title: Gene gain and loss events in Rickettsia and Orientia species.
abstract: BACKGROUND
  Genome degradation is an ongoing process in all members of the Rickettsiales order, which makes these bacterial species an excellent model for studying reductive evolution through interspecies variation in genome size and gene content. In this study, we evaluated the degree to which gene loss shaped the content of some Rickettsiales genomes. We shed light on the role played by horizontal gene transfers in the genome evolution of Rickettsiales.
  
  
  RESULTS
  Our phylogenomic tree, based on whole-genome content, presented a topology distinct from that of the whole core gene concatenated phylogenetic tree, suggesting that the gene repertoires involved have different evolutionary histories. Indeed, we present evidence for 3 possible horizontal gene transfer events from various organisms to Orientia and 6 to Rickettsia spp., while we also identified 3 possible horizontal gene transfer events from Rickettsia and Orientia to other bacteria. We found 17 putative genes in Rickettsia spp. that are probably the result of de novo gene creation; 2 of these genes appear to be functional. On the basis of these results, we were able to reconstruct the gene repertoires of "proto-Rickettsiales" and "proto-Rickettsiaceae", which correspond to the ancestors of Rickettsiales and Rickettsiaceae, respectively. Finally, we found that 2,135 genes were lost during the evolution of the Rickettsiaceae to an intracellular lifestyle.
  
  
  CONCLUSIONS
  Our phylogenetic analysis allowed us to track the gene gain and loss events occurring in bacterial genomes during their evolution from a free-living to an intracellular lifestyle. We have shown that the primary mechanism of evolution and specialization in strictly intracellular bacteria is gene loss. Despite the intracellular habitat, we found several horizontal gene transfers between Rickettsiales species and various prokaryotic, viral and eukaryotic species.
  
  
  BACKGROUND
  Reviewed by Arcady Mushegian, Eugene V. Koonin and Patrick Forterre. For the full reviews please go to the Reviewers' comments section.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE, CNRS-IRD UMR 6236 IFR48 Faculté de Médecine, Université de la Méditerranée, Marseille, France.
authors.forename: Kalliopi
authors.initials: K
authors.lastname: Georgiades
authors.forename: Vicky
authors.initials: V
authors.lastname: Merhej
authors.forename: Khalid
authors.initials: K
authors.lastname: El Karkouri
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
mesh_terms: D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics; D012285:Orientia tsutsugamushi / Q000235:genetics*; D010802:Phylogeny; D012281:Rickettsia / Q000235:genetics*; D013045:Species Specificity