Ando, Shuji

ABSTRACT The genus Rickettsia comprises obligate intracellular bacteria belonging to the class Alphaproteobacteria. Although Rickettsia species have traditionally been classified into several phylogenetic groups, recent genome-based studies have revealed greater diversity within the genus and related Rickettsiaceae lineages than previously recognized. Here, we isolated six rickettsial strains from Ixodes turdus ticks collected at various locations across Japan and performed whole-genome sequencing. A closed-genome sequence was obtained for one of the isolates. The six isolates shared highly similar genomic features and were identified as “ Candidatus Rickettsia mendelii” on the basis of conserved rickettsial marker gene sequences. The genomes of “ Ca . R. mendelii” were smaller (1.05–1.06 Mb) and had lower GC content (29.2–29.3%) than most analyzed rickettsial genomes and were comparable in these respects to those of Typhus Group rickettsiae. Family-wide phylogenomic analysis using a quality-filtered Rickettsiaceae genome data set placed “ Ca . R. mendelii” in a distinct early-diverging lineage within the genus Rickettsia . Chromosome-level comparisons with many other Rickettsia species revealed stretches of conserved synteny distributed across the chromosome of “ Ca . R. mendelii.” Genes encoding major secretion-related and host interaction-associated components were detected, whereas no hits meeting the detection criteria were obtained for the F-type IV secretion system (F-T4SS) proteins encoded by Rickettsiales-amplified genetic elements (RAGEs). These results provide the first genome sequences from cultured “ Ca . R. mendelii” isolates and expand our understanding of genome diversity and evolution within the genus Rickettsia . IMPORTANCE Genome-based studies have expanded the known diversity of the genus Rickettsia and related Rickettsiaceae lineages, but genome information from cultured isolates remains unavailable for some poorly characterized taxa. Here, we report the first whole-genome sequences from six cultured isolates of “ Ca . R. mendelii” and show that this taxon represents a distinct early-diverging lineage within the genus Rickettsia . The genomes of “ Ca . R. mendelii” were smaller and had lower GC content than most analyzed rickettsial genomes and were comparable in these respects to those of Typhus Group rickettsiae, despite the distinct phylogenetic placement. This indicates that similar genome characteristics can occur in phylogenetically distant rickettsial lineages. The low genomic diversity among geographically separated “ Ca . R. mendelii” isolates suggests broad dispersal of closely related strains, which may be facilitated by infected ticks carried by migratory birds. These findings improve our understanding of the genome characteristics and geographic distribution of “ Ca . R. mendelii.”

Abstract Rickettsia species, which constitute obligate intracellular bacteria adapted to a host-dependent lifestyle, have traditionally been classified into four phylogenetic groups. However, the available genomes are biased toward the Typhus and Spotted Fever groups, with early-diverging Ancestral group (AG) lineages being underrepresented. Here, we isolated six Candidatus Rickettsia mendelii strains from Ixodes turdus ticks in Japan. We obtained their whole-genome sequences, including one closed genome, and found that they form a distinct lineage in the AG and have the smallest genome among the known rickettsial species. Gene tree-aware reconstruction of evolutionary events using amalgamated likelihood estimation revealed that the last common ancestor of Rickettsia had a smaller gene family size than modern species do, and Ca . R. mendelii retains the most similar genomic content to this ancestral state. Various patterns of gene gain and loss among Rickettsia lineages were also suggested, highlighting their divergent evolutionary trajectories. These findings increase our understanding of Rickettsia genome evolution.

AbstractMany Rickettsia species of the spotted fever group (SFG) cause tick‐borne diseases known as “spotted fever.” One of the candidate SFG Rickettsia species is “Candidatus Rickettsia kotlanii,” which was first detected in Haemaphysalis concinna in Hungary in 2006. However, its precise phylogenetic position in the SFG is not clear because only single‐gene sequence–based phylogenetic analyses were performed using very limited genes. Here, we present the complete genome sequences of two Japanese “Ca. R. kotlanii” isolates, which differed only by a 135 bp insertion/deletion (InDel). Using these genomes and publicly available whole genome sequences of other Rickettsia species, the precise phylogenetic position of “Ca. R. kotlanii” in Rickettsia was determined to be in a clade of the SFG. The phylogenetic relationships and average nucleotide identity of “Ca. R. kotlanii” relative to the other species indicated that “Ca. R. kotlanii” is an independent taxon in the SFG. Notably, although the genomes of the two isolates were almost identical, the isolates were obtained from different tick species in different regions and years, suggesting extremely low genomic diversity in “Ca. R. kotlanii.” While the genome of “Ca. R. kotlanii” is the smallest in the transitional group and SFG Rickettsia sequenced to date, we identified genes uniquely present or absent in “Ca. R. kotlanii,” but most were apparently degraded. Therefore, analyses of differences at the sequence (single nucleotide polymorphisms and small InDels) or gene expression level will be required to understand the functional or physiological features unique to “Ca. R. kotlanii.”

Mycoplasma haemomuris is causative of infectious anaemia or splenomegaly in rodents. We examined the nucleotide sequences of the non-ribosomal genes, rnpB and dnaK, in strains of the species M. haemomuris detected in small field mice and black rats. rnpB nucleotide sequences in strains of the species M. haemomuris isolated from small field mice and black rats had only 89 % sequence similarity, suggesting their separation into two distinct subgroups. dnaK had a nucleotide sequence similarity of 84 % between the subgroups. These results support the classification of M. haemomuris into two genetically distinct subgroups. Here we propose the establishment of these subgroups as ‘Candidatus Mycoplasma haemomuris subsp. musculi’, detected in small field mice (Apodemus argenteus), and ‘Candidatus Mycoplasma haemomuris subsp. ratti’, detected in black rats (Rattus rattus).