Evolutionary forces affecting synonymous variations in plant genomes

PLoS Genetics
Yves ClémentSylvain Glémin

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 accou...Continue Reading

References

Jun 20, 1991·Nature·J H McDonald, M Kreitman
Oct 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·T Nagylaki
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·L Duret, D Mouchiroud
May 24, 2001·Molecular Biology and Evolution·N G Smith, A Eyre-Walker
Jul 4, 2001·Nature Reviews. Genetics·A Eyre-Walker, L D Hurst
Jun 13, 2003·Trends in Genetics : TIG·Gabriel Marais
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Swaine L ChenHarley H McAdams
Jun 18, 2004·Molecular Biology and Evolution·Stephen I WrightBlake C Meyers
Jan 19, 2006·Nature Reviews. Genetics·J V ChamaryLaurence D Hurst
Apr 10, 2007·Trends in Genetics : TIG·Nicolas Galtier, Laurent Duret
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
May 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Michael Lynch
Jul 28, 2007·Molecular Biology and Evolution·Ryan D HernandezCarlos D Bustamante
Jul 11, 2008·Nature·Eugenio ManceraLars M Steinmetz
Aug 9, 2008·Molecular Biology and Evolution·Paul G Higgs, Wenqi Ran
Jul 14, 2009·PLoS Genetics·Ruth Hershberg, Dmitri A Petrov
Jul 28, 2009·Annual Review of Genomics and Human Genetics·Laurent Duret, Nicolas Galtier
Dec 31, 2009·Journal of Molecular Evolution·Kai Zeng, Brian Charlesworth
Apr 14, 2010·Proceedings of the National Academy of Sciences of the United States of America·Isheng J TsaiVassiliki Koufopanou
Jul 21, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Abhirami RatnakumarMatthew T Webster
Sep 15, 2010·Molecular Biology and Evolution·Nina Stoletzki, Adam Eyre-Walker
Sep 15, 2010·PLoS Genetics·Ruth Hershberg, Dmitri A Petrov
Sep 22, 2010·Molecular Biology and Evolution·Suo QiuDeborah Charlesworth
Nov 26, 2010·Nature Reviews. Genetics·Joshua B Plotkin, Grzegorz Kudla
Mar 30, 2011·Molecular Biology and Evolution·Juan S EscobarNicolas Galtier
Apr 21, 2011·Molecular Biology and Evolution·Aline MuyleSylvain Glémin
Apr 26, 2011·BMC Bioinformatics·Vincent MieleLaurent Duret
Aug 23, 2011·Genome Biology and Evolution·Suo QiuDeborah Charlesworth
Oct 25, 2011·PLoS Genetics·Brian P CusackHugues Roest Crollius
Apr 12, 2012·The Plant Cell·Laurana Serres-GiardiSylvain Glémin
May 26, 2012·Genome Biology and Evolution·Eugénie PessiaGabriel A B Marais
Feb 21, 2013·The New Phytologist·Boris Igic, Jeremiah W Busch
Sep 14, 2013·Molecular Biology and Evolution·Yves Clément, Peter F Arndt
Nov 12, 2013·Molecular Biology and Evolution·Matthew C RobinsonNadia D Singh

❮ Previous
Next ❯

Citations

Feb 3, 2018·Journal of Experimental Botany·Karl J NiklasInmaculada Yruela
Sep 9, 2017·PloS One·Vincent RanwezNathalie Chantret
Aug 1, 2019·PLoS Genetics·Abigail L LaBellaAntonis Rokas
May 3, 2019·Science Advances·Sylvain GléminVincent Ranwez
Jun 14, 2019·The Plant Journal : for Cell and Molecular Biology·Muriel Gros-BalthazardBouchaib Khadari
Jan 14, 2020·The Plant Journal : for Cell and Molecular Biology·Guillaume MartinNabila Yahiaoui
May 18, 2020·Genetics·Tuomas Hämälä, Peter Tiffin
Jul 10, 2020·Genome Biology and Evolution·Marc KrasovecDmitry A Filatov
Nov 21, 2017·Annals of Botany·Purabi MazumdarJennifer Ann Harikrishna
Sep 17, 2021·Frontiers in Plant Science·Concetta BurgarellaDavid Pot

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq

Software Mentioned

SiLiX
read2snp
MACSE
PhyML
codeml

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.