Initial sequencing and comparative analysis of the mouse genome

doi:doi:10.1038/nature01262

Nature 420, 520-562 (5 December 2002) | doi:10.1038/nature01262; Received 18 September 2002; Accepted 31 October 2002

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing ConsortiumAsif T. Chinwalla^1,⁴⁷, Lisa L. Cook¹, Kimberly D. Delehaunty¹, Ginger A. Fewell¹, Lucinda A. Fulton^1,⁴⁷, Robert S. Fulton¹, Tina A. Graves¹, LaDeana W. Hillier^1,⁴⁷, Elaine R. Mardis¹, John D. McPherson¹, Tracie L. Miner¹, William E. Nash¹, Joanne O. Nelson¹, Michael N. Nhan¹, Kymberlie H. Pepin¹, Craig S. Pohl¹, Tracy C. Ponce¹, Brian Schultz¹, Johanna Thompson¹, Evanne Trevaskis¹, Robert H. Waterston^1,⁴⁷, Michael C. Wendl¹, Richard K. Wilson¹ & Shiaw-Pyng Yang^1,⁴⁷ for Genome Sequencing Center:, Peter An², Eric Berry^2,⁴⁷, Bruce Birren², Toby Bloom², Daniel G. Brown^2,^15,⁴⁷, Jonathan Butler^2,⁴⁷, Mark Daly^2,⁴⁷, Robert David², Justin Deri², Sheila Dodge², Karen Foley², Diane Gage², Sante Gnerre^2,⁴⁷, Timothy Holzer², David B. Jaffe^2,⁴⁷, Michael Kamal^2,⁴⁷, Elinor K. Karlsson^2,⁴⁷, Cristyn Kells², Andrew Kirby^2,⁴⁷, Edward J. Kulbokas, III^2,⁴⁷, Eric S. Lander^2,^46,⁴⁷, Tom Landers², J. P. Leger², Rosie Levine², Kerstin Lindblad-Toh^2,⁴⁷, Evan Mauceli^2,⁴⁷, John H. Mayer², Megan McCarthy², Jim Meldrim², Jim Meldrim², Jill P. Mesirov^2,⁴⁷, Robert Nicol², Chad Nusbaum², Steven Seaman², Ted Sharpe², Andrew Sheridan², Jonathan B. Singer^2,⁴⁷, Ralph Santos², Brian Spencer², Nicole Stange-Thomann², Jade P. Vinson^2,⁴⁷, Claire M. Wade^2,⁴⁷, Jamey Wierzbowski², Dudley Wyman² & Michael C. Zody^2,⁴⁷ for Whitehead Institute/MIT Center for Genome Research:, Ewan Birney^3,⁴⁷, Nick Goldman^3,⁴⁷, Arkadiusz Kasprzyk^3,⁴⁷, Emmanuel Mongin³, Alistair G. Rust³, Guy Slater^3,⁴⁷, Arne Stabenau^3,⁴⁷, Abel Ureta-Vidal³ & Simon Whelan^3,⁴⁷ for European Bioinformatics Institute:, Rachel Ainscough⁴, John Attwood⁴, Jonathon Bailey⁴, Karen Barlow⁴, Stephan Beck⁴, John Burton⁴, Michele Clamp^4,⁴⁷, Christopher Clee⁴, Alan Coulson⁴, James Cuff^4,⁴⁷, Val Curwen^4,⁴⁷, Tim Cutts^4,⁴⁷, Joy Davies⁴, Eduardo Eyras^4,⁴⁷, Darren Grafham⁴, Simon Gregory^4,⁴⁷, Tim Hubbard^4,⁴⁷, Adrienne Hunt⁴, Matthew Jones⁴, Ann Joy⁴, Steven Leonard⁴, Christine Lloyd⁴, Lucy Matthews⁴, Stuart