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

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

doi:10.1038/nature03154

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

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

Research output: Contribution to journal › Article › peer-review

2290 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	432
Issue number	7018
DOIs	https://doi.org/10.1038/nature03154
Publication status	Published - 9 Dec 2004

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10.1038/nature03154

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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., ... Wilson, RK. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432(7018), 695-716. https://doi.org/10.1038/nature03154

@article{07a08fe6a5934452bb862d31128c7c8e,

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.",

keywords = "Recent segmental duplications, Non-ltr retrotransposons, Alcohol-dehydrogenase, Olfactory receptor, Gene prediction, Phylogenetic analysis, Interspersed repeats, Functional-analysis, Cr-1 elements, Bitter taste",

author = "LW Hillier and W Miller and E Birney and W Warren and RC Hardison and CP Ponting and P Bork and DW Burt and MAM Groenen and ME Delany and JB Dodgson and AT Chinwalla and PF Cliften and SW Clifton and KD Delehaunty and C Fronick and RS Fulton and TA Graves and C Kremitzki and D Layman and V Magrini and JD McPherson and TL Miner and P Minx and WE Nash and MN Nhan and JO Nelson and LG Oddy and CS Pohl and J Randall-Maher and SM Smith and JW Wallis and S Yang and MN Romanov and CM Rondelli and B Paton and J Smith and D Morrice and L Daniels and HG Tempest and L Robertson and JS Masabanda and DK Griffin and A Vignal and V Fillon and L Jacobbson and S Kerje and L Andersson and RPM Crooijmans and J Aerts and {van der Poel}, JJ and H Ellegren and RB Caldwell and SJ Hubbard and DV Grafham and AM Kierzek and SR McLaren and IM Overton and H Arakawa and KJ Beattie and Y Bezzubov and PE Boardman and JK Bonfield and MDR Croning and RM Davies and MD Francis and SJ Humphray and CE Scott and RG Taylor and C Tickle and WRA Brown and J Rogers and JM Buerstedde and SA Wilson and L Stubbs and I Ovcharenko and L Gordon and S Lucas and MM Miller and H Inoko and T Shiina and J Kaufman and J Salomonsen and K Skjoedt and GKS Wong and J Wang and B Liu and J Wang and J Yu and HM Yang and M Nefedov and M Koriabine and PJ deJong and L Goodstadt and C Webber and NJ Dickens and I Letunic and M Suyama and D Torrents and {von Mering}, C and EM Zdobnov and K Makova and A Nekrutenko and L Elnitski and P Eswara and DC King and S Yang and S Tyekucheva and A Radakrishnan and RS Harris and F Chiaromonte and J Taylor and JB He and M Rijnkels and S Griffiths-Jones and A Ureta-Vidal and MM Hoffman and J Severin and SMJ Searle and AS Law and D Speed and D Waddington and Z Cheng and E Tuzun and E Eichler and ZR Bao and P Flicek and DD Shteynberg and MR Brent and JM Bye and EJ Huckle and S Chatterji and C Dewey and L Pachter and A Kouranov and Z Mourelatos and AG Hatzigeorgiou and AH Paterson and R Ivarie and M Brandstrom and E Axelsson and N Backstrom and S Berlin and MT Webster and O Pourquie and A Reymond and C Ucla and SE Antonarakis and MY Long and JJ Emerson and E Betr{\'a}n and I Dupanloup and H Kaessmann and AS Hinrichs and G Bejerano and TS Furey and RA Harte and B Raney and A Siepel and WJ Kent and D Haussler and E Eyras and R Castelo and JF Abril and S Castellano and F Camara and G Parra and R Guigo and G Bourque and G Tesler and PA Pevzner and A Smit and LA Fulton and ER Mardis and RK Wilson",

year = "2004",

month = dec,

day = "9",

doi = "10.1038/nature03154",

language = "English",

volume = "432",

pages = "695--716",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

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, Minx, P, Nash, WE, Nhan, MN, Nelson, JO, Oddy, LG, Pohl, CS, Randall-Maher, J, Smith, SM, Wallis, JW, Yang, S, 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, HM, 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, JB, 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, ZR, 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, MY, 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, Fulton, LA, Mardis, ER & Wilson, RK 2004, 'Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution', Nature, vol. 432, 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, LW

