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A physical map of the mouse genome

Naturevolume 418, pages743–750 (2002)Cite this article

Abstract

A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human–mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy.

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Figure 1: Construction of human–mouse homology clone map.
Figure 2: Comparison of radiation hybrid and genetic maps to the physical map of mouse chromosome 2.
Figure 3: Conserved segments between human chromosome 6 (Hsa6) and the mouse genome.
Figure 4: Conserved segments between mouse chromosome 11 and the human genome.
Figure 5: Homology maps of the mouse and human genomes.

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Acknowledgements

The authors acknowledge the support of the Wellcome Trust, the National Institutes of Health and the US Department of Energy. We are grateful to the web team at the Sanger Institute for assistance with developing map displays, to P. Deloukas for RH map analysis, and E. Arnold-Berkowits, S. Lo, J. Gill and all present and past members of the Institute for Genomic Research BAC end sequencing team for the sequencing work.

Author information

Authors and Affiliations

  1. The Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, Cambridge, UK

    Simon G. Gregory, Carol E. Scott, Richard S. Evans, Paul W. Burridge, Tony V. Cox, Christopher A. Fox, Richard D. Hutton, Ian R. Mullenger, Kimbly J. Phillips, James Smith, Jim Stalker, Glen J. Threadgold, Tim Hubbard, Jane Rogers & David R. Bentley

  2. Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri, 63108, USA

    Mandeep Sekhon, Kristine Wylie, Asif Chinwalla, John Wallis, LaDeana Hillier, Jason Carter, Tony Gaige, Sara Jaeger, Colin Kremitzki, Dan Layman, Jason Maas, Rebecca McGrane, Kelly Mead, Rebecca Walker, Robert H. Waterston & John D. McPherson

  3. Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 4E6, Canada

    Jacqueline Schein, Steven Jones, Michael Smith, Jennifer Asano, Ian Bosdet, Susanna Chan, Suganthi Chittaranjan, Readman Chiu, Chris Fjell, Noreen Girn, Catharine Gray, Ran Guin, Letticia Hsiao, Martin Krzywinski, Reta Kutsche, Soo Sen Lee, Carrie Mathewson, Candice McLeavy, Steve Messervier, Steven Ness, Pawan Pandoh, Anna-Liisa Prabhu, Parvaneh Saeedi, Duane Smailus, Lorraine Spence, Jeff Stott, Sheryl Taylor, Wesley Terpstra, Miranda Tsai, Jill Vardy, Natasja Wye, George Yang & Marco Marra

  4. The Institute for Genomic Research, Rockville, Maryland, 20850, USA

    Shaying Zhao, Sofiya Shatsman, Bola Ayodeji, Keita Geer, Getahun Tsegaye, Alla Shvartsbeyn, Elizabeth Gebregeorgis, Margaret Krol, Daniel Russell, Larry Overton, Joel A. Malek, Mike Holmes, Michael Heaney, Jyoti Shetty, Tamara Feldblyum, William C. Nierman & Claire M. Fraser

  5. Children's Hospital Oakland Research Institute, Oakland, California, 94609, USA

    Kazutoyo Osoegawa, Joseph J. Catanese & Pieter J. de Jong

  6. EMBL—European Bioinformatics Institute, CB10 1SD, Hinxton, Cambridge, UK

    Ewan Birney

  7. Department of Electrical Engineering, Washington University, St Louis, Missouri, 63130, USA

    Dan Fuhrmann

Authors
  1. Simon G. Gregory

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  2. Mandeep Sekhon

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  3. Jacqueline Schein

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  4. Shaying Zhao

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  5. Kazutoyo Osoegawa

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  6. Carol E. Scott

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  7. Richard S. Evans

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  8. Paul W. Burridge

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  9. Tony V. Cox

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  10. Christopher A. Fox

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  11. Richard D. Hutton

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  12. Ian R. Mullenger

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  13. Kimbly J. Phillips

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  14. James Smith

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  15. Jim Stalker

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  17. Ewan Birney

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  18. Kristine Wylie

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  19. Asif Chinwalla

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  30. Rebecca Walker

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  31. Steven Jones

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  36. Suganthi Chittaranjan

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  41. Catharine Gray

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  86. David R. Bentley

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Corresponding author

Correspondence toDavid R. Bentley.

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Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

41586_2002_BFnature00957_MOESM1_ESM.zip

This file contains a static version of the mouse fingerprint contig (FPC) map; it is an archive representation of the data at the time of publication. (Start with the file bac.1.0.html). A live, updated version of this data can be seen in CytoView at Ensembl (choose 'MapViewer'), and also at the NCBI (use the 'Jump to chr' box to select chromosome; if searching specific features, select 'cytoview' option to view the map). The FPC map was previous displayed in Ensembl before the availability of sequence covering most of the genome. Since then, Ensembl displays have switched to being sequence based, with the FPC data mapped onto it and visible through the CytoView interface. Both the sequence and the FPC map are being refined as the mouse genome is finished. (ZIP 3564 kb)

This file contains a static version of the map derived from the synteny between the mouse and human genomes (Fig. 5); it is an archive representation of the data at the time of publication. (Start with the file hm.1.1.html). A live, updated version of this data can be seen in SyntenyView at Ensembl.

Copies of these data, plus comparisons and discussion of genetic, RH and clone maps, and an interactive version of the synteny displays of Fig. 5, are available at theWellcome Trust Sanger Institute. (ZIP 1541 kb)

Updated views of the map are available from the authors' websites (http://www.ensembl.org/Mus_musculus/cytoview andhttp://www.ncbi.nlm.nih.gov/genome/guide/mouse), as is an archive version for this publication, plus comparisons and discussion of genetic, RH and clone maps, and an interactive version of the synteny displays of Fig. 5 (http://www.sanger.ac.uk/Projects/M_musculus/publications/fpcmap-2002).

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Gregory, S., Sekhon, M., Schein, J.et al. A physical map of the mouse genome.Nature418, 743–750 (2002). https://doi.org/10.1038/nature00957

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