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

BMC Genomics

Software

Ping Xu¹  Fei Su¹  Hongzhi Tang¹  Hong-Yu Ou¹  Fei Tao¹ 

[1] State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 200240, Shanghai, P.R. China;School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P.R. China;

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

DOI  :  10.1186/1471-2164-14-924

 received in 2013-07-24, accepted in 2013-12-26,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundWith 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.ResultsHere 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/.ConclusionsPSP 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.

【 授权许可】

Unknown   
© Su et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.