Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.
Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.
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DOI：
10.3389/fmicb.2018.00067
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发表时间：
2018
影响因子：
5.2
通讯作者：
Son J
中科院分区：
文献类型：
--
作者：
Gupta RS;Lo B;Son J
分枝杆菌属包含188种，包括几种主要的人类病原体以及许多其他环境物种。我们在此报告了对150个分枝杆菌物种基因组的综合系统基因组学和比较基因组学分析，以了解它们的相互关系。根据分枝杆菌属（Mycobacterium）的1941个核心蛋白、放线菌门（Actinobacteria）的136个核心蛋白和其他8个保守蛋白构建了150个物种的系统进化树。此外，根据保守蛋白家族的平均氨基酸身份确定分枝杆菌物种之间的总体基因组相似性。这些分析的结果一致地支持在分枝杆菌属中最高水平存在五个不同的单系类群，它们被指定为“结核-类群”、“terrrae”、“Triviale”、“Fortuitum-Vaccae”和“脓肿- chelonae”分支。其中一些分支在早期的系统发育研究中也被观察到。在这些分支中，“脓肿- chelonae”分支形成了最深的分支谱系，并没有与快速生长的物种“Fortuitum-Vaccae”分支形成单一的类群。与此同时，我们对来自分枝杆菌基因组的蛋白质进行了比较分析，发现了172个保守特征索引和保守特征蛋白形式的分子特征，这些特征是所有分枝杆菌物种或五个已鉴定分支的成员唯一共享的。所鉴定的分子特征（或突触形态）为分枝杆菌属和所描述的五个分支的单系性提供了强有力的独立证据，并为这些分支的划分和诊断提供了可靠的手段。基于我们全面的系统基因组分析结果和大量已确定的分子特征，这些结果一致且强烈地支持将已知的分枝杆菌物种划分为五个描述的分支，我们建议将分枝杆菌属划分为一个修正的分枝杆菌属，包括“结核-类人猿”分支，其中包括所有主要的人类病原体，以及四个新属，即分枝杆菌gen. nov., Mycolicibacter gen. nov., Mycolicibacter gen. nov.和Mycolicibacter gen. nov.。分枝杆菌gen. 11和分枝杆菌gen. 11分别对应于“Fortuitum-Vaccae”、“Terrae”、“Triviale”和“脓肿- chelonae”分支。随着分枝杆菌种类划分为这五个不同的类群，现在可以将注意力集中在区分这些类群成员的独特遗传和分子特征上。
The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the “Tuberculosis-Simiae,” “Terrae,” “Triviale,” “Fortuitum-Vaccae,” and “Abscessus-Chelonae” clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the “Abscessus-Chelonae” clade forms the deepest branching lineage and does not form a monophyletic grouping with the “Fortuitum-Vaccae” clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the “Tuberculosis-Simiae” clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the “Fortuitum-Vaccae,” “Terrae,” “Triviale,” and “Abscessus-Chelonae” clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.