Article

Nature 432, 695-716 (9 December 2004) | doi:10.1038/nature03154; Received 19 July 2004; Accepted 1 November 2004

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

LaDeana W. Hillier1, Webb Miller2, Ewan Birney3, Wesley Warren1, Ross C. Hardison2, Chris P. Ponting4, Peer Bork5,6, David W. Burt7, Martien A. M. Groenen8, Mary E. Delany9, Jerry B. Dodgson10, Genome fingerprint map, sequence and assembly:, Asif T. Chinwalla1, Paul F. Cliften1, Sandra W. Clifton1, Kimberly D. Delehaunty1, Catrina Fronick1, Robert S. Fulton1, Tina A. Graves1, Colin Kremitzki1, Dan Layman1, Vincent Magrini1, John D. McPherson1, Tracie L. Miner, Patrick Minx1, William E. Nash1, Michael N. Nhan1, Joanne O. Nelson1, Lachlan G. Oddy1, Craig S. Pohl1, Jennifer Randall-Maher1, Scott M. Smith1, John W. Wallis1, Shiaw-Pyng Yang1, Mapping :, Michael N. Romanov10, Catherine M. Rondelli10, Bob Paton7, Jacqueline Smith7, David Morrice7, Laura Daniels9, Helen G. Tempest11, Lindsay Robertson11, Julio S. Masabanda11, Darren K. Griffin11, Alain Vignal12, Valerie Fillon12, Lina Jacobbson13, Susanne Kerje13, Leif Andersson13, Richard P. M. Crooijmans8, Jan Aerts8, Jan J. van der Poel8, Hans Ellegren14, cDNA sequencing:, Randolph B. Caldwell15, Simon J. Hubbard16, Darren V. Grafham17, Andrzej M. Kierzek18, Stuart R. McLaren17, Ian M. Overton16, Hiroshi Arakawa15, Kevin J. Beattie19, Yuri Bezzubov15, Paul E. Boardman16, James K. Bonfield17, Michael D. R. Croning17, Robert M. Davies17, Matthew D. Francis17, Sean J. Humphray17, Carol E. Scott17, Ruth G. Taylor17, Cheryll Tickle19, William R. A. Brown20, Jane Rogers17, Jean-Marie Buerstedde15, Stuart A. Wilson21, Other sequencing and libraries:, Lisa Stubbs22, Ivan Ovcharenko22, Laurie Gordon22, Susan Lucas23, Marcia M. Miller24, Hidetoshi Inoko25, Takashi Shiina25, Jim Kaufman26, Jan Salomonsen27, Karsten Skjoedt28, Gane Ka-Shu Wong29,30,31, Jun Wang29,30, Bin Liu29, Jian Wang29,30, Jun Yu29,30, Huanming Yang29,30, Mikhail Nefedov32, Maxim Koriabine32, Pieter J. deJong32, Analysis and annotation:, Leo Goodstadt4, Caleb Webber4, Nicholas J. Dickens4, Ivica Letunic6, Mikita Suyama6, David Torrents6, Christian von Mering6, Evgeny M. Zdobnov6, Kateryna Makova2, Anton Nekrutenko2, Laura Elnitski2, Pallavi Eswara2, David C. King2, Shan Yang2, Svitlana Tyekucheva2, Anusha Radakrishnan2, Robert S. Harris2, Francesca Chiaromonte2, James Taylor2, Jianbin He2, Monique Rijnkels33, Sam Griffiths-Jones17, Abel Ureta-Vidal3, Michael M. Hoffman3, Jessica Severin3, Stephen M. J. Searle17, Andy S. Law7, David Speed7, Dave Waddington7, Ze Cheng34, Eray Tuzun34, Evan Eichler34, Zhirong Bao34, Paul Flicek35, David D. Shteynberg35, Michael R. Brent35, Jacqueline M. Bye17, Elizabeth J. Huckle17, Sourav Chatterji36, Colin Dewey36, Lior Pachter36, Andrei Kouranov37, Zissimos Mourelatos37, Artemis G. Hatzigeorgiou37, Andrew H. Paterson38, Robert Ivarie38, Mikael Brandstrom14, Erik Axelsson14, Niclas Backstrom14, Sofia Berlin14, Matthew T. Webster14, Olivier Pourquie39, Alexandre Reymond40, Catherine Ucla40, Stylianos E. Antonarakis40, Manyuan Long41, J. J. Emerson41, Esther Betrán42, Isabelle Dupanloup43, Henrik Kaessmann43, Angie S. Hinrichs44, Gill Bejerano44, Terrence S. Furey44, Rachel A. Harte44, Brian Raney44, Adam Siepel13, W. James Kent44, David Haussler44,45, Eduardo Eyras46, Robert Castelo46, Josep F. Abril46, Sergi Castellano46, Francisco Camara46, Genis Parra46, Roderic Guigo46, Guillaume Bourque47, Glenn Tesler48, Pavel A. Pevzner49, Arian Smit50, Project management:, Lucinda A. Fulton1, Elaine R. Mardis1 & Richard K. Wilson1 for International Chicken Genome Sequencing Consortium

