A physical map of the mouse genome

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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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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.

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Correspondence to David R. Bentley.

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The authors declare that they have no competing financial interests.

Supplementary information

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 the Wellcome Trust Sanger Institute. (ZIP 1541 kb)

Updated views of the map are available from the authors' websites (http://www.ensembl.org/Mus_musculus/cytoview and http://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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