McLaren⁴, Kirsten McLay⁴, Beverley Meredith⁴, James C. Mullikin^4,⁴⁷, Zemin Ning^4,⁴⁷, Karen Oliver⁴, Emma Overton-Larty⁴, Robert Plumb⁴, Simon Potter^4,⁴⁷, Michael Quail⁴, Jane Rogers⁴, Carol Scott⁴, Steve Searle^4,⁴⁷, Ratna Shownkeen⁴, Sarah Sims⁴, Melanie Wall⁴, Anthony P. West⁴, David Willey⁴ & Sophie Williams⁴ for Wellcome Trust Sanger Institute, Josep F. Abril^5,⁴⁷, Roderic Guigó^5,⁴⁷ & Genís Parra^5,⁴⁷ for Research Group in Biomedical Informatics, Pankaj Agarwal^6,⁴⁷ for Bioinformatics, Richa Agarwala⁷, Deanna M. Church^7,⁴⁷, Wratko Hlavina^7,⁴⁷, Donna R. Maglott^7,⁴⁷ & Victor Sapojnikov^7,⁴⁷ for National Center for Biotechnology Information, Marina Alexandersson^8,⁴⁷ & Lior Pachter^8,⁴⁷ for Department of Mathematics, Stylianos E. Antonarakis^9,⁴⁷, Emmanouil T. Dermitzakis^9,⁴⁷, Alexandre Reymond^9,⁴⁷ & Catherine Ucla^9,⁴⁷ for Division of Medical Genetics, Robert Baertsch^10,⁴⁷, Mark Diekhans^10,⁴⁷, Terrence S. Furey^10,⁴⁷, Angela Hinrichs^10,⁴⁷, Fan Hsu^10,⁴⁷, Donna Karolchik^10,⁴⁷, W. James Kent^10,⁴⁷, Krishna M. Roskin^10,⁴⁷, Matthias S. Schwartz^10,⁴⁷, Charles Sugnet^10,⁴⁷ & Ryan J. Weber^10,⁴⁷ for Center for Biomolecular Science and Engineering, Peer Bork^11,⁴⁷, Ivica Letunic^11,⁴⁷, Mikita Suyama^11,⁴⁷, David Torrents^11,⁴⁷ & Evgeny M. Zdobnov^11,⁴⁷ for EMBL, Marc Botcherby¹², Stephen D. Brown¹², Robert D. Campbell¹² & Ian Jackson¹² for UK MRC Mouse Sequencing Consortium, Nicolas Bray^13,⁴⁷, Olivier Couronne^13,⁴⁷, Inna Dubchak^13,⁴⁷, Alex Poliakov^13,⁴⁷ & Edward M. Rubin¹³ for Lawrence Berkeley National Laboratory, Michael R. Brent^14,⁴⁷, Paul Flicek^14,⁴⁷, Evan Keibler^14,⁴⁷ & Ian Korf^14,⁴⁷ for Department of Computer Science, S. Batalov¹⁵ for School of Computer Science, Carol Bult^16,⁴⁷ & Wayne N. Frankel^16,⁴⁷ for The Jackson Laboratory, Piero Carninci¹⁷, Yoshihide Hayashizaki¹⁷, Jun Kawai¹⁷ & Yasushi Okazaki¹⁷ for Laboratory for Genome Exploration, Simon Cawley^18,⁴⁷, David Kulp^18,⁴⁷ & Raymond Wheeler^18,⁴⁷ for Affymetrix Inc., Francesca Chiaromonte^19,⁴⁷ for Departments of Statistics and Health Evaluation Sciences, Francis S. Collins^20,⁴⁷, Adam Felsenfeld^20,⁴⁷, Mark Guyer²⁰, Jane Peterson²⁰ & Kris Wetterstrand²⁰ for National Human Genome Research Institute, Richard R. Copley^21,⁴⁷ & Richard Mott^21,⁴⁷ for Wellcome Trust Centre for Human Genetics, Colin Dewey^22,⁴⁷ for Department of Electrical Engineering, Nicholas J. Dickens^23,⁴⁷, Richard D. Emes^23,⁴⁷, Leo Goodstadt^23,⁴⁷, Chris P. Ponting^23,⁴⁷ & Eitan Winter^23,⁴⁷ for Department of Human Anatomy and Genetics, Diane M. Dunn²⁴, Andrew C. von Niederhausern²⁴ & Robert B. Weiss²⁴ for Department of Human Genetics, Sean R. Eddy^25,⁴⁷, L. Steven Johnson²⁵ & Thomas A. Jones²⁵ for Howard Hughes Medical Institute and Department of Genetics, Laura Elnitski^26,⁴⁷ & Diana L. Kolbe^26,⁴⁷ for Departments of Biochemistry and Molecular Biology and Computer Science and Engineering, Pallavi Eswara^27,⁴⁷, Webb Miller^27,⁴⁷, Michael J. O'Connor²⁷ & Scott Schwartz^27,⁴⁷ for Department of Computer Science and Engineering, Richard A. Gibbs²⁸ & Donna M. Muzny²⁸ for Baylor College of Medicine, Gustavo Glusman^29,⁴⁷ & Arian Smit^29,⁴⁷ for The Institute for Systems Biology, Eric D. Green^30,⁴⁷ for National Human Genome Research Institute, Ross C. Hardison^31,⁴⁷ & Shan Yang³¹ for Department of Biochemistry and Molecular Biology, David Haussler^32,⁴⁷ for Howard Hughes Medical Institute, Axin Hua³³ & Bruce A. Roe³³ for Department of Chemistry and Biochemistry, Raju S. Kucherlapati³⁴ & Kate T. Montgomery³⁴ for Departments of Genetics and Medicine and Harvard-Partners Center for Genetics and Genomics, Jia Li^35,⁴⁷ for Department of Statistics, Ming Li^36,⁴⁷ for Department of Computer Science, Susan Lucas³⁷ for US DOE Joint Genome Institute, Bin Ma^38,⁴⁷ for Department of Computer Science, W. Richard McCombie³⁹ for Cold Spring Harbor Laboratory, Michael Morgan⁴⁰ for Wellcome Trust, Pavel Pevzner^41,⁴⁷ & Glenn Tesler^41,⁴⁷ for Department of Computer Science and Engineering, Jörg Schultz^42,⁴⁷ for Max Planck Institute for Molecular Genetics, Douglas R. Smith⁴³ for Genome Therapeutics Corporation, John Tromp^44,⁴⁷ for Bioinformatics Solutions Inc., Kim C. Worley^45,⁴⁷ for Department of Molecular and Human Genetics, Eric S. Lander^2,^46,⁴⁷ for Department of Biology & Josep F. Abril^5,⁴⁷, Pankaj Agarwal^6,⁴⁷, Marina Alexandersson^8,⁴⁷, Stylianos E. Antonarakis^9,⁴⁷, Robert Baertsch^10,⁴⁷, Eric Berry^2,⁴⁷, Ewan Birney^3,⁴⁷, Peer Bork^11,⁴⁷, Nicolas Bray^13,⁴⁷, Michael