Suzuki Haruo, Saito Rintaro, Tomita Masaru
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
BMC Bioinformatics. 2009 Jun 1;10:167. doi: 10.1186/1471-2105-10-167.
In 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.
The 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.
We 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.
在许多细菌中，已有报道称基因间同义密码子使用存在基因组内多样性。然而，尚未有定量研究尝试比较不同基因组间的多样性水平。在此，我们引入一种基于平均差异的指数（Dmean），用于量化基因组内所有基因间同义密码子使用的多样性水平。
将Dmean应用于268个细菌基因组表明，在基因组G+C组成极度偏向的细菌中，基因间同义密码子使用的多样性很小。此外，我们的发现与先前的报道相矛盾。例如，先前有报道称幽门螺杆菌基因间密码子使用的多样性水平较低，但基于Dmean，该物种的多样性水平高于此处测试的半数以上细菌。我们的发现与先前报道之间的差异可能是由于测量密码子使用多样性的方法不同。
我们建议使用Dmean来测量基因间密码子使用的多样性水平。该方法可作为一种基因组特征，应用于其他组成特征，如氨基酸使用和二核苷酸相对丰度。
