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Plant Cell Advance Online Publication
Published on January 4, 2008; 10.1105/tpc.107.056309

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Received October 15, 2007
Returned for revision November 21, 2007
Accepted December 12, 2007

Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution

Jérôme Salse 1, Stéphanie Bolot 1, Michaël Throude 1, Vincent Jouffe 1, Benoît Piegu 2, Umar Masood Quraishi 1, Thomas Calcagno 1, Richard Cooke 2, Michel Delseny 2, and Catherine Feuillet 1*

1 Institut National de la Recherche Agronomique/Université Blaise Pascal Unité Mixte de Recherche 1095, Amélioration et Santé des Plantes, 63100 Clermont-Ferrand, France
2 Unité Mixte de Recherche 5096, Centre National de la Recherche Scientifique/Université de Perpignan/Institut de Recherche pour le Developpement, Laboratoire Génome et Développement des Plantes 52, 66860 Perpignan Cedex, France

* To whom correspondence should be addressed. E-mail: catherine.feuillet{at}clermont.inra.fr.

The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.




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