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Variation and selection on codon usage bias across an entire subphylum.

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Synonymous codon usage variation in budding yeasts is shaped by both genetic drift and translational selection. While drift influences global codon usage, selection impacts many genes across most genomes.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Synonymous codon usage varies across codons, genes, and species.
  • Factors influencing this variation include mutational bias, natural selection for translational efficiency, and genetic drift.
  • The interplay of these forces across lineages remains largely unexplored.

Purpose of the Study:

  • To investigate how mutational bias, natural selection, and genetic drift shape codon usage patterns across the Saccharomycotina subphylum.
  • To determine the extent to which codon usage deviates from neutral expectations and identify the role of translational selection.

Main Methods:

  • Analyzed genomic data from 327 species of budding yeast (Saccharomycotina).
  • Correlated genome-wide relative synonymous codon usage (RSCU) with GC content at the third codon position (GC3).
  • Evaluated deviations from neutral expectations using the effective number of codons and GC3 content, and assessed translational selection's imprint on codon usage.

Main Results:

  • Genome-wide codon usage strongly correlated with GC3, but proline, arginine, and glycine codon usage deviated from neutral expectations.
  • A significant proportion of genes (23%) and genomes (94%) showed substantial deviation from neutral codon usage.
  • Translational selection was widespread, influencing codon usage in 81% of genomes.

Conclusions:

  • Both genetic drift and translational selection contribute to synonymous codon usage variation in budding yeasts.
  • Drift is the primary driver of global codon usage patterns, while translational selection significantly influences codon bias in numerous genes and genomes.