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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Recombination, meiotic expression and human codon usage.

Fanny Pouyet1, Dominique Mouchiroud1, Laurent Duret1

  • 1Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard, Villeurbanne, France.

Elife
|August 23, 2017
PubMed
Summary

Synonymous codon usage in human genes is not driven by translation efficiency but by GC-biased gene conversion (gBGC) linked to meiotic recombination. This non-adaptive process explains most codon usage variation in mammalian genomes.

Keywords:
biased gene conversioncodon Usageevolutionary biologygenomicshumanmeiosisrecombinationtranslational selection

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Synonymous codon usage (SCU) varies across human genes and functional categories.
  • Previous interpretations suggested SCU is adaptively constrained for translation efficiency.
  • Distinct codon usage in functional categories was thought to reflect cellular state optimization.

Purpose of the Study:

  • To investigate the primary drivers of synonymous codon usage variation in human genes.
  • To test the hypothesis that GC-biased gene conversion (gBGC) influences SCU.
  • To determine if SCU is adaptively constrained or influenced by non-adaptive processes.

Main Methods:

  • Analysis of large-scale GC-content variation in human genes.
  • Correlation of recombination rates with SCU.
  • Investigation of the role of meiotic recombination and GC-biased gene conversion (gBGC).

Main Results:

  • SCU variation is primarily driven by large-scale GC-content changes, not tRNA abundance.
  • GC-biased gene conversion (gBGC), a non-adaptive process linked to meiotic recombination, is the main driver of SCU.
  • Differences in SCU among functional categories correlate with meiotic transcription levels and recombination rates.

Conclusions:

  • GC-biased gene conversion (gBGC) explains a significant portion (70%) of SCU variance in human genes.
  • SCU is largely shaped by non-adaptive evolutionary forces like gBGC, rather than adaptive optimization of translation efficiency.
  • The heterogeneity of SCU induced by gBGC in mammalian genomes likely prevents tRNA pool optimization to codon usage demands.