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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.

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