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Open Access Software

PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes

Fei Su12, Hong-Yu Ou12, Fei Tao12, Hongzhi Tang12 and Ping Xu12*

Author Affiliations

1 State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, P.R. China

2 School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China

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BMC Genomics 2013, 14:924  doi:10.1186/1471-2164-14-924

Published: 27 December 2013

Abstract

Background

With genomic sequences of many closely related bacterial strains made available by deep sequencing, it is now possible to investigate trends in prokaryotic microevolution. Positive selection is a sub-process of microevolution, in which a particular mutation is favored, causing the allele frequency to continuously shift in one direction. Wide scanning of prokaryotic genomes has shown that positive selection at the molecular level is much more frequent than expected. Genes with significant positive selection may play key roles in bacterial adaption to different environmental pressures. However, selection pressure analyses are computationally intensive and awkward to configure.

Results

Here we describe an open access web server, which is designated as PSP (Positive Selection analysis for Prokaryotic genomes) for performing evolutionary analysis on orthologous coding genes, specially designed for rapid comparison of dozens of closely related prokaryotic genomes. Remarkably, PSP facilitates functional exploration at the multiple levels by assignments and enrichments of KO, GO or COG terms. To illustrate this user-friendly tool, we analyzed Escherichia coli and Bacillus cereus genomes and found that several genes, which play key roles in human infection and antibiotic resistance, show significant evidence of positive selection. PSP is freely available to all users without any login requirement at: http://db-mml.sjtu.edu.cn/PSP/ webcite.

Conclusions

PSP ultimately allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily, and identify the genes undergoing positive selection, which may play key roles in the interactions of host-pathogen and/or environmental adaptation.

Keywords:
Orthologous genes; Positive selection; Synonymous and nonsynonymous substitutions; Bacterial microevolution; Bacillus cereus; Escherichia coli