Scapoli C, Bartolomei E, De Lorenzi S, Carrieri A, Salvatorelli G, Rodriguez-Larralde A, Barrai I
Department of Biology and Evolution, University of Ferrara, Ferrara, Italy.
J Mol Microbiol Biotechnol. 2009;17(2):53-60. doi: 10.1159/000195674. Epub 2009 Jan 21.
The large number of organisms and of genes sequenced at the present time permits now to study molecular evolution in such lower clades as genera, species, and subspecies. Here, we focus our attention on the genus Mycobacterium, in which we examined codon and aminoacid usage in 13 species, and in 12 subspecies for a total of 8,836,513 codons from 26,755 sequences. Within the genus Mycobacterium, frequencies of codon and aminoacid usage correlate between species and between subspecies. In the groups studied, aminoacid molecular weight and codon degeneracy influence correlations between frequencies, while GC content is the main factor influencing the effective number of codons. The coding GC, which is highly correlated with total genomic GC content, seems to be the main factor influencing present synonymous codon usage in the genus. In particular, the GC content at the 3rd base position seems to shape heavily the effective number of codons, giving indication that here mutational bias dominates over translational selection. Evolutionary trees based on codon and aminoacid usage are consistent with traditional phylogenies of species within the genus.
目前大量的生物体和已测序的基因使得现在能够在属、种和亚种等较低分类群中研究分子进化。在这里，我们将注意力集中在分枝杆菌属上，我们研究了该属中13个种和12个亚种的密码子和氨基酸使用情况，共涉及来自26,755个序列的8,836,513个密码子。在分枝杆菌属内，种间和亚种间密码子和氨基酸使用频率存在相关性。在所研究的群体中，氨基酸分子量和密码子简并性影响频率之间的相关性，而GC含量是影响密码子有效数量的主要因素。编码区GC含量与全基因组GC含量高度相关，似乎是影响该属当前同义密码子使用的主要因素。特别是，第3位碱基的GC含量似乎对密码子有效数量有很大影响，这表明在这里突变偏向超过了翻译选择。基于密码子和氨基酸使用情况构建的进化树与该属内物种的传统系统发育一致。
