Abstract
BackgroundIn many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, we introduce a mean dissimilarity-based index (Dmean) for quantifying the level of diversity in synonymous codon usage among all genes within a genome.ResultsThe application of Dmean to 268 bacterial genomes shows that in bacteria with extremely biased genomic G+C compositions there is little diversity in synonymous codon usage among genes. Furthermore, our findings contradict previous reports. For example, a low level of diversity in codon usage among genes has been reported for Helicobacter pylori, but based on Dmean, the diversity level of this species is higher than those of more than half of bacteria tested here. The discrepancies between our findings and previous reports are probably due to differences in the methods used for measuring codon usage diversity.ConclusionWe recommend that Dmean be used to measure the diversity level of codon usage among genes. This measure can be applied to other compositional features such as amino acid usage and dinucleotide relative abundance as a genomic signature.
Highlights
In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported
The D values for B. burgdorferi exhibited a bimodal distribution with a left peak corresponding to within-strand dissimilarities and a right peak corresponding to between-strand dissimilarities (Figure 1A), whereas those for T. pallidum exhibited a monomodal distribution (Figure 1B)
The D values tended to be smaller in B. burgdorferi than in T. pallidum
Summary
Intragenomic diversity in synonymous codon usage among genes has been reported. No quantitative attempt has been made to compare the diversity levels among different genomes. We introduce a mean dissimilarity-based index (Dmean) for quantifying the level of diversity in synonymous codon usage among all genes within a genome. It was shown that in many organisms there are considerable differences in codon usage among genes within a genome [2]. Previous analyses of codon usage diversity in bacteria have mostly focused on individual genomes, with no quantitative attempt to compare the diversity levels among different genomes. It is desirable to quantify the level of codon usage diversity among genes in such a way that the estimates could be compared among genomes
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