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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2004-12-09

AUTHORS

LaDeana W. Hillier, Webb Miller, Ewan Birney, Wesley Warren, Ross C. Hardison, Chris P. Ponting, Peer Bork, David W. Burt, Martien A. M. Groenen, Mary E. Delany, Jerry B. Dodgson, Asif T. Chinwalla, Paul F. Cliften, Sandra W. Clifton, Kimberly D. Delehaunty, Catrina Fronick, Robert S. Fulton, Tina A. Graves, Colin Kremitzki, Dan Layman, Vincent Magrini, John D. McPherson, Tracie L. Miner, Patrick Minx, William E. Nash, Michael N. Nhan, Joanne O. Nelson, Lachlan G. Oddy, Craig S. Pohl, Jennifer Randall-Maher, Scott M. Smith, John W. Wallis, Shiaw-Pyng Yang, Michael N. Romanov, Catherine M. Rondelli, Bob Paton, Jacqueline Smith, David Morrice, Laura Daniels, Helen G. Tempest, Lindsay Robertson, Julio S. Masabanda, Darren K. Griffin, Alain Vignal, Valerie Fillon, Lina Jacobbson, Susanne Kerje, Leif Andersson, Richard P. M. Crooijmans, Jan Aerts, Jan J. van der Poel, Hans Ellegren, Randolph B. Caldwell, Simon J. Hubbard, Darren V. Grafham, Andrzej M. Kierzek, Stuart R. McLaren, Ian M. Overton, Hiroshi Arakawa, Kevin J. Beattie, Yuri Bezzubov, Paul E. Boardman, James K. Bonfield, Michael D. R. Croning, Robert M. Davies, Matthew D. Francis, Sean J. Humphray, Carol E. Scott, Ruth G. Taylor, Cheryll Tickle, William R. A. Brown, Jane Rogers, Jean-Marie Buerstedde, Stuart A. Wilson, Lisa Stubbs, Ivan Ovcharenko, Laurie Gordon, Susan Lucas, Marcia M. Miller, Hidetoshi Inoko, Takashi Shiina, Jim Kaufman, Jan Salomonsen, Karsten Skjoedt, Gane Ka-Shu Wong, Jun Wang, Bin Liu, Jian Wang, Jun Yu, Huanming Yang, Mikhail Nefedov, Maxim Koriabine, Pieter J. deJong, Leo Goodstadt, Caleb Webber, Nicholas J. Dickens, Ivica Letunic, Mikita Suyama, David Torrents, Christian von Mering, Evgeny M. Zdobnov, Kateryna Makova, Anton Nekrutenko, Laura Elnitski, Pallavi Eswara, David C. King, Shan Yang, Svitlana Tyekucheva, Anusha Radakrishnan, Robert S. Harris, Francesca Chiaromonte, James Taylor, Jianbin He, Monique Rijnkels, Sam Griffiths-Jones, Abel Ureta-Vidal, Michael M. Hoffman, Jessica Severin, Stephen M. J. Searle, Andy S. Law, David Speed, Dave Waddington, Ze Cheng, Eray Tuzun, Evan Eichler, Zhirong Bao, Paul Flicek, David D. Shteynberg, Michael R. Brent, Jacqueline M. Bye, Elizabeth J. Huckle, Sourav Chatterji, Colin Dewey, Lior Pachter, Andrei Kouranov, Zissimos Mourelatos, Artemis G. Hatzigeorgiou, Andrew H. Paterson, Robert Ivarie, Mikael Brandstrom, Erik Axelsson, Niclas Backstrom, Sofia Berlin, Matthew T. Webster, Olivier Pourquie, Alexandre Reymond, Catherine Ucla, Stylianos E. Antonarakis, Manyuan Long, J. J. Emerson, Esther Betrán, Isabelle Dupanloup, Henrik Kaessmann, Angie S. Hinrichs, Gill Bejerano, Terrence S. Furey, Rachel A. Harte, Brian Raney, Adam Siepel, W. James Kent, David Haussler, Eduardo Eyras, Robert Castelo, Josep F. Abril, Sergi Castellano, Francisco Camara, Genis Parra, Roderic Guigo, Guillaume Bourque, Glenn Tesler, Pavel A. Pevzner, Arian Smit, Lucinda A. Fulton, Elaine R. Mardis, Richard K. Wilson

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. More... »

