Dichotomy of major bacterial phyla inferred from gene arrangement comparisons

Takashi Kunisawa, Science University of Tokyo, Japan

Currently, more than 350 prokaryotic genomes were completely sequenced and are stored in the major databases GenBank/EMBL/DDBJ. The availability of genomic sequence data allows new challenges to various biological problems. One of such attempts is the extraction of phylogenetic information from gene order data of genomes. As will be discussed here, such an attempt presents a new unexpected feature of the bacterial evolution.

   A computer search for gene arrangements that are present in Gram-positive bacteria but are absent from Proteobacteria and vice versa was carried out. Four such arrangements were detected, based on which major bacterial phyla were divided into two groups; Thermotoga, Deinococcus-Thermus, Chloroflexi (green non-sulfur bacteria), and Fusobacteria, represent Gram-positive bacterial gene arrangements, while Aquifex, Spirochetes, Planctomycetes, Chlorobi (green sulfur bacteria), Bacteroides show Proteobacterial arrangements. The division is almost consistent with another partition of the major phyla based on the comparison of domain architectures of RNA polymerase subunits and sigma factor, suggesting a fundamental split of the major bacterial phyla at an early stage of bacterial evolution.

   The dichotomy of the bacterial major phyla essentially differs from the traditional view of the bacterial evolution based on rRNA sequences, which indicates that hyperthermophilic bacteria, i.e., Aquifex and Thermotoga, emerged first and then the rest of the major phyla radiated at approximately the same origin.


keywords: genome, gene order, bacteria, phylogeny