Evolutionary forces affecting synonymous variations in plant genomes

Clément Yves, Sarah Gautier, Holtz Yan, Homa Félix, Pointet Stéphanie, Contreras Sandy, Nabholz Benoit, Sabot François, Sauné Laure, Ardisson Morgane, Bacilieri Roberto, Besnard Guillaume, Berger Angélique, Cardi Céline, De Bellis Fabien, Fouet Olivier, Jourda Cyril, Khadari Bouchaib, Lanaud Claire, Leroy Thierry, Pot David, Sauvage Christopher, Scarcelli Nora, Tregear James, Vigouroux Yves, Yahiaoui Nabila, Ruiz Manuel, Santoni Sylvain, Labouisse Jean-Pierre, Pham Jean Louis, David Jacques, Glemin Sylvain. 2017. Evolutionary forces affecting synonymous variations in plant genomes. PLoS Genetics, 13 (5):e1006799, 28 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
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Thème(s) HCERES des revues (en SHS) : Anthropologie-Ethnologie

Abstract : Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones. (Résumé d'auteur)

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Clément Yves, Montpellier SupAgro (FRA)
  • Sarah Gautier, INRA (FRA)
  • Holtz Yan, INRA (FRA)
  • Homa Félix, Uppsala University (SWE)
  • Pointet Stéphanie, CIRAD-BIOS-UMR AGAP (FRA)
  • Contreras Sandy, SouthGreen Platform (FRA)
  • Nabholz Benoit, ISEM (FRA)
  • Sabot François, IRD (FRA)
  • Sauné Laure, INRA (FRA)
  • Ardisson Morgane, INRA (FRA)
  • Bacilieri Roberto, INRA (FRA)
  • Besnard Guillaume, CNRS (FRA)
  • Berger Angélique, CIRAD-BIOS-UMR AGAP (FRA)
  • Cardi Céline, CIRAD-BIOS-UMR AGAP (FRA)
  • De Bellis Fabien, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7070-7691
  • Fouet Olivier, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8547-1474
  • Jourda Cyril, CIRAD-BIOS-UMR PVBMT (REU)
  • Khadari Bouchaib, INRA (FRA)
  • Lanaud Claire, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6411-7310
  • Leroy Thierry, CIRAD-BIOS-UMR AGAP (FRA)
  • Pot David, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6144-8448
  • Sauvage Christopher, INRA (FRA)
  • Scarcelli Nora, IRD (FRA)
  • Tregear James, IRD (FRA)
  • Vigouroux Yves, IRD (FRA)
  • Yahiaoui Nabila, CIRAD-BIOS-UMR AGAP (FRA)
  • Ruiz Manuel, CIRAD-BIOS-UMR AGAP (COL) ORCID: 0000-0001-8153-276X
  • Santoni Sylvain, INRA (FRA)
  • Labouisse Jean-Pierre, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5592-6789
  • Pham Jean Louis, IRD (FRA)
  • David Jacques, Montpellier SupAgro (FRA)
  • Glemin Sylvain, ISEM (FRA)

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