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Whole-genome based Archaea phylogeny and taxonomy： A composition vector approach
  • ISSN号：1674-1056
  • 期刊名称：《中国物理B：英文版》
  • 时间：0
  • 分类：Q939.109[生物学—微生物学] Q78[生物学—分子生物学]
  • 作者机构：[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
  • 相关基金：This work was supported by the National Basic Research Program of China （2007CB814800） and Shanghai Leading Academic Discipline Project （B111）.
作者： SUN JianDong[1], XU Zhao[1], HAO BaiLin[1,2,3]
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, Archaea, phylogeny, taxonomy, composition vector, alignment-free, CVTree, 16S rRNA analysis
中文摘要：

最新建议没有排列、没有参数的作文向量(CVtree ) 方法成功地被使用了从他们的整个染色体的数据推断病毒，叶绿体，细菌，和真菌的种系发生的关系。在系统的细菌学的 Bergeys 手册或在细菌和 Archaea (TOBA ) 的分类轮廓在我们对 7 种类一直不是的 56 个 Archaea 在之中染色体的种系发生的位置给予特殊注意的这研究列出了任何一个。由检查稳定的 monophyletic，在 CVTrees 的分叉从 861 个染色体的一个总数重建了(加 797 个细菌的 56 Archaea，把 8 Eukarya 用作外集团) 明确的分类任务为这些 not-fully-classified 种类被建议。Archaea 分类的进一步的开发可以验证 CVTree 途径的预言的种系发生的结果。

英文摘要：

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.

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期刊信息
  • 《中国物理B：英文版》
  • 中国科技核心期刊
  • 主管单位:中国科学院
  • 主办单位:中国物理学会和中国科学院物理研究所
  • 主编：欧阳钟灿
  • 地址：北京 中关村 中国科学院物理研究所内
  • 邮编：100080
  • 邮箱：
  • 电话：010-82649026 82649519
  • 国际标准刊号：ISSN：1674-1056
  • 国内统一刊号：ISSN：11-5639/O4
  • 邮发代号:
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  • 被引量:406