title: Impact of recurrent gene duplication on adaptation of plant genomes.
abstract: 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.
authors.affiliation: INRA, UMR 1334 AGAP, 2 Place Pierre Viala, 34060 Montpellier, France. irisfischer402@gmail.com.
authors.forename: Iris
authors.initials: I
authors.lastname: Fischer
authors.forename: Jacques
authors.initials: J
authors.lastname: Dainat
authors.forename: Vincent
authors.initials: V
authors.lastname: Ranwez
authors.forename: Sylvain
authors.initials: S
authors.lastname: Glémin
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Dufayard
authors.forename: Nathalie
authors.initials: N
authors.lastname: Chantret
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D016000:Cluster Analysis; D003062:Codon / Q000235:genetics; D030541:Databases, Genetic; D020440:Gene Duplication; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D009154:Mutation / Q000235:genetics; D011110:Polymorphism, Genetic; D012641:Selection, Genetic; D013997:Time Factors
chemical_list: D003062:Codon