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Evolutionary forces affecting synonymous variations in plant genomes.

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GC-biased gene conversion (gBGC) is a widespread force shaping plant genomes, often stronger than selection. This process significantly impacts base composition variation, particularly in GC-rich plant species.

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Area of Science:

  • Population Genomics
  • Molecular Evolution
  • Plant Genetics

Background:

  • Plant genomes exhibit significant variation in base composition, especially at synonymous third codon positions.
  • Synonymous codon usage bias is common, even in species with homogeneous base composition.
  • The driving forces behind these variations, including mutational bias, selection, and GC-biased gene conversion (gBGC), are debated.

Purpose of the Study:

  • To jointly estimate the relative strengths of selection, gBGC, and mutational bias in plant genomes.
  • To investigate the variation in these forces across and within angiosperm species.
  • To understand the contribution of gBGC to plant genome base composition heterogeneity.

Main Methods:

  • Utilized a population genetics approach by extending a recently developed method.
  • Applied the method to a large population genomic dataset derived from transcriptome sequencing.
  • Analyzed data from 11 diverse angiosperm species spanning the plant phylogeny.

Main Results:

  • Plant genomes at synonymous positions are frequently far from mutation-drift equilibrium.
  • GC-biased gene conversion (gBGC) was found to be a widespread and dominant evolutionary force, generally stronger than selection.
  • gBGC significantly contributes to the observed base composition variation among plant species.

Conclusions:

  • GC-biased gene conversion (gBGC) plays a crucial role in shaping plant genome base composition.
  • The relative strength of gBGC compared to selection varies across species.
  • gBGC must be considered in plant genome analyses, especially for GC-rich genomes, to accurately interpret evolutionary patterns.