TY - JOUR T1 - Evolutionary forces affecting synonymous variations in plant genomes JF - bioRxiv DO - 10.1101/086231 SP - 086231 AU - Yves Clément AU - Gautier Sarah AU - Yan Holtz AU - Felix Homa AU - Stéphanie Pointet AU - Sandy Contreras AU - Benoit Nabholz AU - François Sabot AU - Laure Sauné AU - Morgane Ardisson AU - Roberto Bacilieri AU - Guillaume Besnard AU - Angélique Berger AU - Céline Cardi AU - Fabien De Bellis AU - Olivier Fouet AU - Cyril Jourda AU - Bouchaib Khadari AU - Claire Lanaud AU - Thierry Leroy AU - David Pot AU - Christopher Sauvage AU - Nora Scarcelli AU - James Tregear AU - Yves Vigouroux AU - Nabila Yahiaoui AU - Manuel Ruiz AU - Sylvain Santoni AU - Jean-Pierre Labouisse AU - Jean-Louis Pham AU - Jacques David AU - Sylvain Glémin Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/11/07/086231.abstract N2 - 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 datasets based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that 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. ER -