Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
PLoS One. 2013 Sep 10;8(9):e74319. doi: 10.1371/journal.pone.0074319. eCollection 2013.
Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, is a highly clonal bacterium showing minimal genetic variability in the genome sequence of individual strains. Nevertheless, genetically characterized syphilis strains can be clearly divided into two groups, Nichols-like strains and SS14-like strains. TPA Nichols and SS14 strains were completely sequenced in 1998 and 2008, respectively. Since publication of their complete genome sequences, a number of sequencing errors in each genome have been reported. Therefore, we have resequenced TPA Nichols and SS14 strains using next-generation sequencing techniques.
METHODOLOGY/PRINCIPAL FINDINGS: The genomes of TPA strains Nichols and SS14 were resequenced using the 454 and Illumina sequencing methods that have a combined average coverage higher than 90x. In the TPA strain Nichols genome, 134 errors were identified (25 substitutions and 109 indels), and 102 of them affected protein sequences. In the TPA SS14 genome, a total of 191 errors were identified (85 substitutions and 106 indels) and 136 of them affected protein sequences. A set of new intrastrain heterogenic regions in the TPA SS14 genome were identified including the tprD gene, where both tprD and tprD2 alleles were found. The resequenced genomes of both TPA Nichols and SS14 strains clustered more closely with related strains (i.e. strains belonging to same syphilis treponeme subcluster). At the same time, groups of Nichols-like and SS14-like strains were found to be more distantly related.
CONCLUSION/SIGNIFICANCE: We identified errors in 11.5% of all annotated genes and, after correction, we found a significant impact on the predicted proteomes of both Nichols and SS14 strains. Corrections of these errors resulted in protein elongations, truncations, fusions and indels in more than 11% of all annotated proteins. Moreover, it became more evident that syphilis is caused by treponemes belonging to two separate genetic subclusters.
苍白密螺旋体亚种苍白密螺旋体（TPA）是梅毒的病原体，是一种高度克隆的细菌，其单个菌株的基因组序列显示出最小的遗传变异性。然而，具有遗传特征的梅毒菌株可以清楚地分为两个组，Nichols 样菌株和 SS14 样菌株。TPA Nichols 和 SS14 菌株分别于 1998 年和 2008 年完全测序。自完整基因组序列发布以来，每个基因组中都报告了一些测序错误。因此，我们使用下一代测序技术重新测序了 TPA Nichols 和 SS14 菌株。
方法/主要发现：使用 454 和 Illumina 测序方法对 TPA 菌株 Nichols 和 SS14 的基因组进行了重新测序，其组合平均覆盖率高于 90x。在 TPA 菌株 Nichols 基因组中，共鉴定出 134 个错误（25 个取代和 109 个插入缺失），其中 102 个影响蛋白质序列。在 TPA SS14 基因组中，共鉴定出 191 个错误（85 个取代和 106 个插入缺失），其中 136 个影响蛋白质序列。在 TPA SS14 基因组中，确定了一组新的菌株间异质区，包括 tprD 基因，其中发现了 tprD 和 tprD2 等位基因。重新测序的 TPA Nichols 和 SS14 菌株的基因组与相关菌株（即属于同一梅毒密螺旋体亚群的菌株）聚类更紧密。同时，发现 Nichols 样和 SS14 样菌株组之间的关系也更远。
结论/意义：我们在所有注释基因中发现了 11.5%的错误，在纠正后，我们发现 Nichols 和 SS14 菌株的预测蛋白质组受到了显著影响。这些错误的纠正导致超过 11%的所有注释蛋白发生蛋白延长、截断、融合和插入缺失。此外，梅毒是由属于两个不同遗传亚群的密螺旋体引起的，这一点变得更加明显。
