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 | |
| Publication status | Published - 9 Dec 2004 |
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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 journal › Article › peer-review
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
VL - 423
SP - 695
EP - 716
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7018
ER -