Table of Contents
International Journal of Evolutionary Biology
Volume 2011, Article ID 376831, 8 pages
http://dx.doi.org/10.4061/2011/376831
Research Article

Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence Comparisons

1Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
2Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-8510, Japan
3Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan

Received 21 September 2010; Accepted 27 November 2010

Academic Editor: Hideaki Nojiri

Copyright © 2011 Kenro Oshima et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Comparisons of gene content and orthologous protein sequence constitute a major strategy in whole-genome comparison studies. It is expected that horizontal gene transfer between phylogenetically distant organisms and lineage-specific gene loss have greater influence on gene content-based phylogenetic analysis than orthologous protein sequence-based phylogenetic analysis. To determine the evolution of the syntrophic bacterium Symbiobacterium thermophilum, we analyzed phylogenetic relationships among Clostridia on the basis of gene content and orthologous protein sequence comparisons. These comparisons revealed that these 2 phylogenetic relationships are topologically different. Our results suggest that each Clostridia has a species-specific gene content because frequent genetic exchanges or gene losses have occurred during evolution. Specifically, the phylogenetic positions of syntrophic Clostridia were different between these 2 phylogenetic analyses, suggesting that large diversity in the living environments may cause the observed species-specific gene content. S. thermophilum occupied the most distant position from the other syntrophic Clostridia in the gene content-based phylogenetic tree. We identified 32 genes (14 under relaxed selection and 18 under functional constraint) evolving under Symbiobacterium-specific selection on the basis of synonymous-to-nonsynonymous substitution ratios. Five of the 14 genes under relaxed selection are related to transcription. In contrast, none of the 18 genes under functional constraint is related to transcription.