Table_6_Identification of region of difference and H37Rv-related deletion in Mycobacterium tuberculosis complex by structural variant detection and genome assembly.XLSX

Mycobacterium tuberculosis complex (MTBC), the main cause of TB in humans and animals, is an extreme example of genetic homogeneity, whereas it is still nevertheless separated into various lineages by numerous typing methods, which differ in phenotype, virulence, geographic distribution, and host preference. The large sequence polymorphism (LSP), incorporating region of difference (RD) and H37Rv-related deletion (RvD), is considered to be a powerful means of constructing phylogenetic relationships within MTBC. Although there have been many studies on LSP already, focusing on the distribution of RDs in MTBC and their impact on MTB phenotypes, a crumb of new lineages or sub-lineages have been excluded and RvDs have received less attention. We, therefore, sampled a dataset of 1,495 strains, containing 113 lineages from the laboratory collection, to screen for RDs and RvDs by structural variant detection and genome assembly, and examined the distribution of RvDs in MTBC, including RvD2, RvD5, and cobF region. Consistent with genealogical delineation by single nucleotide polymorphism (SNP), we identified 125 RDs and 5 RvDs at the species, lineage, or sub-lineage levels. The specificities of RDs and RvDs were further investigated in the remaining 10,218 strains, suggesting that most of them were highly specific to distinct phylogenetic groups, could be used as stable genetic markers in genotyping. More importantly, we identified 34 new lineage or evolutionary branch specific RDs and 2 RvDs, also demonstrated the distribution of known RDs and RvDs in MTBC. This study provides novel details about deletion events that have occurred in distinct phylogenetic groups and may help to understand the genealogical differentiation.

结核分枝杆菌复合群（Mycobacterium tuberculosis complex，简称MTBC），作为人类及动物结核病的主要病原体，堪称遗传同质性之极端范例。尽管如此，众多分型方法仍将其区分为不同的谱系，这些方法在表型、致病力、地理分布和宿主偏好等方面各具差异。大型序列多态性（large sequence polymorphism，简称LSP），包括差异区域（region of difference，简称RD）和H37Rv相关缺失（H37Rv-related deletion，简称RvD），被视为构建MTBC内部系统发育关系的有效手段。尽管已有多项研究关注LSP，聚焦于RDs在MTBC中的分布及其对MTB表型的影响，但仍有许多新的谱系或亚谱系未被纳入，而RvDs亦未得到足够的关注。因此，本研究采集了包含1,495个菌株、113个实验室保存谱系的数据库，通过结构变异检测和基因组组装技术筛选RDs和RvDs，并考察了RvDs在MTBC中的分布，包括RvD2、RvD5和cobF区域。与单核苷酸多态性（single nucleotide polymorphism，简称SNP）的谱系划分一致，我们在物种、谱系或亚谱系水平上识别出125个RDs和5个RvDs。对剩余的10,218个菌株中RDs和RvDs的特异性进行了进一步研究，发现其中大部分对特定的系统发育群具有高度特异性，可作为基因分型中的稳定遗传标记。更重要的是，我们发现了34个新的谱系或进化支特异性RDs和2个RvDs，并展示了已知RDs和RvDs在MTBC中的分布。本研究揭示了在不同系统发育群中发生的缺失事件，有助于理解谱系分化。