Published online 23 February 2005
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Variation in the strength of selected codon usage bias among bacteria
Institute of Genetics, University of Nottingham, Queens Medical Centre Nottingham NG7 2UH, UK
*To whom correspondence should be addressed. Tel: +44 115 9709263; Fax: +44 115 9709906; Email: paul{at}evol.nott.ac.uk
Received December 15, 2004. Revised January 10, 2005. Accepted January 23, 2005.
Among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. However, in other species selection appears to have been ineffective. Here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. The approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. The strength of selected codon usage bias, S, is found to vary substantially among species; in 30% of the genomes examined, there was no significant evidence that selection had been effective. Values of S are highly positively correlated with both the number of rRNA operons and the number of tRNA genes. These results are consistent with the hypothesis that species exposed to selection for rapid growth have more rRNA operons, more tRNA genes and more strongly selected codon usage bias. For example, Clostridium perfringens, the species with the highest value of S, can have a generation time as short as 7 min.
Present addresses: Russell J. Grocock, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
John F. Peden, Cardiovascular Medicine, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
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