Article

Nature 428, 493-521 (1 April 2004) | doi:10.1038/nature02426; Received 31 December 2003; Accepted 20 February 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Rat Genome Sequencing Project Consortium for (Participants are arranged under area of contribution, and then by institution.), Richard A. Gibbs (Co-principal Investigator)1, George M. Weinstock (Principal Investigator)1, Michael L. Metzker1, Donna M. Muzny1, Erica J. Sodergren1, Steven Scherer1, Graham Scott1, David Steffen1, Kim C. Worley1, Paula E. Burch1, Geoffrey Okwuonu1, Sandra Hines1, Lora Lewis1, Christine DeRamo1, Oliver Delgado1, Shannon Dugan-Rocha1, George Miner1, Margaret Morgan1, Alicia Hawes1, Rachel Gill1, Celera, Robert A. Holt (Principal Investigator)2,3, Mark D. Adams3,4, Peter G. Amanatides3,5, Holly Baden-Tillson3,6, Mary Barnstead3,7, Soo Chin3, Cheryl A. Evans3, Steve Ferriera3,8, Carl Fosler3, Anna Glodek3,9, Zhiping Gu3, Don Jennings3, Cheryl L. Kraft3,10, Trixie Nguyen3, Cynthia M. Pfannkoch3,6, Cynthia Sitter3,11, Granger G. Sutton3, J. Craig Venter3,8 & Trevor Woodage3 for DNA sequencing: Baylor College of Medicine, Douglas Smith (Principal Investigator)12,13, Hong-Mei Lee12, Erik Gustafson12,13, Patrick Cahill12, Arnold Kana12, Lynn Doucette-Stamm12,13, Keith Weinstock12 & Kim Fechtel12 for Genome Therapeutics, Robert B. Weiss (Principal Investigator)14 & Diane M. Dunn14 for University of Utah, Eric D. Green15, Robert W. Blakesley15 & Gerard G. Bouffard15 for NISC Comparative Sequencing Program, NHGRI, Pieter J. de Jong (Principal Investigator)16, Kazutoyo Osoegawa16 & Baoli Zhu16 for BAC library production: Children's Hospital Oakland Research Institute, Marco Marra (Principal Investigator)2, Jacqueline Schein (Principal Investigator)2, Ian Bosdet2, Chris Fjell2, Steven Jones2, Martin Krzywinski2, Carrie Mathewson2, Asim Siddiqui2 & Natasja Wye2 for BAC fingerprinting: British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, John McPherson1,17 for Genome Sequencing Center, Washington University School of Medicine, Shaying Zhao (Principal Investigator)18, Claire M. Fraser18, Jyoti Shetty18, Sofiya Shatsman18, Keita Geer18, Yixin Chen18, Sofyia Abramzon18 & William C. Nierman18 for BAC end sequencing: TIGR, Richard A. Gibbs (Principal Investigator)1, George M. Weinstock (Principal Investigator)1, Paul H. Havlak1, Rui Chen1, K. James Durbin1, Amy Egan1, Yanru Ren1, Xing-Zhi Song1, Bingshan Li1, Yue Liu1 & Xiang Qin1 for Sequence assembly: Baylor College of Medicine, Simon Cawley19 for Analysis and annotation: Affymetrix, George M. Weinstock (Coordinator)1, Kim C. Worley (Overall Coordinator)1, A. J. Cooney20, Richard A. Gibbs1, Lisa M. D'Souza1, Kirt Martin1, Jia Qian Wu1, Manuel L. Gonzalez-Garay1, Andrew R. Jackson1, Kenneth J. Kalafus1,58, Michael P. McLeod1, Aleksandar Milosavljevic1, Davinder Virk1, Andrei Volkov1, David A. Wheeler1 & Zhengdong Zhang1 for Baylor College of Medicine, Jeffrey A. Bailey4, Evan E. Eichler4 & Eray Tuzun4 for Case Western Reserve University, Ewan Birney21, Emmanuel Mongin21, Abel Ureta-Vidal21 & Cara Woodwark21 for EBI, Wellcome Trust Genome Campus, Evgeny Zdobnov22, Peer Bork22,23, Mikita Suyama22 & David Torrents22 for EMBL, Heidelberg, Marina Alexandersson24 for Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Barbara J. Trask25 & Janet M. Young25 for Fred Hutchinson Cancer Research Center, Douglas