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Impact of recurrent gene duplication on adaptation of plant genomes

Fischer I., Dainat J., Ranwez V., Glemin S., Dufayard J.F., Chantret N.. 2014. BMC Plant Biology, 14 (151) : 15 p..

Background Recurrent gene duplication and retention played an important role in angiosperm genome evolution. It has been hypothesized that these processes contribute significantly to plant adaptation but so far this hypothesis has not been tested at the genome scale. Results We studied available sequenced angiosperm genomes to assess the frequency of positive selection footprints in lineage specific expanded (LSE) gene families compared to single-copy genes using a dN/dS-based test in a phylogenetic framework. We found 5.38% of alignments in LSE genes with codons under positive selection. In contrast, we found no evidence for codons under positive selection in the single-copy reference set. An analysis at the branch level shows that purifying selection acted more strongly on single-copy genes than on LSE gene clusters. Moreover we detect significantly more branches indicating evolution under positive selection and/or relaxed constraint in LSE genes than in single-copy genes. Conclusions In this - to our knowledge -first genome-scale study we provide strong empirical support for the hypothesis that LSE genes fuel adaptation in angiosperms. Our conservative approach for detecting selection footprints as well as our results can be of interest for further studies on (plant) gene family evolution. (Résumé d'auteur)

Mots-clés : amélioration des plantes; empreinte adn; Évolution; sélection individuelle; génome; séquence nucléotidique; réplication; gène; magnoliophyta

Thématique : Génétique et amélioration des plantes; Physiologie et biochimie végétales; Taxonomie végétale et phyto-géographie

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