Phylogenomic analysis of natural selection pressure in Streptococcus genomes
Date
2007-08
Authors
Anisimova, Maria
Bielawski, Joseph P.
Dunn, Katherine
Yang, Ziheng
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract
Background: In comparative analyses of bacterial pathogens, it has been common practice to
discriminate between two types of genes: (i) those shared by pathogens and their non-pathogenic
relatives (core genes), and (ii) those found exclusively in pathogens (pathogen-specific accessory
genes). Rather than attempting to a priori delineate genes into sets more or less relevant to
pathogenicity, we took a broad approach to the analysis of Streptococcus species by investigating
the strength of natural selection in all clusters of homologous genes. The genus Streptococcus is
comprised of a wide variety of both pathogenic and commensal lineages, and we relate our findings to
the pre-existing knowledge of Streptococcus virulence factors. Results: Our analysis of 1730 gene
clusters revealed 136 cases of positive Darwinian selection, which we suggest is most likely to
result from an antagonistic interaction between the host and pathogen at the molecular level. A
two-step validation procedure suggests that positive selection was robustly identified in our
genomic survey. We found no evidence to support the notion that pathogen specific accessory genes
are more likely to be subject to positive selection than core genes. Indeed, we even uncovered a few
cases of essential gene evolution by positive selection. Among the gene clusters subject to positive
selection, a large fraction (29%) can be connected to virulence. The most striking finding was that
a considerable fraction of the positively selected genes are also known to have tissue specific
patterns of expression during invasive disease. As current expression data is far from
comprehensive, we suggest that this fraction was underestimated. Conclusion: Our findings suggest
that pathogen specific genes, although a popular focus of research, do not provide a complete
picture of the evolutionary dynamics of virulence. The results of this study, and others, support
the notion that the products of both core and accessory genes participate in complex networks that
comprise the molecular basis of virulence. Future work should seek to understand the evolutionary
dynamics of both core and accessory genes as a function of the networks in which they
participate.
Description
Keywords
Citation
Anisimova, Maria, Joseph Bielawski, Katherine Dunn, and Ziheng Yang. 2007. "Phylogenomic analysis of natural selection pressure in Streptococcus genomes." Bmc Evolutionary Biology 7: 154-154.