Takahashi Mahoko, Kryukov Kirill, Saitou Naruya
Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411-8540, Japan.
Genomics. 2009 Jun;93(6):525-33. doi: 10.1016/j.ygeno.2009.01.009. Epub 2009 Feb 12.
Classification of bacteria is mainly based on sequence comparisons of certain homologous genes such as 16S rRNA. Recently there are challenges to classify bacteria using oligonucleotide frequency pattern of nonhomologous sequences. However, the evolutionary significance of oligonucleotides longer than tetra-nucleotide is not studied well. We performed phylogenetic analysis by using the Euclidean distances calculated from the di to deca-nucleotide frequencies in bacterial genomes, and compared these oligonucleotide frequency-based tree topologies with those for 16S rRNA gene and concatenated seven genes. When oligonucleotide frequency-based trees were constructed for bacterial species with similar GC content, their topologies at genus and family level were congruent with those based on homologous genes. Our results suggest that oligonucleotide frequency is useful not only for classification of bacteria, but also for estimation of their phylogenetic relationships for closely related species.
细菌分类主要基于某些同源基因（如16S rRNA）的序列比较。最近，利用非同源序列的寡核苷酸频率模式对细菌进行分类面临挑战。然而，对于长度超过四核苷酸的寡核苷酸的进化意义尚未进行充分研究。我们通过使用从细菌基因组中二核苷酸到十核苷酸频率计算出的欧几里得距离进行系统发育分析，并将这些基于寡核苷酸频率的树形拓扑结构与基于16S rRNA基因和七个串联基因的拓扑结构进行比较。当为具有相似GC含量的细菌物种构建基于寡核苷酸频率的树时，它们在属和科水平的拓扑结构与基于同源基因的拓扑结构一致。我们的结果表明，寡核苷酸频率不仅有助于细菌分类，还可用于估计密切相关物种之间的系统发育关系。
