An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales

BMC Evolutionary Biology

Research Article

Olivier Chabrol¹  Laurent Guijarro¹  Pierre Pontarotti¹  Julien Paganini¹  Philippe Gouret¹  Hemalatha Golaconda Ramulu²  Phuong Thi Le²  Dider Raoult³ 

[1] Evolutionary biology and modeling, LATP UMR-CNRS 7353, Aix-Marseille University, 13331, Marseille, France;Evolutionary biology and modeling, LATP UMR-CNRS 7353, Aix-Marseille University, 13331, Marseille, France;Unit for Research on Emergent and Tropical Infectious Diseases, URMITE UMR CNRS 7278, IRD 198, Inserm 1095, Aix-Marseille University, 13005, Marseille, France;Unit for Research on Emergent and Tropical Infectious Diseases, URMITE UMR CNRS 7278, IRD 198, Inserm 1095, Aix-Marseille University, 13005, Marseille, France;

关键词: Horizontal gene transfer;    Rickettsiales;    Candidatus;    Sympatry;   

DOI  :  10.1186/1471-2148-12-243

 received in 2012-08-23, accepted in 2012-11-22,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundHorizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species.ResultsWe developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as “rhizome-like”.ConclusionsOur analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.

【 授权许可】

Unknown   
© Le et al.; licensee BioMed Central Ltd. 2012. 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.