| Summary: | <p>Abstract</p> <p>Background</p> <p>Genome degradation is an ongoing process in all members of the <it>Rickettsiales </it>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 <it>Rickettsiales </it>genomes. We shed light on the role played by horizontal gene transfers in the genome evolution of <it>Rickettsiales</it>.</p> <p>Results</p> <p>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 <it>Orientia </it>and 6 to <it>Rickettsia </it>spp., while we also identified 3 possible horizontal gene transfer events from <it>Rickettsia </it>and <it>Orientia </it>to other bacteria. We found 17 putative genes in <it>Rickettsia </it>spp. that are probably the result of <it>de novo </it>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-<it>Rickettsiales</it>" and "proto-<it>Rickettsiaceae</it>", which correspond to the ancestors of <it>Rickettsiales </it>and <it>Rickettsiaceae</it>, respectively. Finally, we found that 2,135 genes were lost during the evolution of the <it>Rickettsiaceae </it>to an intracellular lifestyle.</p> <p>Conclusions</p> <p>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 <it>Rickettsiales </it>species and various prokaryotic, viral and eukaryotic species.</p> <p>Open peer review</p> <p>Reviewed by Arcady Mushegian, Eugene V. Koonin and Patrick Forterre. For the full reviews please go to the Reviewers' comments section.</p>
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