Smith (Principal Investigator)12,13, Hui Huang12, Kim Fechtel12, Huajun Wang12, Heming Xing12 & Keith Weinstock12 for Genome Therapeutics, Sue Daniels26, Darryl Gietzen26, Jeanette Schmidt26, Kristian Stevens26, Ursula Vitt26 & Jim Wingrove26 for Incyte Corporation, Francisco Camara27, M. Mar Albà27, Josep F. Abril27 & Roderic Guigo27 for Institut Municipal d'Investigacio Medica, Barcelona>, Arian Smit28 for The Institute for Systems Biology, Inna Dubchak29,30, Edward M. Rubin29,30, Olivier Couronne29,30 & Alexander Poliakov29 for Lawrence Berkeley National Laboratory, Norbert Hübner23, Detlev Ganten23, Claudia Goesele23,31, Oliver Hummel23,31, Thomas Kreitler23,31, Young-Ae Lee23, Jan Monti23, Herbert Schulz23 & Heike Zimdahl23 for Max Delbrück Center for Molecular Medicine, Heinz Himmelbauer31 & Hans Lehrach31 for Max Planck Institute for Molecular Genetics, Berlin, Howard J. Jacob (Principal Investigator)32, Susan Bromberg33, Jo Gullings-Handley32, Michael I. Jensen-Seaman32, Anne E. Kwitek32, Jozef Lazar32, Dean Pasko33, Peter J. Tonellato32 & Simon Twigger32 for Medical College of Wisconsin, Chris P. Ponting (Leader, Genes and Proteins Analysis Group)34, Jose M. Duarte34, Stephen Rice34, Leo Goodstadt34, Scott A. Beatson34, Richard D. Emes34, Eitan E. Winter34 & Caleb Webber34 for MRC Functional Genetics Unit, University of Oxford, Petra Brandt35 & Gerald Nyakatura35 for MWG-Biotech, Margaret Adetobi36, Francesca Chiaromonte36, Laura Elnitski36, Pallavi Eswara36, Ross C. Hardison36, Minmei Hou36, Diana Kolbe36, Kateryna Makova36, Webb Miller36, Anton Nekrutenko36, Cathy Riemer36, Scott Schwartz36, James Taylor36, Shan Yang36 & Yi Zhang36 for Pennsylvania State University, Klaus Lindpaintner37 for Roche Genetics and Roche Center for Medical Genomics, T. Dan Andrews38, Mario Caccamo38, Michele Clamp38, Laura Clarke38, Valerie Curwen38, Richard Durbin38, Eduardo Eyras38 & Stephen M. Searle38 for Sanger Institute, Gregory M. Cooper (Co-Leader, Evolutionary Analysis Group)39, Serafim Batzoglou40, Michael Brudno40, Arend Sidow39 & Eric A. Stone39 for Stanford University, J. Craig Venter3,8 for The Center for the Advancement of Genomics, Bret A. Payseur41 for University of Arizona, Guillaume Bourque42 for Université de Montréal, Carlos López-Otín43 & Xose S. Puente43 for Universidad de Oviedo, Kushal Chakrabarti44, Sourav Chatterji44, Colin Dewey44, Lior Pachter45, Nicolas Bray45, Von Bing Yap45 & Anat Caspi46 for University of California, Berkeley, Glenn Tesler47 & Pavel A. Pevzner48 for University of California, San Diego, David Haussler (Co-Leader, Evolutionary Analysis Group)49, Krishna M. Roskin50, Robert Baertsch50, Hiram Clawson50, Terrence S. Furey50, Angie S. Hinrichs50, Donna Karolchik50, William J. Kent50, Kate R. Rosenbloom50, Heather Trumbower50 & Matt Weirauch36,50 for University of California, Santa Cruz, David N. Cooper51 & Peter D. Stenson51 for University of Wales College of Medicine, Bin Ma52 for University of Western Ontario, Michael Brent53, Manimozhiyan Arumugam53 & David Shteynberg53 for Washington University, Richard R. Copley54 & Martin S. Taylor54 for Wellcome Trust Centre for Human Genetics, University of Oxford, Harold Riethman55 & Uma Mudunuri55 for The Wistar Institute, Jane Peterson56, Mark Guyer56, Adam Felsenfeld56, Susan Old57, Stephen Mockrin57 & Francis Collins56 for Scientific management: & for

