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Open Access Highly Accessed Research article

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

Phuong Thi Le12, Hemalatha Golaconda Ramulu12, Laurent Guijarro1, Julien Paganini1, Philippe Gouret1, Olivier Chabrol1, Dider Raoult2 and Pierre Pontarotti1*

Author Affiliations

1 Evolutionary biology and modeling, LATP UMR-CNRS 7353, Aix-Marseille University, Marseille, 13331, France

2 Unit for Research on Emergent and Tropical Infectious Diseases, URMITE UMR CNRS 7278, IRD 198, Inserm 1095, Aix-Marseille University, Marseille, 13005, France

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BMC Evolutionary Biology 2012, 12:243  doi:10.1186/1471-2148-12-243

Published: 12 December 2012

Abstract

Background

Horizontal 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.

Results

We 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”.

Conclusions

Our 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.

Keywords:
Horizontal gene transfer; Rickettsiales; Candidatus Pelagibacter ubique; Sympatry