Complete genomes of two Ikeda-genotype Orientia tsutsugamushi isolates from South Korea reveal within-lineage divergence and contrast with the Boryong reference strain

Figures

• 

  Fig 1. Single-locus and multilocus phylogenetic placement of the South Korean Ikeda-genotype Orientia tsutsugamushi isolates. Maximum-likelihood trees were constructed using (a) the 56-kDa TSA gene (single gene), (b) multilocus sequence analysis (MLSA) based on concatenated sequences of the seven MLST loci (gpsA, mdh, nrdF, nuoF, ppdK, sucB, and sucD). For the study isolates, 56-kDa TSA and MLST locus sequences were extracted from the whole-genome assemblies, and MLST alleles and sequence types were assigned in silico using the O. tsutsugamushi PubMLST database. For some reference genomes, no exact PubMLST sequence type match was available based on the in silico allele profile, theses strains are labeled as ‘no exact PubMLST ST match’. The two South Korean Ikeda-genotype strains (CH219 and K4-135) are highlighted.

• 

  Fig 2. Core-genome phylogeny before and after recombination filtering. Maximum-likelihood phylogenies were inferred from (a) the Roary concatenated core-gene nucleotide alignment (540 core genes, pre-filtering) and (b) the Gubbins recombination-filtered polymorphic-sites alignment derived from the same core gene alignment (post-filtering). Node labels indicate standard bootstrap support (%) from 1,000 replicates. The two South Korean Ikeda-genotype strains (CH219 and K4-135) are highlighted.

• 

  Fig 3. Pairwise Average Nucleotide Identity (ANI) heatmap for 18 Orientia tsutsugamushi strains, including the two South Korean strains from this study (CH219 and K4-135) and 16 publicly available genomes. ANI was calculated using FastANI, and higher nucleotide identity values are represented by darker blue colour. The color scale indicates ANI values among the genomes, with grey shading representing ANI values below 98.5%. The two South Korean strains CH219 and K4-135 are highlighted with *.

• 

  Fig 4. Pairwise whole-genome dot plots of four Orientia tsutsugamushi genomes. Dot plots were generated using MUMmer (nucmer) pairwise alignments filtered to retain matches with ≥ 95% nucleotide identity and ≥ 2 kb alignment length. Each panel shows genome-wide alignments between the indicated genome pair; forward matches are shown as purple and reverse-oriented matches in blue. The two South Korean Ikeda-genotype strains (CH219 and K4-135) are highlighted in bold.