An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales
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
BMC Evolutionary Biology 2012, 12:243 doi:10.1186/1471-2148-12-243Published: 12 December 2012
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.
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”.
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.