Advertisement

Mammalian Genome

, Volume 18, Issue 5, pp 287–299 | Cite as

A comparative location database (CompLDB): map integration within and between species

  • Webber Liao
  • Andrew Collins
  • Matthew Hobbs
  • Mehar S. Khatkar
  • Junhong Luo
  • Frank W. NicholasEmail author
Article

Abstract

We have adapted the Location Database (LDB) map-integration strategy of Morton et al. [Ann Hum Genet 56:223–232] (1992) as above to create an integrated map for each of several species for which fully annotated genome sequences are not yet available (sheep, cattle, pig, wallaby), using all types of partial maps for that species, including cytogenetic, linkage, somatic-cell hybrid, and radiation hybrid maps. An integrated map provides not only predictions of the kilobase location of every locus, but also predicts locations (in cM) and cytogenetic band locations for every locus. In this way a comprehensive linkage map and a comprehensive cytogenetic map are created, including all loci, irrespective of whether they have ever been linkage mapped or physically mapped, respectively. High-resolution physical maps from annotated sequenced species have also been placed alongside the integrated maps. This has created a powerful tool for comparative genomics. The LDB map-integration strategy has been extended to make use of zoo-FISH comparative information. It has also been extended to enable the creation of a “virtual” map for each species not yet sequenced by using mapping data from fully sequenced species. All of the partial maps, together with the integrated map, for each species have been placed in a database called Comparative Location Database (CompLDB), which is available for querying, browsing, or download in tabular form at http://medvet.angis.org.au/ldb/.

Keywords

Radiation Hybrid Band File Anchor Locus Cytogenetic Band Comparative Mapping Data 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This work was supported in part by the Cooperative Research Centre for Innovative Dairy Products and by SheepGenomics. The authors thank the many researchers who have generated the data incorporated into the integrated maps. In particular, they thank Dr. Jill Maddox for much of the data on which the example of OAR18 was based. The authors also thank the referees for many helpful suggestions.

Supplementary material

335_2007_9020_MOESM1_ESM.pdf (229 kb)
ESM1 (PDF 205350 kb)

References

  1. Anon. (2006) Nature Collections: Human Genome (London: Nature Publishing Group)Google Scholar
  2. Collins A, Frezal J, Teague J, Morton NE (1996) A metric map of humans: 23,500 loci in 850 bands. Proc Natl Acad Sci U S A 93:14771–14775PubMedCrossRefGoogle Scholar
  3. de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T (2005) CARTHAGENE: multipopulation integrated genetic and radiated hybrid mapping. Bioinformatics 21:1703–1704PubMedCrossRefGoogle Scholar
  4. De Gortari MJ, Freking BA, Cuthbertson RP, Kappes SM, Keele JW, et al. (1998) A second-generation linkage map of the sheep genome. Mamm Genome 9:204–209PubMedCrossRefGoogle Scholar
  5. Demeure O, Renard C, Yerle M, Faraut T, Riquet J, et al. (2003) Rearranged gene order between pig and human in a QTL region on SSC 7. Mamm Genome 14:71–80PubMedCrossRefGoogle Scholar
  6. Edwards JH (1991) The Oxford grid. Ann Hum Genet 55:17–31PubMedGoogle Scholar
  7. Furey TS, Haussler D (2003) Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet 12:1037–1044PubMedCrossRefGoogle Scholar
  8. Iannuzzi L, Di Meo GO, Perucatti A, Incarnato D (1999) Comparison of the human with the sheep genomes by use of human chromosome-specific painting probes. Mamm Genome 10:719–723PubMedCrossRefGoogle Scholar
  9. ISCNDB (2000) International system for chromosome nomenclature of domestic bovids. In: Di Berardino D, Di Miro DP, Gallagher DS, Hayes H, Iannuzzi L (coordinator) (eds) Cytogenetics and cell genetics, vol 92. pp 283–299Google Scholar
  10. Ke X, Tapper W, Collins A (2001) LDB2000: Sequence based integrated maps of the human genome. Bioinformatics 17:1581–1586Google Scholar
  11. Maddox JF, Davies KP, Crawford AM, Hulme DJ, Vaiman D, et al. (2001) An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res 11:1275–1289PubMedCrossRefGoogle Scholar
  12. Maniatis N, Collins A, Ku X-F, McCarthy LC, Hewett DR, et al. (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc Natl Acad Sci U S A 99:2228–2233PubMedCrossRefGoogle Scholar
  13. McCoard SA, Fahrenkrug SC, Alexander LJ, Freking BA, Rohrer GA, et al. (2002) An integrated comparative map of the porcine X chromosome. Anim Genet 33:178–185PubMedCrossRefGoogle Scholar
  14. Morton NE (1991) Parameters of the human genome. Proc Natl Acad Sci U S A 88:7474–7476PubMedCrossRefGoogle Scholar
  15. Morton NE, Collins A, Lawrence S, Shields DC (1992) Algorithms for a location database. Ann Hum Genet 56:223–232PubMedGoogle Scholar
  16. Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, et al. (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613–617PubMedCrossRefGoogle Scholar
  17. Nievergelt CM, Smith DW, Kohlenberg JB, Schork NJ (2004) Large-scale integration of human genetic and physical maps. Genome Res 14:1199–1205PubMedCrossRefGoogle Scholar
  18. Perrocheau M, Boutreux V, Chadi S, Mata X, Decaunes P, et al. (2006) Construction of a medium-density horse gene map. Anim Genet 37:145–155PubMedCrossRefGoogle Scholar
  19. Snelling WM, Gautier M, Keele JW, Smith TP, Stone RT, et al. (2004) Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. BMC Genomics 5:77PubMedCrossRefGoogle Scholar
  20. Tapper W, Maniatis N, Morton NE, Collins A (2003) A metric linkage disequilibrium map of a human chromosome. Ann Hum Genet 67:487–494PubMedCrossRefGoogle Scholar
  21. Tapper W, Collins A, Gibson J, Maniatis N, Ennis S, et al. (2005) A map of the human genome in linkage disequilibrium units. Proc Natl Acad Sci U S A 102:11835–11839PubMedCrossRefGoogle Scholar
  22. Yap IV, Schneider D, Kleinberg J, Matthews D, Cartinhour S, et al. (2003) A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps. Genetics 165:2235–2247PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Webber Liao
    • 1
  • Andrew Collins
    • 2
    • 3
  • Matthew Hobbs
    • 1
    • 3
  • Mehar S. Khatkar
    • 1
    • 3
  • Junhong Luo
    • 1
    • 4
  • Frank W. Nicholas
    • 1
    • 3
    • 4
    Email author
  1. 1.Reprogen, Faculty of Veterinary ScienceUniversity of SydneyNew South WalesAustralia
  2. 2.Genetic Epidemiology and Bioinformatics Research Group, Human Genetics Division, School of MedicineUniversity of SouthamptonSouthamptonUK
  3. 3.Cooperative Research Centre for Innovative Dairy Products, Faculty of Veterinary ScienceUniversity of SydneyNew South WalesAustralia
  4. 4.SheepGenomics, Faculty of Veterinary ScienceUniversity of SydneyNew South WalesAustralia

Personalised recommendations