Phylogenic position and low genomic diversity of “<i>Candidatus Rickettsia kotlanii</i>” inferred by complete genome sequences of two Japanese isolates

<jats:title>Abstract</jats:title><jats:p>Many <jats:italic>Rickettsia</jats:italic> species of the spotted fever group (SFG) cause tick‐borne diseases known as “spotted fever.” One of the candidate SFG <jats:italic>Rickettsia</jats:italic> species is “<jats:italic>Candidatus Rickettsia kotlanii</jats:italic>,” which was first detected in <jats:italic>Haemaphysalis concinna</jats:italic> 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 “<jats:italic>Ca</jats:italic>. <jats:italic>R. kotlanii</jats:italic>” isolates, which differed only by a 135 bp insertion/deletion (InDel). Using these genomes and publicly available whole genome sequences of other <jats:italic>Rickettsia</jats:italic> species, the precise phylogenetic position of “<jats:italic>Ca</jats:italic>. <jats:italic>R. kotlanii</jats:italic>” in <jats:italic>Rickettsia</jats:italic> was determined to be in a clade of the SFG. The phylogenetic relationships and average nucleotide identity of “<jats:italic>Ca</jats:italic>. <jats:italic>R. kotlanii</jats:italic>” relative to the other species indicated that “<jats:italic>Ca</jats:italic>. <jats:italic>R. kotlanii</jats:italic>” 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 “<jats:italic>Ca</jats:italic>. <jats:italic>R. kotlanii</jats:italic>.” While the genome of “<jats:italic>Ca</jats:italic>. <jats:italic>R. kotlanii</jats:italic>” is the smallest in the transitional group and SFG <jats:italic>Rickettsia</jats:italic> sequenced to date, we identified genes uniquely present or absent in “<jats:italic>Ca</jats:italic>. <jats:italic>R. kotlanii</jats:italic>,” 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 “<jats:italic>Ca</jats:italic>. <jats:italic>R. kotlanii</jats:italic>.”</jats:p>