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

by: LW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, P Bork, DW Burt, MA 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, Randall J Maher, SM Smith, JW Wallis, SP 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, RP 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, MD Croning, RM Davies, MD Francis, SJ Humphray, CE Scott, RG Taylor, C Tickle, WR 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, GK Wong, J Wang, B Liu, J Wang, J Yu, H 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, J He, M Rijnkels, Griffiths S Jones, Ureta A Vidal, MM Hoffman, J Severin, SM Searle, AS Law, D Speed, D Waddington, Z Cheng, E Tuzun, E Eichler, Z 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, M 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, And RK Wilson

Nature, Vol. 432, No. 7018. (9 December 2004), pp. 695-716.

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DOI, Nature, Pubmed, Hubmed, DOI, http://dx.doi.org/10.1038/nature03154

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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.

@article{hillier04, 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.}, address = {Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.}, author = {Hillier, L. W. and Miller, W. and Birney, E. and Warren, W. and Hardison, R. C. and Ponting, C. P. and Bork, P. and Burt, D. W. and Groenen, M. A. and Delany, M. E. and Dodgson, J. B. and Chinwalla, A. T. and Cliften, P. F. and Clifton, S. W. and Delehaunty, K. D. and Fronick, C. and Fulton, R. S. and Graves, T. A. and Kremitzki, C. and Layman, D. and Magrini, V. and Mcpherson, J. D. and Miner, T. L. and Minx, P. and Nash, W. E. and Nhan, M. N. and Nelson, J. O. and Oddy, L. G. and Pohl, C. S. and Maher, Randall J. and Smith, S. M. and Wallis, J. W. and Yang, S. P. and Romanov, M. N. and Rondelli, C. M. and Paton, B. and Smith, J. and Morrice, D. and Daniels, L. and Tempest, H. G. and Robertson, L. and Masabanda, J. S. and Griffin, D. K. and Vignal, A. and Fillon, V. and Jacobbson, L. and Kerje, S. and Andersson, L. and Crooijmans, R. P. and Aerts, J. and van der Poel, J. J. and Ellegren, H. and Caldwell, R. B. and Hubbard, S. J. and Grafham, D. V. and Kierzek, A. M. and Mclaren, S. R. and Overton, I. M. and Arakawa, H. and Beattie, K. J. and Bezzubov, Y. and Boardman, P. E. and Bonfield, J. K. and Croning, M. D. and Davies, R. M. and Francis, M. D. and Humphray, S. J. and Scott, C. E. and Taylor, R. G. and Tickle, C. and Brown, W. R. and Rogers, J. and Buerstedde, J. M. and Wilson, S. A. and Stubbs, L. and Ovcharenko, I. and Gordon, L. and Lucas, S. and Miller, M. M. and Inoko, H. and Shiina, T. and Kaufman, J. and Salomonsen, J. and Skjoedt, K. and Wong, G. K. and Wang, J. and Liu, B. and Wang, J. and Yu, J. and Yang, H. and Nefedov, M. and Koriabine, M. and Dejong, P. J. and Goodstadt, L. and Webber, C. and Dickens, N. J. and Letunic, I. and Suyama, M. and Torrents, D. and von Mering, C. and Zdobnov, E. M. and Makova, K. and Nekrutenko, A. and Elnitski, L. and Eswara, P. and King, D. C. and Yang, S. and Tyekucheva, S. and Radakrishnan, A. and Harris, R. S. and Chiaromonte, F. and Taylor, J. and He, J. and Rijnkels, M. and Jones, Griffiths S. and Vidal, Ureta A. and Hoffman, M. M. and Severin, J. and Searle, S. M. and Law, A. S. and Speed, D. and Waddington, D. and Cheng, Z. and Tuzun, E. and Eichler, E. and Bao, Z. and Flicek, P. and Shteynberg, D. D. and Brent, M. R. and Bye, J. M. and Huckle, E. J. and Chatterji, S. and Dewey, C. and Pachter, L. and Kouranov, A. and Mourelatos, Z. and Hatzigeorgiou, A. G. and Paterson, A. H. and Ivarie, R. and Brandstrom, M. and Axelsson, E. and Backstrom, N. and Berlin, S. and Webster, M. T. and Pourquie, O. and Reymond, A. and Ucla, C. and Antonarakis, S. E. and Long, M. and Emerson, J. J. and Betr\'{a}n, E. and Dupanloup, I. and Kaessmann, H. and Hinrichs, A. S. and Bejerano, G. and Furey, T. S. and Harte, R. A. and Raney, B. and Siepel, A. and Kent, W. J. and Haussler, D. and Eyras, E. and Castelo, R. and Abril, J. F. and Castellano, S. and Camara, F. and Parra, G. and Guigo, R. and Bourque, G. and Tesler, G. and Pevzner, P. A. and Smit, A. and Fulton, L. A. and Mardis, E. R. and Wilson, And R. K. }, citeulike-article-id = {444856}, doi = {http://dx.doi.org/10.1038/nature03154}, issn = {1476-4687}, journal = {Nature}, keywords = {bird, chicken, comparative\_genomics, genome, sequence, whole\_genome}, month = {December}, number = {7018}, pages = {695--716}, posted-at = {2005-12-19 22:25:32}, priority = {5}, title = {Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.}, url = {http://dx.doi.org/10.1038/nature03154}, volume = {432}, year = {2004} }

RIS record

TY - JOUR ID - hillier04 L3 - citeulike-article-id:444856 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. IS - 7018 JF - Nature SN - 1476-4687 AD - Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. EP - 716 TI - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. VL - 432 SP - 695 KW - bird KW - chicken KW - comparative_genomics KW - genome KW - sequence KW - whole_genome 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, MA 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 - Maher, Randall AU - Smith, SM AU - Wallis, JW AU - Yang, SP 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, RP 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, MD AU - Davies, RM AU - Francis, MD AU - Humphray, SJ AU - Scott, CE AU - Taylor, RG AU - Tickle, C AU - Brown, WR 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, GK AU - Wang, J AU - Liu, B AU - Wang, J AU - Yu, J AU - Yang, H 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, J AU - Rijnkels, M AU - Jones, Griffiths AU - Vidal, Ureta AU - Hoffman, MM AU - Severin, J AU - Searle, SM AU - Law, AS AU - Speed, D AU - Waddington, D AU - Cheng, Z AU - Tuzun, E AU - Eichler, E AU - Bao, Z 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, M 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, And PY - 2004/December/09/ UR - http://dx.doi.org/10.1038/nature03154 ER -

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