Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, Japan.
PLoS One. 2013 Jul 26;8(7):e70290. doi: 10.1371/journal.pone.0070290. Print 2013.
Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.
已经使用基因序列信息为广泛的生物构建了系统发育树，特别是通过鉴定垂直遗传的同源基因。可用的完整基因组序列的数量正在迅速增加，并且已经提出了许多基于全基因组序列构建基因组树的工具。然而，尚未建立使用完整基因组序列构建系统发育树的合理方法。我们已经开发了一种基于全基因组序列平均序列相似性的系统发育树构建方法。我们使用该方法检查了 115 种光合原核生物，即蓝细菌、绿弯菌门、变形菌门、绿菌门、厚壁菌门和包括古菌在内的非光合生物的系统发育。尽管由于横向基因转移和饱和突变，门的分支顺序的自举值较低，但获得的树与先前报道的系统发育树大体一致，表明该方法是传统系统发育方法的可靠替代方法。
