The genome of
R. africae consists of two replicons: a circular chromosome of 1,278,540 base pairs (bp) (Figure ) and a 12,377 bp circular plasmid (Table , Figure [
25,
26]). We acknowledge the fact that the ESF-5 strain, first isolated in 1966 [
27], may have undergone loss or rearrangement of plasmid or chromosomal genes during multiple passages in cell culture. Sequences were deposited in GenBank under accession number [GenBank:
NZ_AAUY01000001]. The chromosome has a G + C content of 32.4%, in the range of other SFG rickettsial genomes (32.3 – 32.5%), whereas the plasmid has a G + C content of 33.4%, similar to those of
R. felis (33.2 and 33.6%) [
28] but higher than that of
R. massiliae plasmids (31.4%). The predicted total complement of 1,271 open reading frames (ORFs), 1,260 chromosomal (78.26% coding sequence), and 11 plasmidic (81.3% coding sequence) ORFs [see Additional file
1], is in the range of genomes from SFG rickettsiae with the exception of
R. felis, which exhibits a larger genome (Table ). Of these, 1,117 (87.9%) exhibited homologs in the non-redundant database, and 1,024 (80.5%) were assigned putative functions [see Additional file
2]. Overall, the 1,260 chromosomal ORFs encoded 1,112 protein-coding genes, with 87 of these being split into 2 to 10 ORFs by the presence of one to several stop codons. By comparison with other SFG genomes,
R. africae had fewer split genes than any other species with the exception of
R. felis (Table ). In addition,
R. africae exhibited a single rRNA operon, with non-contiguous 16S and 23S rRNA genes as in other rickettsial genomes, 33 tRNAs and another three RNAs. The
R. africae chromosome exhibited an almost perfect colinearity with the
R. conorii genome [
23], with the exception of a 88,459-bp inversion [see Additional file
3]. At both extremities of the inversion, there were repeats of the
Rickettsia palindromic element – 6 (RPE-6) familly. In this inverted fragment,
R. africae exhibited 20 ORFs and 10 RPEs that were absent from
R. conorii. Among these 20 ORFs, a cluster of 11 consecutive ORFs had orthologs in the 3'-extremity of the Tra cluster previously identified in the
R. massiliae genome [
29]. These 11 ORFs included
traDF (ORF0650), a transposase (ORF0651),
spoT15 (ORF0652), a split
spoT13 (ORF0653/ORF0654), a split
spoT6 (ORF0655/ORF0656), a split signal transduction histidine kinase (ORF0657/ORF0658),
dam2, a site-specific DNA adenine methylase (ORF0659), and ORF0660 of unknown function (Figure ). In addition to the orthologs in
R. massiliae, these genes had orthologs in similar clusters in
R. felis,
R. bellii,
R. canadensis and
O. tsutsugamushi but were absent from all other species. As in
R. massiliae,
R. bellii and
R. canadensis, the
R. africae cluster was bounded at its 3'-end by a tRNA-Val, but, in contrast with these three species, neither an integrase with its
attI site nor a tRNA-Val fragment marker of integration was present at the 5' end (Figure ). The presence of a similar gene cluster inserted at the same position in several
Rickettsia species, with a GC content different from that of the genome (29.78%
vs 32.4%, respectively, in
R. africae) suggests that it was acquired horizontally from a common ancestor and then transmitted vertically. In
R. africae, an
attC site, specific to integron-inserted gene cassettes, located at the 3'-end (coordinates: 687890–688018) of the
spoT15 gene (ORF652), supports the role of integration in the insertion of this gene cluster.
AttC sites were also identified in
R. massiliae (coordinates: 743029–743145),
R. felis (coordinates: 407889–408017), and
R. bellii (coordinates 468143–468211). Nevertheless, the presence of transposases in all species and the fact that, in
R. felis, nine of these genes are located in the pRF plasmid support the role of several genetic mechanisms at the origin of this cluster, possibly involving plasmids, integrons and transposons. In comparison with other species containing this gene cluster,
R. africae had the smallest number of genes. In particular, it lacked most of the Tra cluster, with the exception of
traDF, but retained three
spoT genes, including two degraded to pseudogenes. In
R. bellii and
R. massiliae,
tra genes were described as encoding components of a type IV secretion system (T4SS) for conjugal DNA transfer [
15,
29]. In terms of gene content, the
R. africae cluster was more similar to those of
R. felis and
R. canadensis, with the loss of the Tra cluster, the conservation of
spoT genes and the presence of pseudogenes, than to those of
R. massiliae and
R. bellii, in which the Tra cluster was intact but
spoT genes were partially degraded. Such findings suggest that species-specific evolution of this gene cluster occurred, which likely resulted from gene excisions in
R. africae,
R. felis and
R. canadensis, or gene expansion by transposase duplication in
R. massiliae.
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