AU - Miller, W

AU - Birney, E

AU - Warren, W

AU - Hardison, RC

AU - Ponting, CP

AU - Bork, P

AU - Burt, DW

AU - Groenen, MAM

AU - Delany, ME

AU - Dodgson, JB

AU - Chinwalla, AT

AU - Cliften, PF

AU - Clifton, SW

AU - Delehaunty, KD

AU - Fronick, C

AU - Fulton, RS

AU - Graves, TA

AU - Kremitzki, C

AU - Layman, D

AU - Magrini, V

AU - McPherson, JD

AU - Miner, TL

AU - Minx, P

AU - Nash, WE

AU - Nhan, MN

AU - Nelson, JO

AU - Oddy, LG

AU - Pohl, CS

AU - Randall-Maher, J

AU - Smith, SM

AU - Wallis, JW

AU - Yang, S

AU - Romanov, MN

AU - Rondelli, CM

AU - Paton, B

AU - Smith, J

AU - Morrice, D

AU - Daniels, L

AU - Tempest, HG

AU - Robertson, L

AU - Masabanda, JS

AU - Griffin, DK

AU - Vignal, A

AU - Fillon, V

AU - Jacobbson, L

AU - Kerje, S

AU - Andersson, L

AU - Crooijmans, RPM

AU - Aerts, J

AU - van der Poel, JJ

AU - Ellegren, H

AU - Caldwell, RB

AU - Hubbard, SJ

AU - Grafham, DV

AU - Kierzek, AM

AU - McLaren, SR

AU - Overton, IM

AU - Arakawa, H

AU - Beattie, KJ

AU - Bezzubov, Y

AU - Boardman, PE

AU - Bonfield, JK

AU - Croning, MDR

AU - Davies, RM

AU - Francis, MD

AU - Humphray, SJ

AU - Scott, CE

AU - Taylor, RG

AU - Tickle, C

AU - Brown, WRA

AU - Rogers, J

AU - Buerstedde, JM

AU - Wilson, SA

AU - Stubbs, L

AU - Ovcharenko, I

AU - Gordon, L

AU - Lucas, S

AU - Miller, MM

AU - Inoko, H

AU - Shiina, T

AU - Kaufman, J

AU - Salomonsen, J

AU - Skjoedt, K

AU - Wong, GKS

AU - Wang, J

AU - Liu, B

AU - Wang, J

AU - Yu, J

AU - Yang, HM

AU - Nefedov, M

AU - Koriabine, M

AU - deJong, PJ

AU - Goodstadt, L

AU - Webber, C

AU - Dickens, NJ

AU - Letunic, I

AU - Suyama, M

AU - Torrents, D

AU - von Mering, C

AU - Zdobnov, EM

AU - Makova, K

AU - Nekrutenko, A

AU - Elnitski, L

AU - Eswara, P

AU - King, DC

AU - Yang, S

AU - Tyekucheva, S

AU - Radakrishnan, A

AU - Harris, RS

AU - Chiaromonte, F

AU - Taylor, J

AU - He, JB

AU - Rijnkels, M

AU - Griffiths-Jones, S

AU - Ureta-Vidal, A

AU - Hoffman, MM

AU - Severin, J

AU - Searle, SMJ

AU - Law, AS

AU - Speed, D

AU - Waddington, D

AU - Cheng, Z

AU - Tuzun, E

AU - Eichler, E

AU - Bao, ZR

AU - Flicek, P

AU - Shteynberg, DD

AU - Brent, MR

AU - Bye, JM

AU - Huckle, EJ

AU - Chatterji, S

AU - Dewey, C

AU - Pachter, L

AU - Kouranov, A

AU - Mourelatos, Z

AU - Hatzigeorgiou, AG

AU - Paterson, AH

AU - Ivarie, R

AU - Brandstrom, M

AU - Axelsson, E

AU - Backstrom, N

AU - Berlin, S

AU - Webster, MT

AU - Pourquie, O

AU - Reymond, A

AU - Ucla, C

AU - Antonarakis, SE

AU - Long, MY

AU - Emerson, JJ

AU - Betrán, E

AU - Dupanloup, I

AU - Kaessmann, H

AU - Hinrichs, AS

AU - Bejerano, G

AU - Furey, TS

AU - Harte, RA

AU - Raney, B

AU - Siepel, A

AU - Kent, WJ

AU - Haussler, D

AU - Eyras, E

AU - Castelo, R

AU - Abril, JF

AU - Castellano, S

AU - Camara, F

AU - Parra, G

AU - Guigo, R

AU - Bourque, G

AU - Tesler, G

AU - Pevzner, PA

AU - Smit, A

AU - Fulton, LA

AU - Mardis, ER

AU - Wilson, RK

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.

KW - Recent segmental duplications

KW - Non-ltr retrotransposons

KW - Alcohol-dehydrogenase

KW - Olfactory receptor

KW - Gene prediction

KW - Phylogenetic analysis

KW - Interspersed repeats

KW - Functional-analysis

KW - Cr-1 elements

KW - Bitter taste

UR - https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=anu_research_portal_plus2&SrcAuth=WosAPI&KeyUT=WOS:000225597200038&DestLinkType=FullRecord&DestApp=WOS_CPL

U2 - 10.1038/nature03154

DO - 10.1038/nature03154

M3 - Article

C2 - 15592404

SN - 0028-0836

VL - 432

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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