searle, Stephen M J ; Law, Andy S. ; Speed, David ; Waddington, Dave ; Cheng, Ze ; Tuzun, Eray ; Eichler, Evan ; Bao, Zhirong ; Flicek, Paul ; Shteynberg, David D. ; Brent, Michael R. ; Bye, Jacqueline M. ; Huckle, Elizabeth J. ; Chatterji, Sourav ; Dewey, Colin ; Pachter, Lior ; Kouranov, Andrei ; Mourelatos, Zissimos ; Hatzigeorgiou, Artemis G. ; Paterson, Andrew H. ; Ivarie, Robert ; Brandstrom, Mikael ; Axelsson, Erik ; Backstrom, Niclas ; Berlin, Sofia ; Webster, Matthew T. ; Pourquie, Olivier ; Reymond, Alexandre ; Ucla, Catherine ; Antonarakis, Stylianos E. ; Long, Manyuan ; Emerson, J. J. ; Betran, Esther ; Dupanloup, Isabelle ; Kaessmann, Henrik ; Hinrichs, Angie S. ; Bejerano, Gill ; Furey, Terrence S. ; Harte, Rachel A. ; Raney, Brian ; Siepel, Adam ; Kent, W. James ; Haussler, David ; Eyras, Eduardo ; Castelo, Robert ; Abril, Josep F. ; Castellano, Sergi ; Camara, Francisco ; Parra, Genis ; Guigo, Roderic ; Bourque, Guillaume ; Tesler, Glenn ; Pevzner, Pavel A. ; Smit, Arian ; Fulton, Lucinda A. ; Mardis, Elaine R. ; Wilson, Richard K. ; Minx, Patrick. / Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. In: Nature. 2004 ; Vol. 423, No. 7018. pp. 695-716.
    @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",
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    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

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

    In: Nature, Vol. 423, No. 7018, 09.12.2004, p. 695-716.

    Research output: Contribution to journalArticle

    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

    VL - 423

    SP - 695

    EP - 716

    JO - Nature

    JF - Nature

    SN - 0028-0836

    IS - 7018

    ER -

    Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;423(7018):695-716. https://doi.org/10.1038/nature03154