Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. [Erratum: 2005 Feb. 17, v. 433, no. 7027, p. 777.]

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 genomecomposed of approximately one billion base pairs of sequence an...

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Published in:	Nature (London) Vol. 432; no. 7018; pp. 695 - 716
Main Authors:	Hillier, L.W., Miller, W., Birney, E., Warren, Wesley, Hardison, R.C., Ponting, C.P., Bork, Peer, 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., Layman, D., Magrini, V., Mcpherson, J.D., Miner, T.L., Minx, P., Nash, W.E., Nhan, M.N., Nelson, J.O., Oddy, L.G., Pohl, C.S., Randall-Maher, J., Smith, S.M., Wallis, J.W., Yang, S.P., Romanov, M.N., Rondelli, C.M., Paton, B., Smith, J., Morrice, D., Daniels, L., Tempest, H.G., Robertson, L., Masabanda, J.S., Griffin, D.K., Vignal, Alain, Fillon, Valerie, Jacobbson, L., Kerje, S., Andersson, Leif, Crooijmans, R.P.M.A., Aerts, J., van Der Poel, J.J., Ellegren, H., Caldwell, R.B., Hubbard, S.J., Grafham, D.V., Kierzek, A.M., Mclaren, S.R., Overton, I.M., Arakawa, H., Beattie, K.J., Bezzubov, Y., Boardman, P.E., Bonfield, J.K., Croning, M.D.R., Davies, R.M., Francis, M.D., Humphray, S.J., Scott, C.E., Taylor, R.G., Tickle, C., Brown, W.R.A., Rogers, J., Buerstedde, J.M., Wilson, S.A., Stubbs, L., Ovcharenko, I., Gordon, Laurence, Lucas, S., Miller, M.M., Inoko, H., Shiina, T., Kaufman, Jim, Salomonsen, J., Skjoedt, K., Wong, G.K.S., Wang, J., Liu, B., Yu, J., Yang, H.M., Nefedov, M., Koriabine, M., Dejong, P.J., Goodstadt, L., Webber, C., Dickens, N.J., Letunic, I., Suyama, M., Torrents, D., von Mering, C., Zdobnov, E.M.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 09.12.2004 Nature Publishing Nature Publishing Group
Subjects:	alcohol-dehydrogenase Animals Avian Proteins - genetics Biologi Biological and medical sciences Biology Birds brown-norway rat Cell and molecular biology Cell- och molekylärbiologi Chickens Chickens - genetics Chromosomes Classical genetics, quantitative genetics, hybrids Comparative Study Conserved Sequence - genetics Dinosaurs DNA Transposable Elements - genetics Evolution Evolution, Molecular Fundamental and applied biological sciences. Psychology Gallus gallus Gene Duplication Gene expression genes Genes - genetics Genetic diversity Genetics Genetics of eukaryotes. Biological and molecular evolution Genetik Genome Genomics Humanities and Social Sciences Humans Life Sciences Long Interspersed Nucleotide Elements - genetics major histocompatibility complex mammalian evolution Mammals molecular sequence data mouse genome multidisciplinary Multigene Family - genetics Mutagenesis - genetics NATURAL SCIENCES NATURVETENSKAP non-coding RNA genes non-ltr retrotransposons nucleotide sequences olfactory receptor phylogenetic analysis Physical Chromosome Mapping protein-coding genes pseudogenes Pseudogenes - genetics recent segmental duplications repetitive sequences retrotransposons Retroviridae - genetics RNA, Untranslated - genetics Science Science (multidisciplinary) Sequence Analysis, DNA Short Interspersed Nucleotide Elements - genetics Synteny tissue-specific genes transposons Vertebrata Vertebrates Vertebrates - genetics Molecular evolution Vertebrata Nucleotide sequence Aves Genome Gallus gallus Research Support P.H.S RNA DNA Evolution Untranslated/genetics U.S. Gov't Sequence Analysis Molecular Non-U.S. Gov't Non-P.H.S
ISSN:	0028-0836, 1476-4687, 1476-4687
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Summary:	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 genomecomposed 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.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 content type line 23 ObjectType-Article-1 ObjectType-Feature-2
ISSN:	0028-0836 1476-4687 1476-4687
DOI:	10.1038/nature03154