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Initial sequencing and comparative analysis of the mouse genome

Waterston, Robert H. and Pachter, Lior (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420 (6915). pp. 520-562. ISSN 0028-0836. doi:10.1038/nature01262. https://resolver.caltech.edu/CaltechAUTHORS:20170309-090859678

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Abstract

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.


Item Type:Article
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http://dx.doi.org/10.1038/nature01262DOIArticle
http://www.nature.com/nature/journal/v420/n6915/abs/nature01262.htmlPublisherArticle
http://www.readcube.com/articles/10.1038/nature01262PublisherFree ReadCube access
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2002 Macmillan Publishers Limited. Received 18 September 2002; Accepted 31 October 2002. We thank J. Takahashi and M. Johnston for comments on the manuscript; the Mouse Liaison Group for strategic advice; L. Gaffney, D. Leja and K.-S. Toh for graphical help; B. Graham and G. Roberts for administrative work on sequencing of individual mouse BACs; and P. Kassos and M. McMurtry for secretarial assistance. We thank D. Hill and L. Corbani of the Mouse Genome Informatics Group for their contributions to the GO analysis for mouse and human, and the members of the Bork group at EMBL for discussions. Funding was provided by the National Institutes of Health (National Human Genome Research Institute, National Cancer Institute, National Institute of Dental and Craniofacial Research, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of General Medical Sciences, National Eye Institute, National Institute of Environmental Health Sciences, National Institute of Aging, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute on Deafness and Other Communication Disorders, National Institute of Mental Health, National Institute on Drug Abuse, National Center for Research Resources, the National Heart Lung and Blood Institute and The Fogarty International Center); the Wellcome Trust; the Howard Hughes Medical Institute; the United States Department of Energy; the National Science Foundation; the Medical Research Council; NSERC; BMBF (German Ministry for Research and Education); the European Molecular Biology Laboratory; Plan Nacional de I + D and Instituto Carlos III; Swiss National Science Foundation, NCCR Frontiers in Genetics, the Swiss Cancer League and the ‘Childcare’ and ‘J. Lejeune’ Foundations; and the Ministry of Education, Culture, Sports, Science and Technology of Japan. The initial threefold sequence coverage was partly supported by the Mouse Sequencing Consortium (GlaxoSmithKline, Merck and Affymetrix) through the Foundation for the National Institutes of Health. We acknowledge A. Holden for coordinating the Mouse Sequencing Consortium. We thank the Sanger Institute systems group for maintenance and provision of the computer resource. The MGSC also used Hewlett-Packard Company's BioCluster, a configuration of 27 HP AlphaServer ES40 systems with 100 CPUs and 1 terabyte of storage. The BioCluster is housed in Hewlett-Packard's IQ Solutions Center, and was accessed remotely. The computing resource greatly accelerated the analysis. 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. Availability of sequence and assembly data: Unprocessed sequence reads are available from the NCBI trace archive (ftp://ftp.ncbi.nih.gov/pub/TraceDB/mus_musculus/). Raw assembly data (before removal of contaminants, anchoring to chromosomes, and addition of finished sequence) are available from the Whitehead Institute for Biomedical Research (WIBR) (ftp://wolfram.wi.mit.edu/pub/mouse_contigs/Mar10_02/). The released assembly MGSCv3 is available from Ensembl (http://www.ensembl.org/Mus_musculus/), NCBI (ftp://ftp.ncbi.nih.gov/genomes/M_musculus/MGSCv3_Release1/), UCSC (http://genome.ucsc.edu/downloads.html) and WIBR (ftp://wolfram.wi.mit.edu/pub/mouse_contigs/MGSC_V3/). (See Supplementary Information for detailed Methods.) The author declares no competing financial interests.
Funders:
Funding AgencyGrant Number
NIHUNSPECIFIED
Wellcome TrustUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
NSFUNSPECIFIED
Medical Research Council (UK)UNSPECIFIED
Natural Sciences and Engineering Research Council of Canada (NSERC)UNSPECIFIED
Bundesministerium für Bildung und Forschung (BMBF)UNSPECIFIED
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
Plan Nacional de I + D (Spain)UNSPECIFIED
Instituto Carlos IIIUNSPECIFIED
Swiss National Science Foundation (SNSF)UNSPECIFIED
Swiss Cancer LeagueUNSPECIFIED
ChildCare FoundationUNSPECIFIED
Jerome Lejeune FoundationUNSPECIFIED
Ministry of Education, Culture, Sports, Science and Technology (MEXT)UNSPECIFIED
Mouse Sequencing ConsortiumUNSPECIFIED
Issue or Number:6915
DOI:10.1038/nature01262
Record Number:CaltechAUTHORS:20170309-090859678
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170309-090859678
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74965
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:09 Mar 2017 17:49
Last Modified:15 Nov 2021 16:29

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