ArticlePLoS genetics2017
Evolutionary forces affecting synonymous variations in plant genomes.
Article in PLoS genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- Comparative analysis of the complete mitochondrial and chloroplast genomes of Krascheninnikovia arborescens reveals its evolutionary features in Amaranthaceae.BMC plant biology · 2026Article
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
- Evolution of GC-biased gene conversion by natural selection.Genetics · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Incorporating genetic load contributes to predicting Arabidopsis thaliana's response to climate change.Nature communications · 2025Article
- Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives.Evolution letters · 2024Article
- Deciphering the complex organelle genomes of two Rhododendron species and insights into adaptive evolution patterns in high-altitude.BMC plant biology · 2024Article
- Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes.Molecular biology and evolution · 2024Article
- Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction.Science advances · 2024Article
- Half a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution.Genome biology and evolution · 2024Article
- Rapid Targeted Assembly of the Proteome Reveals Evolutionary Variation of GC Content in Avian Lice.Bioinformatics and biology insights · 2024Article
- Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.PLoS genetics · 2022Article
- Article
- Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana.Scientific reports · 2021Article
- The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns.Frontiers in plant science · 2021Article
- Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae).Scientific reports · 2020Article
- Evolution of Mutation Rate in Astronomically Large Phytoplankton Populations.Genome biology and evolution · 2020Article
- Biased Gene Conversion Constrains Adaptation inGenetics · 2020Article
- Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana.The Plant journal : for cell and molecular biology · 2020Article
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32 authors.
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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.
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