Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach  

作　　者：SUN JianDong XU Zhao HAO BaiLin 

机构地区：[1]T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China [2]Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China [3]Santa Fe Institute, Santa Fe, New Mexico 87501, USA

出　　处：《Chinese Science Bulletin》2010年第22期2323-2328,共6页

基　　金：supported by the National Basic Research Program of China (2007CB814800);Shanghai Leading Academic Discipline Project (B111)

摘　　要：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.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.

关 键 词：细菌分类学 全基因组 系统发育 矢量方法 组分 古细菌 亲缘关系 真核生物 

分 类 号：Q939.109[生物学—微生物学] Q78