  1. Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA;
  2. 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, University Park, Pennsylvania 16802, USA;
  3. EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK;
  4. MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK;
  5. Max-Delbrueck-Center for Molecular Medicine, 13025 Berlin, Robert-Roessle-Strasse 10, Germany;
  6. EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany;
  7. Genomics and Genetics and Bioinformatics, Roslin Institute (Edinburgh), Midlothian EH25 9PS, UK;
  8. Animal Breeding and Genetics Group, Wageningen University, Marijkeweg 40, 6709PG Wageningen, The Netherlands;
  9. Department of Animal Science, 2131D Meyer Hall, One Shields Avenue, University of California, Davis, California 95616, USA;
  10. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA;
  11. Cell and Chromosome Biology Group, Department of Biological Sciences, Brunel University, Uxbridge, Middlesex UB8 3PH, UK;
  12. Laboratoire de Genetique Cellulaire, Centre INRA de Toulouse, BP 27 Auzeville, 31326 Castanet Tolosan, France;
  13. Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Center, Box 597, SE-751 24 Uppsala, Sweden;
  14. Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvegen 18D, SE-752 36 Uppsala, Sweden;
  15. Institut fuer Molekulare Strahlenbiologie, GSF–Forschungszentrum, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany;
  16. Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester, M60 1QD, UK;
  17. The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK;
  18. Laboratory of Systems Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland;
  19. Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD15EH, UK;
  20. Institute of Genetics, Nottingham University, Queen's Medical Centre, Nottingham NG7 2UH, UK;
  21. Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK;
  22. EEBI Division and Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA;
  23. DOE Joint Genome Institute, Walnut Creek, California 94598, USA;
  24. Division of Molecular Biology, Beckman Research Institute, City of Hope National Medical Center, 1450 E. Duarte Road, Duarte, California 91010, USA;
  25. Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1143, Japan;
  26. Institute for Animal Health, Compton, Berkshire RG20 7NN, UK;
  27. The Royal Veterinary and Agricultural University, Department of Veterinary Pathobiology, Laboratory of Immunology, Stigboejlen 7, Frederiksberg, Copenhagen DK-1870, Denmark;
  28. Department of Immunology and Medical Microbiology, University of Odense, Winslovparken 19, Odense, Copenhagen DK-5000, Denmark;
  29. Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China;
  30. James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou Genomics Institute, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China;
  31. Genome Center, Department of Medicine, University of Washington, Seattle, Washington 98195, USA;
  32. Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, California 94609, USA;
  33. Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Street, Houston, Texas 77030-2600, USA;
  34. Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA;
  35. Laboratory for Computational Genomics, Campus Box 1045, Washington University, St Louis, Missouri 63130, USA;
  36. Departments of Computer Science and Mathematics, U.C. Berkeley, Berkeley, California 94720-3840, USA;
  37. Center for Bioinformatics, Departments of Genetics and Pathology, University of Pennsylvania, Medical School, Philadelphia, Pennsylvania 19104-6021, USA;
  38. Plant Genome Mapping Laboratory and Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
  39. Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA;
  40. Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland;
  41. Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA;
  42. Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA;
  43. Center for Integrative Genomics, BEP, University of Lausanne, CH-1015 Lausanne, Switzerland;
  44. UCSC Genome Bioinformatics Group, Center for Biomolecular Science & Engineering, Mailstop SOE, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA;
  45. Howard Hughes Medical Institute, Center for Biomolecular Science & Engineering, Mailstop SOE, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA;
  46. Grup de Recerca en Informatica Biomedica, Institut Municipal d'Investigacio Medica, Universitat Pompeu Fabra, and Programa de Bioinfomatica i Genomica, Centre de Regulacio Genomica, C/Dr. Aiguader 80, 08003 Barcelona, Catalonia, Spain;
  47. Genome Institute of Singapore, 60 Biopolis Street, 02-01 Genome, 138672, Singapore;
  48. University of California, San Diego, Department of Mathematics, 9500 Gilman Drive, La Jolla, California 92093-0112, USA;
  49. University of California, San Diego, Department of Computer Science and Engineering, 9500 Gilman Drive, La Jolla, California 92093-0114, USA;
  50. Computational Biology Group, The Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA

Top

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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