TY - JOUR
T1 - Functional bias of positively selected genes in Streptococcus genomes
AU - Suzuki, Haruo
AU - Stanhope, Michael J.
N1 - Funding Information:
We thank Tristan Lefébure for helpful discussion, Sergei L. Kosakovsky Pond for his advice on HyPhy, and Robert Bukowski, Andrew Dolgert, and Linda Woodard for their help with the parallelization of the analyses on a Linux cluster at the Computational Biology Service Unit (CBSU) and Center for Advanced Computing (CAC) of Cornell University. This work was supported by the National Institute of Allergy and Infectious Disease , US National Institutes of Health, under Grant No. AI073368-01A2 awarded to M.J.S.
Copyright:
Copyright 2012 Elsevier B.V., All rights reserved.
PY - 2012/3
Y1 - 2012/3
N2 - Rates of nonsynonymous substitution (dN) significantly higher than rates of synonymous substitution (dS) have been used as evidence of positive selection for the fixation of advantageous point mutations. It has been suggested that positive selection contributes to the evolution of virulence factors and certain functional categories in bacterial pathogens. The genus Streptococcus contains a number of important human and agricultural pathogens. Here we assessed positive selection across 13 Streptococcus species, and their relationship with virulence factors and functional categories. We found that known virulence genes were subject to positive selection pressure as much as other genes. After false discovery rate correction for multiple comparisons, no functional categories were significantly over- or under-represented in positively selected genes relative to other genes. Our results suggest that within the genus Streptococcus positive selection based on dN/dS ratios is not distributed with bias across biological functions.
AB - Rates of nonsynonymous substitution (dN) significantly higher than rates of synonymous substitution (dS) have been used as evidence of positive selection for the fixation of advantageous point mutations. It has been suggested that positive selection contributes to the evolution of virulence factors and certain functional categories in bacterial pathogens. The genus Streptococcus contains a number of important human and agricultural pathogens. Here we assessed positive selection across 13 Streptococcus species, and their relationship with virulence factors and functional categories. We found that known virulence genes were subject to positive selection pressure as much as other genes. After false discovery rate correction for multiple comparisons, no functional categories were significantly over- or under-represented in positively selected genes relative to other genes. Our results suggest that within the genus Streptococcus positive selection based on dN/dS ratios is not distributed with bias across biological functions.
KW - Gene functional categories
KW - Positive selection
KW - Streptococcus
KW - Virulence factor
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U2 - 10.1016/j.meegid.2011.11.004
DO - 10.1016/j.meegid.2011.11.004
M3 - Article
C2 - 22155358
AN - SCOPUS:84863408547
VL - 12
SP - 274
EP - 277
JO - Infection, Genetics and Evolution
JF - Infection, Genetics and Evolution
SN - 1567-1348
IS - 2
ER -
