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Immunogenetics

, Volume 55, Issue 3, pp 141–148 | Cite as

Conservation of the MHC-like region throughout evolution

  • Etienne G. J. DanchinEmail author
  • Laurent Abi-Rached
  • André Gilles
  • Pierre Pontarotti
Original Paper

Abstract

Identification of conserved regions between the genomes of distant species is a crucial step in the reconstruction of the genomic organization of their last common ancestor. Here we confirm for the first time with robust evidence, the existence of a region of conserved synteny between the human genome and the Drosophila genome. This evolutionarily conserved synteny involves the human MHC and paralogous regions, and we identified 19 conserved genes between these two species in a Drosophila genomic region of less than 2 Mb. The statistical analysis of the distribution of these 19 genes between the Drosophila and human genomes shows that it cannot be explained by chance. Our study constitutes a first step towards the reconstruction of the genome of Urbilateria (the ancestor of all bilaterian) and allows for a better understanding of the evolutionary history of our genome as well as other metazoan genomes.

Keywords

Comparative genomics MHC Evolution Phylogenomics Conserved syntenies 

Notes

Acknowledgements

We would like to thank Jeffrey Rasmussen and Michael F. Mc Dermott for helpful discussion and critical reading of the manuscript. Part of this research has been conducted at INSERM U119 Marseille, France. E.G.J. Danchin is a M.R.T. (French National Research and Technology Ministry) fellow.

References

  1. Abi-Rached L, Gilles A, Shiina T, Pontarotti P, Inoko H (2002) Evidence for en bloc duplication in vertebrate genomes. Nat Genet 31:100–105CrossRefGoogle Scholar
  2. Adoutte A, Balavoine G, Lartillot N, Lespinet O, Prud'homme B, de Rosa R (2000) The new animal phylogeny: reliability and implications. Proc Natl Acad Sci USA 97:4453–4456CrossRefGoogle Scholar
  3. Altschul S-F, Gish W, Miller W, Myers E-W, Lipman, D-J (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefGoogle Scholar
  4. Coghlan A, Wolfe K-H (2002) Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res 12:857–867CrossRefGoogle Scholar
  5. DeRobertis E-M, Sasai Y (1996) A common plan for dorsoventral patterning in Bilateria. Nature 380:37–40CrossRefGoogle Scholar
  6. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  7. Fitch W- M (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  8. Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543–548PubMedGoogle Scholar
  9. Graham A, Papalopulu N, Krumlauf R (1989) The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57:367–378CrossRefGoogle Scholar
  10. Gu Z, Cavalcanti A, Chen F-C, Bouman P, Li W-H (2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 3:256–262CrossRefGoogle Scholar
  11. Ku H-M, Vision T, Liu J, Tanksley S-D (2000) Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 97:9121–9126CrossRefGoogle Scholar
  12. Ruvkun G, Hobert O (1998) The taxonomy of developmental control in Caenorhabditis elegans. Science 282:2033–2041CrossRefGoogle Scholar
  13. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  14. Seoighe C, Wolfe K-H (1998) Extent of genomic rearrangement after genome duplication in yeast. Proc Natl Acad Sci USA 95:4447–4452CrossRefGoogle Scholar
  15. Thompson J-D, Higgins D-G, Gibson T-J (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRefGoogle Scholar
  16. Thompson J-D, Gibson T-J, Plewniak F, Jeanmougin F, Higgins D-G (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefGoogle Scholar
  17. Trachtulec Z, Forejt J (2001) Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast. Mamm Genome 12:227–231CrossRefGoogle Scholar
  18. Trachtulec Z, Hamvas R-M, Forejt J, Lehrach H-R, Vincek V, Klein J (1997) Linkage of TATA-binding protein and proteasome subunit C5 genes in mice and humans reveals synteny conserved between mammals and invertebrates. Genomics 44:1–7CrossRefGoogle Scholar
  19. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al. (2001) The sequence of the human genome. Science 16:1304–1351CrossRefGoogle Scholar
  20. Vision T-J, Brown D-G, Tanksley S-D (2000) The origins of genomic duplications in Arabidopsis. Science 290:2114–2117CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • Etienne G. J. Danchin
    • 1
    Email author
  • Laurent Abi-Rached
    • 2
  • André Gilles
    • 1
  • Pierre Pontarotti
    • 1
  1. 1.EA Biodiversité 2202, Phylogenomics LaboratoryUniversité de ProvenceMarseilles Cedex 3France
  2. 2.Department of Structural BiologyStanford UniversityStanfordUSA

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