Gene gain and loss events in Rickettsia and Orientiaspecies

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.

Reassessment of the Listeria monocytogenespan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome

“…Other studies on Rickettsia/Orienta species and E.coli/Shigella found considerable differences in the respective phylogenies indicating more distinct evolutionary histories for the gene repertoires involved [44,76]. The relative correspondence of SNPs and gene-scale indels in genus Listeria could be a result of differential acquisition and loss of genes in accordance to various evolutionary descents as previously described considering other genera [77,78].…”

Small Regulatory RNAs of Rickettsia conorii

“…The inference of this study that sequences homologous to most R. conorii trans-acting sRNAs are confined to only a few other rickettsial genomes excluding those from the typhus group, is expected owing to the genetic diversity resulting from gene degradation, transposon mutagenesis, repetitive and insertion sequences, mobile genetic elements, and lateral gene transfer1333. Computational comparison of rickettsial genomes reveals that nearly 50% of the genes encoded by each species/strain are unique to its genome with approximately 700 protein coding genes shared across all genomes1112.…”

What contemporary viruses tell us about evolution: a personal view

“…Also, bacteria became obligatory intracellular symbionts as mitochondria or chloroplasts of eukaryotic cells and delegated most of their genes to the nucleus, while the residual 300 genes, about 10 % of the total, were maintained and used for special functions. Is specialization traded off for loss of mobility [39, 66, 67]? Gene reduction or loss of genes may correlate with acquisition of special functions.…”