PAGES

695-716

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  • Journal

    TITLE

    Nature

    ISSUE

    7018

    VOLUME

    432

    Author Affiliations

  • Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Avenue, Campus Box 8501, 63108, St Louis, Missouri, USA
  • Center for Comparative Genomics and Bioinformatics, Departments of Biology, Statistics, Biochemistry and Molecular Biology, Computer Science and Engineering, and Health Evaluation Sciences, The Pennsylvania State University, 16802, University Park, Pennsylvania, USA
  • EMBL-EBI, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
  • MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, OX1 3QX, Oxford, UK
  • EMBL, Meyerhofstrasse 1, 69012, Heidelberg, Germany
  • Genomics and Genetics and Bioinformatics, Roslin Institute (Edinburgh), EH25 9PS, Midlothian, UK
  • Animal Breeding and Genetics Group, Wageningen University, Marijkeweg 40, 6709PG, Wageningen, The Netherlands
  • Department of Animal Science, University of California, 2131D Meyer Hall, One Shields Avenue, 95616, Davis, California, USA
  • Department of Microbiology and Molecular Genetics, Michigan State University, 48824, East Lansing, Michigan, USA
  • Cell and Chromosome Biology Group, Department of Biological Sciences, Brunel University, UB8 3PH, Uxbridge, Middlesex, UK
  • Laboratoire de Genetique Cellulaire, Centre INRA de Toulouse, Auzeville, BP 27, 31326, Castanet Tolosan, France
  • Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Center, Box 597, SE-751 24, Uppsala, Sweden
  • Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvegen 18D, SE-752 36, Uppsala, Sweden
  • Institut fuer Molekulare Strahlenbiologie, GSF–Forschungszentrum, Ingolstaedter Landstrasse 1, D-85764, Neuherberg, Germany
  • Department of Biomolecular Sciences, UMIST, PO Box 88, M60 1QD, Manchester, UK
  • The Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA, Hinxton, Cambridgeshire, UK
  • Laboratory of Systems Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warszawa, Poland
  • Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
  • Institute of Genetics, Nottingham University, Queen's Medical Centre, NG7 2UH, Nottingham, UK
  • Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, S10 2TN, Sheffield, UK
  • EEBI Division and Genome Biology Division, Lawrence Livermore National Laboratory, 94550, Livermore, California, USA
  • DOE Joint Genome Institute, 94598, Walnut Creek, California, USA
  • Division of Molecular Biology, Beckman Research Institute, City of Hope National Medical Center, 1450 E. Duarte Road, 91010, Duarte, California, USA
  • Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, 259-1143, Isehara, Japan
  • Institute for Animal Health, RG20 7NN, Compton, Berkshire, UK
  • The Royal Veterinary and Agricultural University, Department of Veterinary Pathobiology, Laboratory of Immunology, Stigboejlen 7, DK-1870, Frederiksberg, Copenhagen, Denmark
  • Department of Immunology and Medical Microbiology, University of Odense, Winslovparken 19, DK-5000, Odense, Copenhagen, Denmark
  • Genome Center, Department of Medicine, University of Washington, 98195, Seattle, Washington, USA
  • James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou Genomics Institute, Key Laboratory of Bioinformatics of Zhejiang Province, 310007, Hangzhou, China
  • Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, 101300, Beijing, China
  • Children's Hospital Oakland Research Institute, 747 52nd Street, 94609, Oakland, California, USA
  • Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Street, 77030-2600, Houston, Texas, USA
  • Genome Sciences, University of Washington School of Medicine, 98195, Seattle, Washington, USA
  • Laboratory for Computational Genomics, Campus Box 1045, Washington University, 63130, St Louis, Missouri, USA
  • Departments of Computer Science and Mathematics, U.C. Berkeley, 94720-3840, Berkeley, California, USA
  • Center for Bioinformatics, Departments of Genetics and Pathology, University of Pennsylvania, Medical School, 19104-6021, Philadelphia, Pennsylvania, USA
  • Plant Genome Mapping Laboratory and Department of Genetics, University of Georgia, 30602, Athens, Georgia, USA
  • Stowers Institute for Medical Research, 1000 East 50th Street, 64110, Kansas City, Missouri, USA
  • Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211, Geneva, Switzerland
  • Department of Ecology and Evolution, University of Chicago, 60637, Chicago, Illinois, USA
  • Department of Biology, University of Texas at Arlington, 76019, Arlington, Texas, USA
  • Center for Integrative Genomics, BEP, University of Lausanne, CH-1015, Lausanne, Switzerland
  • UCSC Genome Bioinformatics Group, Center for Biomolecular Science & Engineering, Mailstop SOE, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, 95064, Santa Cruz, California, USA
  • Howard Hughes Medical Institute, Center for Biomolecular Science & Engineering, Mailstop SOE, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, 95064, Santa Cruz, California, USA
  • Programa de Bioinfomatica i Genomica, Centre de Regulacio Genomica, C/Dr. Aiguader 80, 08003, Barcelona, Catalonia, Spain
  • Genome Institute of Singapore, 60 Biopolis Street, 02-01138672, Genome, Singapore
  • Department of Mathematics, University of California, San Diego, 9500 Gilman Drive, 92093-0112, La Jolla, California, USA
  • Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, 92093-0114, La Jolla, California, USA
  • Computational Biology Group, The Institute for Systems Biology, 1441 North 34th Street, 98103, Seattle, Washington, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature03154

    DOI

    http://dx.doi.org/10.1038/nature03154

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1006367901

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/15592404


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