A tree of life based on protein domain organizations
A tree of life based on protein domain organizations
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DOI：
10.1093/molbev/msm034
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发表时间：
2007-05-01
影响因子：
10.7
通讯作者：
Nishikawa, Ken
中科院分区：
文献类型：
--
作者：
Fukami-Kobayashi, Kaoru;Minezaki, Yoshiaki;Nishikawa, Ken
我们希望利用全基因组信息，而不是有限数量的基因，来估计一棵生命树，一棵物种树，包括3个超级王国（古生物、细菌和真核生物）中所有可用的物种。在这里，我们报告了一种新的方法，用于构建一个生命树的基础上的蛋白质结构域的组织，即，在蛋白质中的结构域的顺序，在一个生物体的基因组中检测到的所有蛋白质。该方法不需要对同源基因集进行识别，因此不需要繁重且容易出错的计算。通过对17种古细菌、136种细菌和14种真核生物的蛋白质结构域组织进行成对比较，我们计算了它们之间的进化距离，并构建了一棵生命树。我们的树显示单系在真核生物，细菌，真核生物，然后单系在每个真核生物界和大多数细菌门。此外，我们的树中细菌门的分支模式与广泛接受的细菌分类学一致，并且非常接近其他基于基因组的树。然而，传统的树和基于基因组的树之间的一些不一致的方面，包括我们的，也许会敦促修改传统的观点，特别是在超嗜热菌的系统发育位置。
It is desirable to estimate a tree of life, a species tree including all available species in the 3 superkingdoms, Archaea, Bacteria, and Eukaryota, using not a limited number of genes but full-scale genome information. Here, we report a new method for constructing a tree of life based on protein domain organizations, that is, sequential order of domains in a protein, of all proteins detected in a genome of an organism. The new method is free from the identification of orthologous gene sets and therefore does not require the burdensome and error-prone computation. By pairwise comparisons of the repertoires of protein domain organizations of 17 archaeal, 136 bacterial, and 14 eukaryotic organisms, we computed evolutionary distances among them and constructed a tree of life. Our tree shows monophyly in Archaea, Bacteria, and Eukaryota and then monophyly in each of eukaryotic kingdoms and in most bacterial phyla. In addition, the branching pattern of the bacterial phyla in our tree is consistent with the widely accepted bacterial taxonomy and is very close to other genome-based trees. A couple of inconsistent aspects between the traditional trees and the genome-based trees including ours, however, would perhaps urge to revise the conventional view, particularly on the phylogenetic positions of hyperthermophiles.