R. Brent^14,⁴⁷, Daniel G. Brown^2,^15,⁴⁷, Jonathan Butler^2,⁴⁷, Carol Bult^16,⁴⁷, Francesca Chiaromonte^19,⁴⁷, Asif T. Chinwalla^1,⁴⁷, Deanna M. Church^7,⁴⁷, Michele Clamp^4,⁴⁷, Francis S. Collins^20,⁴⁷, Richard R. Copley^21,⁴⁷, Olivier Couronne^13,⁴⁷, Simon Cawley^18,⁴⁷, James Cuff^4,⁴⁷, Val Curwen^4,⁴⁷, Tim Cutts^4,⁴⁷, Mark Daly^2,⁴⁷, Emmanouil T. Dermitzakis^9,⁴⁷, Colin Dewey^22,⁴⁷, Nicholas J. Dickens^23,⁴⁷, Mark Diekhans^10,⁴⁷, Inna Dubchak^13,⁴⁷, Sean R. Eddy^25,⁴⁷, Laura Elnitski^26,⁴⁷, Richard D. Emes^23,⁴⁷, Pallavi Eswara^27,⁴⁷, Eduardo Eyras^4,⁴⁷, Adam Felsenfeld^20,⁴⁷, Paul Flicek^14,⁴⁷, Wayne N. Frankel^16,⁴⁷, Lucinda A. Fulton^1,⁴⁷, Terrence S. Furey^10,⁴⁷, Sante Gnerre^2,⁴⁷, Gustavo Glusman^29,⁴⁷, Nick Goldman^3,⁴⁷, Leo Goodstadt^23,⁴⁷, Eric D. Green^30,⁴⁷, Simon Gregory^4,⁴⁷, Roderic Guigó^5,⁴⁷, Ross C. Hardison^31,⁴⁷, David Haussler^32,⁴⁷, LaDeana W. Hillier^1,⁴⁷, Angela Hinrichs^10,⁴⁷, Wratko Hlavina^7,⁴⁷, Fan Hsu^10,⁴⁷, Tim Hubbard^4,⁴⁷, David B. Jaffe^2,⁴⁷, Michael Kamal^2,⁴⁷, Donna Karolchik^10,⁴⁷, Elinor K. Karlsson^2,⁴⁷, Arkadiusz Kasprzyk^3,⁴⁷, Evan Keibler^14,⁴⁷, W. James Kent^10,⁴⁷, Andrew Kirby^2,⁴⁷, Diana L. Kolbe^26,⁴⁷, Ian Korf^14,⁴⁷, Edward J. Kulbokas, III^2,⁴⁷, David Kulp^18,⁴⁷, Eric S. Lander^2,^46,⁴⁷, Ivica Letunic^11,⁴⁷, Ming Li^36,⁴⁷, Kerstin Lindblad-Toh^2,⁴⁷, Bin Ma^38,⁴⁷, Donna R. Maglott^7,⁴⁷, Evan Mauceli^2,⁴⁷, Jill P. Mesirov^2,⁴⁷, Webb Miller^27,⁴⁷, Richard Mott^21,⁴⁷, James C. Mullikin^4,⁴⁷, Zemin Ning^4,⁴⁷, Lior Pachter^8,⁴⁷, Genís Parra^5,⁴⁷, Pavel Pevzner^41,⁴⁷, Alex Poliakov^13,⁴⁷, Chris P. Ponting^23,⁴⁷, Simon Potter^4,⁴⁷, Alexandre Reymond^9,⁴⁷, Krishna M. Roskin^10,⁴⁷, Victor Sapojnikov^7,⁴⁷, Jörg Schultz^42,⁴⁷, Matthias S. Schwartz^10,⁴⁷, Scott Schwartz^27,⁴⁷, Steve Searle^4,⁴⁷, Jonathan B. Singer^2,⁴⁷, Guy Slater^3,⁴⁷, Arian Smit^29,⁴⁷, Arne Stabenau^3,⁴⁷, Charles Sugnet^10,⁴⁷, Mikita Suyama^11,⁴⁷, Glenn Tesler^41,⁴⁷, David Torrents^11,⁴⁷, John Tromp^44,⁴⁷, Catherine Ucla^9,⁴⁷, Jade P. Vinson^2,⁴⁷, Claire M. Wade^2,⁴⁷, Ryan J. Weber^10,⁴⁷, Raymond Wheeler^18,⁴⁷, Eitan Winter^23,⁴⁷, Shiaw-Pyng Yang^1,⁴⁷, Evgeny M. Zdobnov^11,⁴⁷, Robert H. Waterston^1,⁴⁷, Simon Whelan^3,⁴⁷, Kim C. Worley^45,⁴⁷ & Michael C. Zody^2,⁴⁷ for Members of the Mouse Genome Analysis Group

