钟鸣
(2025-08-31 15:27):
#paper doi:10.7554/eLife.97870.3.sa2 The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference 结核分枝杆菌复合群 (MTBC) 是指结核分枝杆菌及其所有变种,MTBC 以其克隆种群结构和不同菌株之间较低的遗传多样性而闻名,这是由于缺乏水平基因转移和质粒造成的。泛基因组代表一个物种中所有基因的集合,包含核心基因组和附属基因组,附属基因组分为壳基因组和云基因组。泛基因组进一步分为开放基因组和封闭基因组。原核生物泛基因组学分析往往不侧重于全基因组比较,而是侧重于蛋白质编码序列,这种关注忽略了非编码 RNA 和假基因以及基因间区域的必需元素,如启动子、终止子和调控结合位点。作者分析了339 株长读长MTBC基因组测序数据,覆盖几乎全部谱系。作者的分析思路/角度/流程值得参考,但结果更多的是描述和概括,缺少深入的、具体的、能推动研究逻辑的结果和发现。
eLife,
2025/8/22.
DOI: 10.7554/eLife.97870.3
The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
翻译
结核分枝杆菌复合体泛基因组很小,由亚谱系特异性差异区域形成
Abstract:
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulence, and antibiotic resistance. While it is known that within-MTBC diversity is characterised by large deletions found only in certain lineages (regions of difference [RDs]), a comprehensive pangenomic analysis incorporating both coding and non-coding regions remains unexplored. We utilised a curated dataset representing various MTBC genomes, including under-represented lineages, to quantify the full diversity of the MTBC pangenome. The MTBC was found to have a small, closed pangenome with distinct genomic features and RDs both between lineages (as previously known) and between sub-lineages. The accessory genome was identified to be a product of genome reduction, showing both divergent and convergent deletions. This variation has implications for traits like virulence, drug resistance, and metabolism. The study provides a comprehensive understanding of the MTBC pangenome, highlighting the importance of genome reduction in its evolution, and underlines the significance of genomic variations in determining the pathogenic traits of different MTBC lineages.
翻译
结核分枝杆菌复合体 (MTBC) 是一组引起人类和动物结核病 (TB) 的细菌。了解 MTBC 遗传多样性对于深入了解其适应性以及与生存、毒力和抗生素耐药性相关的特征至关重要。虽然已知 MTBC 内多样性的特征是仅在某些谱系(差异区域 [RD])中发现大量缺失,但包含编码和非编码区域的综合泛基因组分析仍未得到探索。我们利用代表各种 MTBC 基因组(包括代表性不足的谱系)的精选数据集来量化 MTBC 泛基因组的全部多样性。发现 MTBC 具有一个小的、封闭的泛基因组,具有不同的基因组特征,并且谱系之间(如先前已知)和亚谱系之间都有 RD。辅助基因组被鉴定为基因组减少的产物,显示出发散和收敛缺失。这种变化对毒力、耐药性和新陈代谢等性状有影响。该研究提供了对 MTBC 泛基因组的全面了解,强调了基因组还原在其进化中的重要性,并强调了基因组变异在确定不同 MTBC 谱系致病性状方面的重要性。