Table 1.
Summary of the genomic features of the Treponema pallidum subsp. endemicum Bosnia A strain and four T. pallidum subsp. pertenue strains (Samoa D, CDC-2, Gauthier and Fribourg-Blanc).
Table 2.
Frameshift mutations and substitutions resulting in significant protein truncations, elongations and novel annotations in the Bosnia A genome in comparison with TPA and TPE strains.
Figure 1.
Unrooted tree based on the alignment of the Bosnia A genome with additional treponemal genomes.
An unrooted tree was constructed from the complete genome sequences of TPA strains (Nichols, Chicago, DAL-1, SS14, and Mexico A), TPE strains (CDC-2, Gauthier, Samoa D, and Fribourg-Blanc), and the TEN strain (Bosnia A) using the Maximum Parsimony method and MEGA5 software [25]. The bar scale corresponds to a difference of 200 nucleotides. Bootstrap values based on 1,000 replications are shown next to the branches. All positions containing indels in at least one genome sequence were omitted from the analysis. There were a total of 1,128,391 nucleotide positions aligned in the final dataset.
Table 3.
Calculated nucleotide identity and nucleotide diversity (π ± standard deviation) between Bosnia A strain and individual TPA and TPE strainsa.
Table 4.
Calculated nucleotide diversity (π ± standard deviation) between TPA and TPE strains, within individual TPE strains, within TPA strains, and between Bosnia A strain and TPA and TPE strains.
Figure 2.
Representation of the Bosnia A chromosome with location of Bosnia A-, TPE-, and TPA-specific sequences.
Bosnia A-specific sequences are shown in green while TPE-specific sequences (TPA and Bosnia A sequences are identical in these loci) are shown in blue. TPA-specific sequences (TPE and Bosnia A sequences are identical in these loci) are shown in red. Bosnia A-specific sequences comprised 406 loci (encompassing a total of 2772 bp) while TPE- and TPA-specific sequences were found in 197 (635 bp) and 1422 (2335 bp) loci, respectively.
Table 5.
Genome differences specific for the TEN Bosnia A straina.
Table 6.
Genome sequences of Bosnia A strain identical to TPE strains and different from TPA strainsa.
Table 7.
Genome sequences of Bosnia A strain identical to TPA strains and different from TPE strainsa.
Figure 3.
Sequence alignments of TENDBA_0133, TENDBA_0968, TENDBA_0577, TENDBA_0326 and TENDBA_0856 loci with the orthologous sequences of TPA and TPE genomes.
Sequences of five TPA strains (Nichols, DAL-1, Chicago, Mexico A and SS14) and four TPE strains (CDC-2, Gauthier, Samoa D and Fribourg-Blanc) are shown. Numbers above the alignment represent gene coordinates in the re-sequenced TPA Nichols strain (CP004010.2 [14]). While the alignment of TENDBA_0133 showed locus completely identical to TPE strains, TENDBA_0968, TENDBA_0577 and TENDBA_0326 loci showed the presence of TPA sequences in the genome of Bosnia A. The TENDBA_0856 locus represent Bosnia A specific region with sporadic nucleotide positions identical to TPA sequences. The TPE-like sequence was found in most of the Bosnia A loci while the pattern found in TENDBA_0968 was also found in TENDBA_0858 (not shown) and the pattern identified in the TENDBA_0577 was found also in the TENDBA_1031 (not shown). The alignment pattern in TENDBA_0326 was previously found in TENDBA_0488 [12] and the pattern in TENDBA_0856 in TENDBA_0865.