Jul 27, 2010

Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto group of yeasts

Molecular Biology and Evolution
Richard J Harrison, Brian Charlesworth

Abstract

Patterns of synonymous codon usage vary between organisms and are controlled by neutral processes (such as drift and mutation) as well as by selection. Here we show that an additional neutral process, GC-biased gene conversion (gBGC), plays a part in shaping patterns of both synonymous codon usage and amino acid composition in a manner dependent upon the local recombination rate. We obtain estimates of the strength of gBGC acting on synonymous sites in five species of yeast, which we find to be a much weaker force than selection. We use this to correct estimates of the strength of selection on codon usage bias, which are normally confounded by the action of gBGC. Our estimate of the rate of gBGC agrees well with an experimentally determined value obtained from Saccharomyces cerevisiae. We also find that, contrary to expectation, codon usage bias is highest in areas of intermediate levels of recombination for GC-ending optimal codons. Possible reasons for this are discussed.

  • References55
  • Citations14

References

Mentioned in this Paper

Saccharomyces cerevisiae allergenic extract
Polaron
Recombination, Genetic
Yeasts
Saccharomyces
Phylogeny
Sense Codon
Codon Genus
Codon (Nucleotide Sequence)
Unassigned Reading Frames

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