  1. Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA <http://www.hgsc.bcm.tmc.edu>;
  2. British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada <http://www.bcgsc.ca>;
  3. Celera, 45 West Gude Drive, Rockville, Maryland 20850, USA;
  4. Department of Genetics and the Center for Computational Genomics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA;
  5. DSM Pharmaceuticals Inc., 5900 NW Greenville Blvd, Greenville, North Carolina 27834, USA;
  6. The Institute for Biological Energy Alternatives (IBEA), 1901 Research Blvd, Rockville, Maryland 20850, USA;
  7. Intronn, Inc., 910 Clopper Road, South Building, Gaithersburg, Maryland 20878, USA;
  8. The Center for the Advancement of Genomics (TCAG), 1901 Research Blvd, Suite 600, Rockville, Maryland 20850, USA;
  9. Avalon Pharmaceuticals, 20358 SenecaMeadows Parkway, Germantown, Maryland 20876, USA;
  10. Basic Immunology Branch, Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, DHHS, 6610 Rockledge Blvd, Room 3005, Bethesda, Maryland 20892-7612, USA;
  11. DynPort Vaccine Company, LLC, 64 Thomas Jefferson Drive, Frederick, Maryland 21702, USA;
  12. Genome Therapeutics Corporation, 100 Beaver Street, Waltham, Massachusetts 02453, USA;
  13. Agencourt Bioscience Corporation, 100 Cummings Center, Beverly, Massachusetts 01915, USA;
  14. Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA;
  15. NIH Intramural Sequencing Center (NISC) and Genome Technology Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, Maryland 20892, USA;
  16. BACPAC Resources, Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, California 94609, USA <http://bacpac.chori.org>;
  17. Genome Sequencing Centre, Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, Missouri 63108, USA <http://genome.wustl.edu>;
  18. The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, Maryland 20850, USA<http://www.tigr.org>;
  19. Affymetrix, 6550 Vallejo St, Suite 100, Emeryville, California 94608, USA;
  20. Department of Cell Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA;
  21. EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK;
  22. EMBL, Meyerhofstrasse 1, Heidelberg 69117, Germany;
  23. Max Delbrück Center for Molecular Medicine (MDC), Experimental Genetics of Cardiovascular Disease, Robert-Rössle-Strasse 10, Berlin 13125, Germany <http://www.mdc-berlin.de/ratgenome/>;
  24. Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Chalmers Science Park, S-412 88 Gothenburg, Sweden;
  25. Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., C3-168, Seattle, Washington 98109, USA <http://www.fhcrc.org/labs/trask/>;
  26. Incyte Corporation, 3160 Porter Drive, Palo Alto, California 94304, USA <http://www.incyte.com>;
  27. Grup de Recerca en Informàtica Biomèdia, 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;
  28. Computational Biology Group, The Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA;
  29. Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA <http://www.lbl.gov>;
  30. US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA <http://jgi.doe.gov>;
  31. Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany;
  32. Human and Molecular Genetics Center, Bioinformatics Research Center, and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA;
  33. Rat Genome Database, Bioinformatics Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA;
  34. MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK;
  35. MWG-Biotech, Anzinger Strasse 7a, Ebersberg 85560, Germany;
  36. Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, 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;
  37. Roche Genetics and Roche Center for Medical Genomics, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland;
  38. Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK;
  39. Departments of Pathology and Genetics, Stanford University, Stanford, California 94305, USA;
  40. S256 James H. Clark Center, Department of Computer Science, Stanford University, Stanford, California 94305, USA;
  41. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA;
  42. Centre de Recherches Mathématiques, Université de Montréal, 2920 Chemin de la tour, Montréal, Quebec H3T 1J8, Canada <http://www.crm.umontreal.ca>;
  43. Departamento de Bioquimica y Biologia Molecular, Instituto Universitario de Oncologia, Universidad de Oviedo, 33006 Oviedo, Spain <http://web.uniovi.es/degradome>;
  44. Department of Electrical Engineering and Computer Science, University of California Berkeley, Berkeley, California 94720, USA;
  45. Department of Mathematics, University of California Berkeley, Berkeley, California 94720, USA;
  46. Bioengineering Graduate Group, University of California Berkeley, Berkeley, California 94720, USA;
  47. University of California, San Diego, Department of Mathematics, 9500 Gilman Drive, San Diego, California 92093-0112, USA <http://www-cse.ucsd.edu/groups/bioinformatics>;
  48. University of California, San Diego, Department of Computer Science and Engineering, 9500 Gilman Drive, San Diego, California 92093-0114, USA <http://www-cse.ucsd.edu/groups/bioinformatics>;
  49. 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;
  50. UCSC Genome Bioinformatics Group, Center for Biomolecular Science and Engineering, Mailstop SOE, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA;
  51. Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, CF14 4XN, UK;
  52. Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B7, Canada;
  53. Laboratory for Computational Genomics, Campus Box 1045, Washington University, St Louis, Missouri 63130, USA, <http://genes.cse.wustl.edu>;
  54. Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK;
  55. The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsyvania 19104, USA;
  56. US National Institutes of Health, National Human Genome Research Institute, 31 Center Drive, Bethesda, Maryland 20892, USA;
  57. US National Institutes of Health, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, USA;
  58. Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA

Correspondence to: Email: agibbs@bcm.tmc.edu
The genomic sequence is available under accession numbers AABR03000000 to AABR03137910 in the international sequence databases (GenBank, DDBJ and EMBL).

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The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

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