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. 2020 Apr 1;15(4):e0230926. doi: 10.1371/journal.pone.0230926

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© 2020 Mikalová et al

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Fig 2 — A. A schematic representation of a chromosomal region of the Treponema pallidum subsp. endemicum (TEN) Iraq B containing the TP0314-TP0318 genes. The entire genome region shown was amplified as two overlapping regions (25BA, 25BB), and each of these two loci contained one specific (Sp) and one non-specific (NSp) primer. Specific primers recognized unique sequences in the TEN Iraq B genome, while non-specific primers recognized binding sites in the paralogous TP0619-TP0621 region. The 25BA region was amplified in a one-step PCR, while the 25BC region was amplified in a second step with the template 25BB DNA (the 25BB template DNA did not have sufficient concentration for sequencing). The use of specific primers verified the amplification from the correct genome part. A 2.3 kb-long deletion present in a portion of the TEN population is shown and covers considerable parts of the tprFG loci (TP0316, TP0317). The paralogous sequence covering TP0314-TP0316 is also shown (see Fig 2B), and this sequence is identical to the region containing the tprIJ loci (TP0619-TP0621). Direct 75-bp long repetitions were found in the DNA regions flanking the deletion. B. A schematic representation of a paralogous sequence covering the TP0314-TP0316 and TP0619-TP0621 regions among available sequences from TEN and T. pallidum subsp. pertenue (TPE) genomes. Whereas the regions covering TP0314-TP0316 and TP0619-TP0621 are identical (or nearly identical) within a single TEN or TPE genome, intragenomic sequences of these regions are different among T. pallidum subsp. pallidum(TPA) strains [28]. Whereas individual TPE strains differed in 5–8 nucleotides from the reference sequence of TPE Samoa D within TP0314-TP0316 and TP0619-TP0621, TEN strains differed from TPE Samoa D in 15 nt positions. Two TPE strains (TPE Kampung Dalan, TPE CDC-2) did not have identical TP0314-TP0316 and TP0619-TP0621 loci and differed between them in 2 and 2 nucleotides, respectively. Some of the nucleotide differences were shared between both TEN and some TPE strains.