Sun JianDong, Xu Zhao, Hao BaiLin
1T-Life Research Center & Department of Physics, Fudan University, Shanghai, 200433 China.
2Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, 100190 China.
Chin Sci Bull. 2010;55(22):2323-2328. doi: 10.1007/s11434-010-3008-8. Epub 2010 Aug 11.
The newly proposed alignment-free and parameter-free composition vector (CVtree) method has been successfully applied to infer phylogenetic relationship of viruses, chloroplasts, bacteria, and fungi from their whole-genome data. In this study we pay special attention to the phylogenetic positions of 56 Archaea genomes among which 7 species have not been listed either in Bergey's Manual of Systematic Bacteriology or in Taxonomic Outline of Bacteria and Archaea (TOBA). By inspecting the stable monophyletic branchings in CVTrees reconstructed from a total of 861 genomes (56 Archaea plus 797 Bacteria, using 8 Eukarya as outgroups) definite taxonomic assignments were proposed for these not-fully-classified species. Further development of Archaea taxonomy may verify the predicted phylogenetic results of the CVTree approach.
新提出的无比对和无参数的成分向量（CVtree）方法已成功应用于从病毒、叶绿体、细菌和真菌的全基因组数据推断它们的系统发育关系。在本研究中，我们特别关注56个古菌基因组的系统发育位置，其中有7个物种在《伯杰氏系统细菌学手册》或《细菌和古菌分类大纲》（TOBA）中均未列出。通过检查从总共861个基因组（56个古菌加797个细菌，以8个真核生物作为外类群）重建的CVTree中稳定的单系分支，为这些未完全分类的物种提出了明确的分类学归属。古菌分类学的进一步发展可能会验证CVTree方法预测的系统发育结果。
