Synonymous codon usage is subject to selection in thermophilic bacteria

David J. Lynn, Gregory A.C. Singer, Donal A. Hickey

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156 Citations (Scopus)


The patterns of synonymous codon usage, both within and among genomes, have been extensively studied over the past two decades. Despite the accumulating evidence that natural selection can shape codon usage, it has not been possible to link a particular pattern of codon usage to a specific external selective force. Here, we have analyzed the patterns of synonymous codon usage in 40 completely sequenced prokaryotic genomes. By combining the genes from several genomes (more than 80 000 genes in all) into a single dataset for this analysis, we were able to investigate variations in codon usage, both within and between genomes. The results show that synonymous codon usage is affected by two major factors: (i) the overall G+C content of the genome and (ii) growth at high temperature. This study focused on the relationship between synonymous codon usage and the ability to grow at high temperature. We have been able to eliminate both phylogenetic history and lateral gene transfer as possible explanations for the characteristic pattern of codon usage among the thermophiles. Thus, these results demonstrate a clear link between a particular pattern of codon usage and an external selective force.

Original languageEnglish
Pages (from-to)4272-4277
Number of pages6
JournalNucleic Acids Research
Issue number19
Publication statusPublished or Issued - 1 Oct 2002
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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