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The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

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Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA;
Whitehead Institute/MIT Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA;
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK;
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK;
Research Group in Biomedical Informatics, Institut Municipal d'Investigacio, Medica/Universitat Pompeu Fabra, Centre de Regulacio Genomica, Barcelona, Catalonia, Spain;
Bioinformatics, GlaxoSmithKline, UW2230, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA;
National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20892, USA;
Department of Mathematics, University of California at Berkeley, 970 Evans Hall, Berkeley, California 94720, USA;
Division of Medical Genetics, University of Geneva Medical School, 1 rue Michel-Servet, CH-1211 Geneva, Switzerland;
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA;
EMBL, Meyerhofstrasse 1, Heidelberg 69117, Germany;
UK MRC Mouse Sequencing Consortium, MRC Mammalian Genetics Unit, Harwell OX11 0RD, UK;
Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 84-171, Berkeley, California 94720, USA;
Department of Computer Science, Washington University, Box 1045, St Louis, Missouri 63130, USA;
School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada;
The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA;
Laboratory for Genome Exploration, RIKEN Genomic Sciences Center, Yokohama Institute, 1-7-22 Suchiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan;
Affymetrix Inc., Emeryville, California 94608, USA;
Departments of Statistics and Health Evaluation Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
National Human Genome Research Institute, National Institutes of Health, 31 Center Drive, Room 4B09, Bethesda, Maryland 20892, USA;
Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK;
Department of Electrical Engineering, University of California, Berkeley, 231 Cory Hall, Berkeley, California 94720, USA;
Department of Human Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, South Parks Road, Oxford OX1 3QX, UK;
Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA;
Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA;
Departments of Biochemistry and Molecular Biology and Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
Baylor College of Medicine, Human Genome Sequencing Center, One Baylor Plaza, MSC-226, Houston, Texas 77030, USA;
The Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA;
National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50, Room 5523, Bethesda, Maryland 20892, USA;
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA;
Department of Chemistry and Biochemistry, University of Oklahoma Advanced Center for Genome Technology, University of Oklahoma, 620 Parrington Oval, Room 311, Norman, Oklahoma 73019, USA;
Departments of Genetics and Medicine and Harvard-Partners Center for Genetics and Genomics, Harvard Medical School, Boston, Massachusetts 02115, USA;
Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
Department of Computer Science, University of California, Santa Barbara, California 93106, USA;
US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA;
Department of Computer Science, University of Western Ontario, London, Ontario N6A 5B7, Canada;
Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA;
Wellcome Trust, 183 Euston Road, London NW1 2BE, UK;
Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0114, USA;
Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany;
Genome Therapeutics Corporation, 100 Beaver Street, Waltham, Massachusetts 02453, USA;
Bioinformatics Solutions Inc., 145 Columbia Street W, Waterloo, Ontario N2L 3L2, Canada;
Department of Molecular and Human Genetics, Baylor College of Medicine, Mailstop BCM226, Room 1419.01, One Baylor Plaza, Houston, Texas 77030, USA;
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138, USA
Members of the Mouse Genome Analysis Group

Correspondence to: Correspondence and requests for materials should be addressed to R.H.W. (e-mail: Email: waterston@gs.washington.edu), K.L.T. (e-mail: Email: kersli@genome.wi.mit.edu) or E.S.L. (e-mail: Email: lander@genome.wi.mit.edu).
Authors' contributions: The following authors contributed to project leadership: R. H. Waterston, K. Lindblad-Toh, E. Birney, J. Rogers, M. R. Brent, F. S. Collins, R. Guigó, R. C. Hardison, D. Haussler, D. B. Jaffe, W. J. Kent, W. Miller, C. P. Ponting, A. Smit, M. C. Zody and E. S. Lander.

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Initial sequencing and comparative analysis of the mouse genome

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the mouse genome

Initial sequencing and comparative analysis of the mouse genome

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