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

Abstract

AbstractBackgroundHorizontal 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 inRickettsialesgenomes. 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 intoRickettsialesspecies.ResultsWe developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) intoRickettsialesgenomes. 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 completeRickettsialesgenomes, of which 38 were previously unidentified instances of HGT fromAnaplasma,Wolbachia,CandidatusPelagibacter ubique andRickettsiagenomes. 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.