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

Hillier, LaDeana W. and Pachter, Lior (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432 (7018). pp. 695-716. ISSN 0028-0836.

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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.

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Pachter, Lior0000-0002-9164-6231
Additional Information:© 2004 Macmillan Publishers Limited. Received 19 July 2004; Accepted 1 November 2004. The Gallus gallus sequence and map generation at Washington University School of Medicine's Genome Sequencing Center was supported by grants from the National Human Genome Research Institute (NHGRI). For work from other groups, we acknowledge the support of the Biotechnology and Biological Sciences Research Council, Center for Integrative Genomics Funds, Childcare and Lejeune Foundations, Chinese Academy of Sciences and Ministry of Science and Technology, Department of Energy, Desiree and Niels Yde Foundation, European Union, European Molecular Biology Laboratory, Fonds Quebeçois de la Recherche sur la Nature et les Technologies, Howard Hughes Medical Institute, National Institute for Diabetes and Digestive and Kidney Diseases, NHGRI, National Institutes of Health, National Natural Science Foundation of China, National Science Foundation, Novo Nordisk Foundation, Stowers Institute for Medical Research, Swedish Research Council, Swiss NCCR Frontiers in Genetics, Swiss National Science Foundation, USDA/CSREES National Research Initiative, USDA/CSREES National Animal Genome Research Program, Wallenberg Consortium North and the AgriFunGen program at the Swedish University of Agricultural Sciences, UK Medical Research Council, University of California Presidential Chair Fund, University of Pennsylvania Genomics Institute Award, University of Texas at Arlington, and the Wellcome Trust. Resources for exploring the sequence and annotation data are available on browser displays available at Ensembl (, UCSC ( and the NCBI ( We thank R. Waterston for advice regarding the manuscript. Correspondence and requests for materials should be addressed to R.K.W. (Email: This G. gallus whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the project accession number AADN00000000. The version described in this paper is the first version, AADN01000000.
Errata:In Table 5 of this Article, the last four values listed in the 'Copy number' column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper.
Funding AgencyGrant Number
National Human Genome Research InstituteUNSPECIFIED
Biotechnology and Biological Sciences Research Council (BBSRC)UNSPECIFIED
Center for Integrative Genomics FundsUNSPECIFIED
ChildCare FoundationUNSPECIFIED
Lejeune FoundationUNSPECIFIED
Chinese Academy of SciencesUNSPECIFIED
Ministry of Science and Technology (China)UNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
Desiree and Niels Yde FoundationUNSPECIFIED
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
Fonds Quebeçois de la Recherche sur la Nature et les Technologies (FQRNT)UNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
National Institute for Diabetes and Digestive and Kidney DiseasesUNSPECIFIED
National Natural Science Foundation of ChinaUNSPECIFIED
Novo Nordisk FoundationUNSPECIFIED
Stowers Institute for Medical ResearchUNSPECIFIED
Swedish Research CouncilUNSPECIFIED
Swiss NCCR Frontiers in GeneticsUNSPECIFIED
Swiss National Science Foundation (SNSF)UNSPECIFIED
U.S. Department of AgricultureUNSPECIFIED
Swedish University of Agricultural SciencesUNSPECIFIED
Medical Research Council (UK)UNSPECIFIED
University of CaliforniaUNSPECIFIED
University of PennsylvaniaUNSPECIFIED
University of Texas at ArlingtonUNSPECIFIED
Issue or Number:7018
Record Number:CaltechAUTHORS:20170308-130340353
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74905
Deposited By: George Porter
Deposited On:08 Mar 2017 21:44
Last Modified:24 Feb 2020 10:30

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