Evolutionary forces affecting synonymous variations in plant genomes

• DOI: 10.1371/journal.pgen.1006799
• Publication Date: 2017-05-22T17:35:31Z
• Authors: Yves Clément; Gautier Sarah; Yan Holtz; Felix Homa; Stéphanie Pointet; Sandy Contreras; Benoit Nabholz; François Sabot; Laure Sauné; Morgane Ardisson; Roberto Bacilieri; Guillaume Besnard; Angélique Berger; Céline Cardi; Fabien De Bellis; Olivier Fouet; Cyril Jourda; Bouchaib Khadari; Claire Lanaud; Thierry Leroy; David Pot; Christopher Sauvage; Nora Scarcelli; James Tregear; Yves Vigouroux; Nabila Yahiaoui; Manuel Ruiz; Sylvain Santoni; Jean-Pierre Labou...; Jean-Louis Pham; Jacques David; Sylvain Glémin
• Keywords: [SDV]Life Sciences [q-bio]; http://aims.fao.org/aos/agrovoc/c_1723; génome végétal; QH426-470; phylogeny; Musa acuminata; F30 - Génétique et amélioration des plantes; [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics; Elaeis guineensis; évolution; Olea europaea; http://aims.fao.org/aos/agrovoc/c_3224; http://aims.fao.org/aos/agrovoc/c_4994; http://aims.fao.org/aos/agrovoc/c_34326; 2. Zero hunger; 0303 health sciences; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; génétique des populations; Genetik och genomik; http://aims.fao.org/aos/agrovoc/c_92382; [SDE]Environmental Sciences; Genome, Plant; Research Article; 570; Gene Conversion; génomique; [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics; Evolution, Molecular; Magnoliopsida; 03 medical and health sciences; Coffea canephora; séquençage; http://aims.fao.org/aos/agrovoc/c_3081; phylogénie; [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; Genetics; Theobroma cacao; Genetik; analyse du transcriptome; Selection, Genetic; http://aims.fao.org/aos/agrovoc/c_13325; 580; http://aims.fao.org/aos/agrovoc/c_2509; Polymorphism, Genetic; génome; http://aims.fao.org/aos/agrovoc/c_2745; Genetics and Genomics; 15. Life on land; GC Rich Sequence; http://aims.fao.org/aos/agrovoc/c_5014; http://aims.fao.org/aos/agrovoc/c_7713; http://aims.fao.org/aos/agrovoc/c_5339; analyse fonctionnelle du génome; mutation

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