Initial sequencing and comparative analysis of the mouse genome
Open accessAbstract
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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In 2002, the mouse reference genome was based on a single inbred mouse strain, C57BL/6J (BL6).
“In 2002, the mouse reference genome was based on a single inbred mouse strain, namely, C57BL/6J (BL6).3”
From High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape (2026) · cites this paper as [3]
The median synonymous substitution rate (Ks) of 1:1 opossum-human orthologues is 1.02.
“The median value of K S is 1.02.”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [7]
Most evolutionarily conserved sequence in eutherian genomes is not protein-coding but consists of conserved non-coding elements.
“The most surprising discovery to emerge from comparative analyses of eutherian genomes is the finding that the majority of evolutionarily conserved sequence does not represent protein-coding genes, but rather are conserved non-coding elements (CNEs) 7,10 .”
From Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) · cites this paper as [7]
Sequencing of mouse and human genomes reveals great conservation of function and only about 300 unique genes.
“sequencing of mouse and human genomes reveals great conservation of function and only about 300 unique genes”
From Retinal ultrastructure of murine models of dry age-related macular degeneration (AMD) (2010) · cites this paper as Waterston et al., 2002
Comparative genome analysis has shown that 5% of the human genome is evolutionarily conserved and thus functional; less than one-third of this 5% consists of genes that encode proteins.
“Comparative genome analysis has shown that 5% of the human genome is evolutionarily conserved and thus functional; less than one-third of this 5% consists of genes that encode proteins (108).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [108]
Useful tools will include maps of evolutionary conservation and chromatin state, as well as databases of cell-state signatures, such as genome-wide expression patterns.
“Useful tools will include maps of evolutionary conservation (108) and chromatin state (140), as well as databases of cell-state signatures, such as genome-wide expression patterns, that may integrate aspects of cell biology under resting and provoked conditions (141).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [108]
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Flagged first, then by citations
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- Charles Street, Cambridge, Massachusetts 02141, USA; 3, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; 4, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK; 5, Research Group in Biomedical Informatics, Institut Municipal d'Investigacio, Medica/Universitat Pompeu Fabra, Centre de Regulacio Genomica, Barcelona, Catalonia, Spain; 6, Bioinformatics, GlaxoSmithKline, UW2230, 709
- Evans Hall, Berkeley, California 94720, USA; 9, Division of Medical Genetics, University of Geneva Medical School, 1 rue Michel-Servet, CH-1211 Geneva, Switzerland; 10, Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA; 11, EMBL, Meyerhofstrasse 1, Heidelberg 69117, Germany; 12, UK MRC Mouse Sequencing Consortium, MRC Mammalian Genetics Unit, Harwell OX11 0RD, UK; 13, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 84-171, Berkeley, California 94720, USA; 14, Department of Computer Science, Washington University, Box 1045, St Louis, Missouri 63130, USA; 15, School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada; 16, The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA; 17, Laboratory for Genome Exploration, RIKEN Genomic Sciences Center, Yokohama Institute, 1-7-22 Suchiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; 18, Affymetrix Inc., Emeryville, California 94608, USA; 19, Departments of Statistics and Health Evaluation Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 20, National Human Genome Research Institute, National Institutes of Health, 31 Center Drive, Room 4B09, Bethesda, Maryland 20892, USA; 21, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; 22, Department of Electrical Engineering, University of California, Berkeley, 231
- Cory Hall, Berkeley, California 94720, USA; 23, Department of Human Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, South Parks Road, Oxford OX1 3QX, UK; 24, Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA; 25, Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA; 26, Departments of Biochemistry and Molecular Biology and Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 27, Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 28, Baylor College of Medicine, Human Genome Sequencing Center, One Baylor Plaza, MSC-226, Houston, Texas 77030, USA; 29, The Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA; 30, National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50, Room 5523, Bethesda, Maryland 20892, USA; 31, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 32, Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA; 33, Department of Chemistry and Biochemistry, University of Oklahoma Advanced Center for Genome Technology, University of Oklahoma, 620
- Gilman Drive, La Jolla, California 92093-0114, USA; 42, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany; 43, Genome Therapeutics Corporation, 100 Beaver Street, Waltham, Massachusetts 02453, USA; 44, Bioinformatics Solutions Inc., 145 Columbia Street W, Waterloo, Ontario N2L 3L2, Canada; 45, Department of Molecular and Human Genetics, Baylor College of Medicine, Mailstop BCM226, Room 1419.01, One Baylor Plaza, Houston, Texas 77030, USA; 46, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138, USA * Members of the Mouse Genome Analysis
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- Authors
- Mouse Genome Sequencing Consortium
- Venue
- Nature
- Published
- 2002-12
- Volume
- 420
- Issue
- 6915
- Pages
- 520-562
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2151464048
- Cited by
- 7,187
- References
- 330
- Citations by year
- 2026: 111 · 2025: 171 · 2024: 209 · 2023: 173 · 2022: 212 · 2021: 237 · 2020: 204 · 2019: 234 · 2018: 214 · 2017: 182 · 2016: 214 · 2015: 262 · 2014: 268 · 2013: 300 · 2012: 298
- FWCI
- 181.79
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- Foundation for the National Institutes of Health
- Howard Hughes Medical Institute
- U.S. Department of Energy
- GlaxoSmithKline
- Wellcome Trust
- European Molecular Biology Laboratory
- Ministry of Education, Culture, Sports, Science and Technology
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Bundesministerium für Bildung und Forschung
- National Institutes of Health
- Natural Sciences and Engineering Research Council of Canada
- Medical Research Council
- National Institute of Mental Health
- National Cancer Institute
- National Institute on Deafness and Other Communication Disorders
- National Institute of General Medical Sciences
- Fogarty International Center
- National Institute of Diabetes and Digestive and Kidney Diseases
- National Center for Research Resources
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- mouse genome, genome sequencing, comparative genomics, human genome, synteny, positive selection, protein-coding genes, gene family expansion, protein evolution, genome evolution
- MeSH terms
- Animals, Base Composition, Gene Expression Regulation, Genes, Multigene Family, Humans, Mice, Transgenic, Neoplasms, Pseudogenes, Repetitive Sequences, Nucleic Acid, Selection, Genetic, Sex Chromosomes, Species Specificity, Genetic Variation, Genome, Human, Mutagenesis, Genome, Conserved Sequence, Sequence Analysis, DNA, Mice, Knockout, CpG Islands, Evolution, Molecular, Physical Chromosome Mapping, Proteome, RNA, Untranslated, Genomics, Models, Animal, Synteny, Chromosomes, Mammalian, Quantitative Trait Loci, Mice
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