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Selection Shapes Synonymous Stop Codon Use in Mammals.

Cathal Seoighe1, Stephen J Kiniry2, Andrew Peters3

  • 1School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland. Cathal.Seoighe@nuigalway.ie.

Journal of Molecular Evolution
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Summary
This summary is machine-generated.

Selection influences stop codon usage in mammals, with nearly 60% of genes showing conserved stop codons, particularly UGA. This suggests evolutionary pressures, not just mutation, shape stop codon preference.

Keywords:
Evolutionary modelSelectionStop codon

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Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Genomics

Background:

  • Phylogenetic models analyze protein-coding sequence evolution and selection pressures.
  • Synonymous nucleotide substitutions are often treated as neutral, proxying the neutral rate of evolution.
  • Nonsynonymous/synonymous substitution rate ratios categorize protein selective regimes.

Purpose of the Study:

  • Extend the Muse and Gaut model to investigate purifying selection on synonymous stop codon substitutions.
  • Quantify the extent of selection acting on stop codon preference in mammalian genes.

Main Methods:

  • Applied an extended Muse and Gaut model to coding sequence alignments.
  • Analyzed a large collection of mammalian coding sequence alignments.
  • Compared characteristics of genes with and without selection on stop codons.

Main Results:

  • Approximately 57% of mammalian genes show evidence of selection on stop codon preference.
  • UGA stop codons are significantly more conserved than other synonymous stop codons.
  • Genes under selection on stop codons exhibit longer untranslated regions and shorter mRNA half-lives.
  • These genes are also under stronger purifying selection in their coding regions.

Conclusions:

  • Stop codon preference in multicellular eukaryotes, especially for UGA, is likely driven by selection, not solely by mutation.
  • Synonymous stop codon usage is under functional constraint and evolutionary pressure.
  • Stop codon selection impacts gene regulation and coding region evolution.