Impact of recurrent gene duplication on adaptation of plant genomes

BMC Plant Biology

Research Article

Sylvain Glémin¹  Jean-François Dufayard²  Nathalie Chantret³  Iris Fischer⁴  Vincent Ranwez⁵  Jacques Dainat⁶ 

[1] Institut des Sciences de l'Evolution CC64, Université Montpellier II, Place Eugène Bataillon, 34095, Montpellier, France;UMR 1334 AGAP, CIRAD, Avenue Agropolis, 34398, Montpellier, France;UMR 1334 AGAP, INRA, 2 Place Pierre Viala, 34060, Montpellier, France;UMR 1334 AGAP, INRA, 2 Place Pierre Viala, 34060, Montpellier, France;UMR 232 DIADE, IRD, 911 Avenue Agropolis, 34394, Montpellier, France;UMR 1334 AGAP, Montpellier SupAgro, 2 Place Pierre Viala, 34060, Montpellier, France;UMR 1334 AGAP, Montpellier SupAgro, 2 Place Pierre Viala, 34060, Montpellier, France;Department of Medical Biochemistry, Microbiology, Genomics, Uppsala University, Husargatan 3, 75123, Uppsala, Sweden;

关键词: Lineage specific expansion (LSE);    Gene duplication;    Gene retention;    Ultraparalogs (UP);    Superorthologs (SO);    Comparative genomics;    Positive selection;    Adaptation;   

DOI  :  10.1186/1471-2229-14-151

 received in 2014-03-10, accepted in 2014-05-23,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundRecurrent 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.ResultsWe 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.ConclusionsIn 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.

【 授权许可】

CC BY   
© Fischer et al.; licensee BioMed Central Ltd. 2014