A tree of life based on protein domain organizations.
Fukami-Kobayashi K, Minezaki Y, Tateno Y, Nishikawa K.
RIKEN BioResource Center, RIKEN Tsukuba Institute, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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