Abstract
Introduction Orientia tsutsugamushi, the causative agent of scrub typhus, can be isolated in Vero or L929 cells and has a small genome (2 to 2.5 Mb). However, genome assembly is challenging due to the presence of host DNA contamination and a high proportion of repeat regions (up to 51%). Current global data includes 11 fully annotated genomes, with none from India. Here, we present the first whole genome sequences of O. tsutsugamushi from India. Methods Five O. tsutsugamushi strains were cultured in Vero cells and confirmed by 47kDa realtime PCR. Genomic DNA was extracted after removal of host DNA and sequencing libraries were prepared. Whole genome sequencing was performed using the PacBio Sequel II system in CCS/HiFi mode. The raw reads were assembled using Flye, and genome completeness was assessed with QUAST and BUSCO. Annotation was performed using the NCBI PGAP pipeline and comparative genome analysis by Roary. Phylogenetic analysis was based on the complete 56kDa gene, which contains four variable domains. Results We report five complete genomes of O. tsutsugamushi, four of which are circular and one linear. Genome sizes range from 2.1 to 2.4 Mb. The total number of predicted genes falls between 2,379 and 2,715, with an average of 1,824 coding genes and 613 pseudogenes. Repeat regions constitute 53 to 59% of the genome, a higher proportion than previously reported. All five genomes have been submitted to NCBI GenBank (Accession Numbers: CP166954 to 58). Phylogenetic analysis based on the full length 56kDa gene revealed that two strains belong to the Karp genogroup, two to Kato, and one to TA763. Conclusion This study presents the first whole genome sequencing data of O. tsutsugamushi from India. Notably, the repetitive regions in these genomes are more extensive than previously reported. Further analyses with additional isolates are necessary to validate this observation. Comprehensive phylogenomic studies, particularly to elucidate evolutionary dynamics and potential recombination events will provide further information.
Competing Interest Statement
The authors have declared no competing interest.
