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Evidence of en bloc duplication in vertebrate genomes

Nature Genetics volume 31, pages 100–105 (2002) Cite this article

Abstract

It has been 30 years since it was first proposed that the vertebrate genome evolved through several rounds of genome-wide duplications (polyploidizations)1. Despite rapid advances in genetics, including sequencing of the complete genomes of several divergent species, this hypothesis has not been tested rigorously and is still a matter of debate2. If polyploidizations occurred during chordate evolution, there should be a network of paralogous regions in the present-day jawed vertebrate (Gnathostomata) genomes3. Here we present an investigation of the major histocompatibility complex (MHC) paralogous regions, which we accomplished by characterizing the corresponding region in amphioxus by identifying nine anchor genes and sequencing both the anchor genes and the regions that flank them (a total of 400 kb). Phylogenetic analysis of 31 genes (including the anchor genes) in these regions shows that duplications occurred after the divergence of cephalochordates and vertebrates but before the Gnathostomata radiation. The distribution of human and amphioxus orthologs in their respective genomes and the relationship between these distributions support the en bloc duplication events. Our analysis represents the first step towards demonstrating that the human ancestral genome has undergone polyploidization. Moreover, reconstruction of the pre-duplicated region indicates that one of the duplicated regions retains the ancestral organization.

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Figure 1: Definition of the anchor genes.
The alternative text for this image may have been generated using AI.
Figure 2: Analysis of amphioxus anchor-gene phylogenetic relationships; phylogenetic reconstructions for the nine amphioxus anchor genes.
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Figure 3: Summary of the cosmid gene organizations.
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Figure 4: Evolution of the chordate proto-MHC region and its genes.
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Acknowledgements

We would like to thank E. Faure for help in cloning the amphioxus RXR gene; M. Flajnik, C. Mawas, F. Birg, J. Berry, D. Birnbaum and L. Du Pasquier for critical reading of the manuscript; E. Danchin for helpful discussions, as well as all the members of the lab for their support; and M. Clark for the Takifugu rubripes BRD2 sequence. L. Abi-Rached is an M.R.T. fellow. This work was supported by INSERM.

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Authors and Affiliations

  1. INSERM Unité 119, 27 bd Leï Roure, Marseille, 13009, France

    Laurent Abi-Rached, André Gilles & Pierre Pontarotti

  2. UPRES Biodiversité 2202, Université de Provence, Pl. V. Hugo, 13331, Marseille, Cedex 3, France

    André Gilles

  3. Department of Molecular Life Science, Tokai University School of Medicine, Bosheidei, Isehara, 259-1193, Kanagawa, Japan

    Takashi Shiina & Hidetoshi Inoko

Authors
  1. Laurent Abi-Rached
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  2. André Gilles
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  4. Pierre Pontarotti
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Correspondence to Laurent Abi-Rached or Pierre Pontarotti.

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Abi-Rached, L., Gilles, A., Shiina, T. et al. Evidence of en bloc duplication in vertebrate genomes. Nat Genet 31, 100–105 (2002). https://doi.org/10.1038/ng855

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