Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

  1. Benoit Piegu1,
  2. Romain Guyot1,
  3. Nathalie Picault1,
  4. Anne Roulin1,
  5. Abhijit Saniyal3,
  6. Hyeran Kim4,
  7. Kristi Collura4,
  8. Darshan S. Brar2,
  9. Scott Jackson3,
  10. Rod A. Wing4, and
  11. Olivier Panaud1,1
  1. 1Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD, Université de Perpignan, Perpignan 66860, France;
  2. 2Plant Breeding Genetics and Biochemistry Division, International Rice Research Institute, Manila 1099, Philippines, USA;
  3. 3Agricultural Genomics, Purdue University, West Lafayette, Indiana 47907, USA;
  4. 4Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA

    Abstract

    Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a “copy and paste” mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis, a wild relative of the Asian cultivated rice O. sativa, has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus.

    Footnotes

    • ↵5 Corresponding author.

      ↵5 E-mail panaud{at}univ-perp.fr; fax 33-04-468664899.

    • Supplemental material is available online at www.genome.org.

    • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.5290206.

      • Received May 9, 2006.
      • Accepted August 2, 2006.
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    1. Published in Advance September 8, 2006, doi: 10.1101/gr.5290206 Genome Res. 16: 1262-1269 Copyright © 2006, Cold Spring Harbor Laboratory Press

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