Evolutionary forces affecting synonymous variations in plant genomes.
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 compo...
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2017-05-01
|
Series: | PLoS Genetics |
Online Access: | http://europepmc.org/articles/PMC5460877?pdf=render |
id |
doaj-edce069e3de2433c97f8464b80235b4b |
---|---|
record_format |
Article |
spelling |
doaj-edce069e3de2433c97f8464b80235b4b2020-11-25T02:06:26ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042017-05-01135e100679910.1371/journal.pgen.1006799Evolutionary forces affecting synonymous variations in plant genomes.Yves ClémentGautier SarahYan HoltzFelix HomaStéphanie PointetSandy ContrerasBenoit NabholzFrançois SabotLaure SaunéMorgane ArdissonRoberto BacilieriGuillaume BesnardAngélique BergerCéline CardiFabien De BellisOlivier FouetCyril JourdaBouchaib KhadariClaire LanaudThierry LeroyDavid PotChristopher SauvageNora ScarcelliJames TregearYves VigourouxNabila YahiaouiManuel RuizSylvain SantoniJean-Pierre LabouisseJean-Louis PhamJacques DavidSylvain GléminBase 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.http://europepmc.org/articles/PMC5460877?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 Labouisse Jean-Louis Pham Jacques David Sylvain Glémin |
spellingShingle |
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 Labouisse Jean-Louis Pham Jacques David Sylvain Glémin Evolutionary forces affecting synonymous variations in plant genomes. PLoS Genetics |
author_facet |
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 Labouisse Jean-Louis Pham Jacques David Sylvain Glémin |
author_sort |
Yves Clément |
title |
Evolutionary forces affecting synonymous variations in plant genomes. |
title_short |
Evolutionary forces affecting synonymous variations in plant genomes. |
title_full |
Evolutionary forces affecting synonymous variations in plant genomes. |
title_fullStr |
Evolutionary forces affecting synonymous variations in plant genomes. |
title_full_unstemmed |
Evolutionary forces affecting synonymous variations in plant genomes. |
title_sort |
evolutionary forces affecting synonymous variations in plant genomes. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Genetics |
issn |
1553-7390 1553-7404 |
publishDate |
2017-05-01 |
description |
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. |
url |
http://europepmc.org/articles/PMC5460877?pdf=render |
work_keys_str_mv |
AT yvesclement evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT gautiersarah evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT yanholtz evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT felixhoma evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT stephaniepointet evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT sandycontreras evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT benoitnabholz evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT francoissabot evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT lauresaune evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT morganeardisson evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT robertobacilieri evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT guillaumebesnard evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT angeliqueberger evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT celinecardi evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT fabiendebellis evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT olivierfouet evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT cyriljourda evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT bouchaibkhadari evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT clairelanaud evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT thierryleroy evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT davidpot evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT christophersauvage evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT norascarcelli evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT jamestregear evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT yvesvigouroux evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT nabilayahiaoui evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT manuelruiz evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT sylvainsantoni evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT jeanpierrelabouisse evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT jeanlouispham evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT jacquesdavid evolutionaryforcesaffectingsynonymousvariationsinplantgenomes AT sylvainglemin evolutionaryforcesaffectingsynonymousvariationsinplantgenomes |
_version_ |
1724933911635558400 |