Looking for positive selection in recently duplicated genes in plant genomes

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Fischer, Iris | Dufayard, Jean-François | Ranwez, Vincent | Chantret, Nathalie

Edité par CCSD -

Whole genome duplications (WGDs) as well as small-scale duplications (SSDs) occurred frequently in plant evolution. In combination with a relatively high retention rate of novel genes, duplication events seem to be an important factor in plant genome evolution. Indeed, a large fraction of angiosperm diversity was suggested to stem from duplication followed by adaptive specialization of paralogous gene copies. Thanks to recent progress in genome sequencing, we can now address the question whether positive selection is a driving force in the evolution of duplicated genes. We searched a plant genome database for cases where recent successive duplication events followed by retention resulted in at least six gene copies. Those ultraparalogous gene clusters were tested for positive selection using codon substitution models implemented in PAML. We found that choosing the appropriate alignment and cleaning method is crucial as the codeml site-model is highly sensitive to alignment errors. Overall, 5-10% of all clusters showed evidence for positive selection. The banana genome shows very little evidence for selection at ultraparalogs, whereas duplicated genes in rice and Brachypodium seem to have undergone positive selection more frequently than the average. However, these results could also be explained by differences in genome coverage and quality.

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