Table 1.
Characteristics of bejel patients and the corresponding samples.
Fig 1.
Comparison of breadth coverage of individual genomes.
Sequenced genomic region of Cuban isolates with marked total sequenced genome length. Gray represents regions of Ns with length at least 5 kb, which were not interrupted with more than 1 kb of sequenced nucleotides. Regions containing SNVs and indels in Cuban bejel genomes are shown as symbols (●, ♦).
Table 2.
Sequencing results of four samples containing TEN isolated from Cuban patients.
Fig 2.
Genetic diversity among Cuban treponemal isolates.
(A) Detailed visualization of genetic differences among Cuban bejel strains. N, the corresponding nucleotide was not determined. (B) Phylogenetic analysis of available TEN genomes or sequences. The evolutionary history was inferred using the Maximum Likelihood method based on the Tamura-Nei model [34]. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The percentage of trees in which the associated taxa clustered together is shown next to the branches. The analysis involved 13 nucleotide sequences. There were a total of 2299 positions in the final dataset with 119 variable positions.
Table 3.
Nucleotide diversity among Cuban bejel genomes.
Nucleotide diversity was calculated as the number of nucleotide substitutions per 100,000 bp.
Fig 3.
Overview of recombinant tprC in the C279 genome.
Recombinant sites within the tprC gene and the resulting tprCI chimera of C279. Black lines represent nucleotides identical to tprC, while red lines nucleotides to tprI. White color represents nucleotides shared between both tprC and tprI genes.
Fig 4.
Comparison of region TP0127-TP0129.
A. Comparison between TEN Bosnia A/TPE Samoa D and TEN C279. B. Region of TP0127-TP0129 in selected strains of other subspecies. TEN Bosnia A was used as the reference strain, and the TPE Samoa D strain was identical to TEN Bosnia A. The TEN genome C279 showed a 72 bp deletion and a 53 bp duplication compared to TP0129 of TEN Bosnia A. TPA Nichols strain in IGR showed a 6 bp deletion and a 30 bp insertion compared to Bosnia A. Most of the sequence of Cuniculi A showed deletions, except for 225 bp, which was sequentially unrelated to TP0127-TP0128 in the other strains.