title: An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales.
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.
authors.affiliation: Evolutionary biology and modeling, LATP UMR-CNRS 7353, Aix-Marseille University, 13331, Marseille, France.
authors.forename: Phuong Thi
authors.initials: PT
authors.lastname: Le
authors.forename: Hemalatha Golaconda
authors.initials: HG
authors.lastname: Ramulu
authors.forename: Laurent
authors.initials: L
authors.lastname: Guijarro
authors.forename: Julien
authors.initials: J
authors.lastname: Paganini
authors.forename: Philippe
authors.initials: P
authors.lastname: Gouret
authors.forename: Olivier
authors.initials: O
authors.lastname: Chabrol
authors.forename: Dider
authors.initials: D
authors.lastname: Raoult
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
mesh_terms: D020561:Alphaproteobacteria / Q000235:genetics*; D001499:Bayes Theorem; D001330:Electronic Data Processing; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D020543:Proteome / Q000032:analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D020543:Proteome; D012336:RNA, Ribosomal, 16S