Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Indonesia: Modular structure of several treponemal genes

Abstract

BackgroundTreponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multistage disease endemic in tropical regions in Africa, Asia, Oceania, and South America. To date, seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) and two TPE strains isolated from the baboons (Fribourg-Blanc and LMNP-1). This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes.Methodology/principal findingsThe genomes were determined using the pooled segment genome sequencing method combined with the Illumina sequencing platform resulting in an average coverage depth of 1,021x and 644x for the TPE Kampung Dalan K363 and TPE Sei Geringging K403 genomes, respectively. Both Indonesian TPE strains were genetically related to each other and were more distantly related to other, previously characterized TPE strains. The modular character of several genes, including TP0136 and TP0858 gene orthologs, was identified by analysis of the corresponding sequences. To systematically detect genes potentially having a modular genetic structure, we performed a whole genome analysis-of-occurrence of direct or inverted repeats of 17 or more nucleotides in length. Besides in tpr genes, a frequent presence of repeats was found in the genetic regions spanning TP0126–TP0136, TP0856–TP0858, and TP0896 genes.Conclusions/significanceComparisons of genome sequences of TPE Kampung Dalan K363 and Sei Geringging K403 with other TPE strains revealed a modular structure of several genomic loci including the TP0136, TP0856, and TP0858 genes. Diversification of TPE genomes appears to be facilitated by intra-strain genome recombination events.

Whole genome sequence of the Treponema pallidum subsp. endemicum strain Iraq B: A subpopulation of bejel treponemes contains full-length tprF and tprG genes similar to those present in T. p. subsp. pertenue strains

“…endemicum (TEN). The genome was assembled using the previously described PSGS technique [2,[15][16][17]20,21] and Illumina sequencing. The average coverage depth was greater than 3000× and all sequencing ambiguities were resolved with Sanger sequencing of the corresponding PCR products.…”

“…Whole genome alignment of treponemal sequences was constructed with Geneious [19] and SeqMan (DNASTAR, Madison, WI, USA) software using the following genomes: TEN Iraq B (CP032303.1), TEN Bosnia A (CP007548.1; [2]), TPE CDC-2 (CP002375.1; [16]), TPE Gauthier (CP002376.1; [16]), TPE Samoa D (CP002374.1; [16]), TPE Ghana-051 (CP020365.1; [20]), TPE CDC 2575 (CP020366.1; [20]), TPE LMNP-1 (CP021113.1; [13]), TPE Kampung Dalan K363 (CP024088.1; [21]), TPE Sei Geringging K403 (CP024089.1; [21]), TPE Fribourg-Blanc (CP003902.1; [17]), and TPA SS14 (CP004011.1; [22]). Complete genome sequences, except for chromosomal regions showing recombination (tprK sequences, tRNA-Ile and tRNA-Ala intergenic spacers of both rRNA operons, tprD gene) or containing repetitions (arp, and TP0470 genes), were used to construct a phylogenetic tree.…”

“…Genetic heterogeneity was identified according to the protocol described elsewhere [20,21,26,27]. Briefly, individual Illumina reads were mapped to the final version of the TEN Iraq B genome sequence using SeqMan NGen (v4.1.0) software with default parameters.…”

“…The TEN Iraq B genome was assessed for the presence of intrastrain heterogeneity [20,21,26,27], with a frequency cutoff for minor alleles of 8% or more [20,21]. Altogether, 12 such sites were identified in TEN Iraq B, and the list of heterogeneous sites is shown in Table 3.…”

Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe

“…Prior to the final phylogenetic analyses, genes containing recombining regions identified through the above-mentioned procedure were excluded from the sequence alignment (Data S3). Additionally, 18 genes previously reported as hypervariable, carrying many repetitive regions and inducing recombination-like effects in mapping were considered to potentially bias the phylogenetic signal [38,[141][142][143][144][145] and were also removed. Those included the arp gene (TPANIC_0433), FadL homolog genes (TPANIC_0548 TPANIC_0856, TPANIC_0858, TPANIC_0859, TPANIC_0865) and all tpr genes TPANIC_0009, TPANIC_0011, TPANIC_0117, TPANIC_0131, TPANIC_0313, TPANIC_0316, TPANIC_0317, TPANIC_0610, TPANIC_0620, TPANIC_0621, TPANIC_0897, TPANIC_1031).…”