Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.
Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.
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DOI：
10.1186/s12864-022-08927-5
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发表时间：
2022-10-15
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
分枝杆菌属包括至少192个命名的物种，其中许多导致严重的疾病，如结核病。非结核分枝杆菌（NTM）也可以感染人类和动物。有些是新出现的问题，因为它们显示出对常用抗生素的高耐药性，而另一些则在生物修复中使用和评估，或包含在抗癌疫苗中。我们提供了114个分枝杆菌型菌株的基因组序列，并与130个可用的分枝杆菌基因组一起，我们生成了基于387个核心基因的系统发育树，并得到了平均核苷酸同一性（ANI）数据的支持。244个基因组序列覆盖了构成分枝杆菌属的大多数物种。基因组大小范围为3.2至8.1 Mb，平均5.7 Mb，我们确定了14个新的质粒。此外，分枝杆菌基因组由噬菌体样序列组成，范围在0和4.64%之间，依赖于分枝杆菌，而IS元件的数量在1和290之间变化。我们的数据还显示，根据分枝杆菌，tRNA和非编码（NC）RNA基因的数量不同，它们在染色体上的位置也不同。我们确定了一个保守的核心集的12个ncRNA，43个tRNA和18个氨酰-tRNA合成酶之间的分枝杆菌。噬菌体，IS元件，tRNA和ncRNA似乎有助于分枝杆菌属的进化，其中几个tRNA和ncRNA基因已被水平转移。根据我们的系统发育分析，我们将几个未命名物种的分离株鉴定为新的分支杆菌物种或已知分支杆菌菌株。预测的编码序列的数量与基因组大小相关，而tRNA、rRNA和ncRNA基因的数量则不相关。总之，这些发现扩展了我们对分枝杆菌属进化的见解，因此它们建立了一个平台来了解分枝杆菌致病性，它们的进化，抗生素耐药性/耐受性以及分枝杆菌中ncRNA的功能和进化。在线版本包含补充材料，可通过10.1186/s12864-022-08927-5获得。
The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines. We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria. Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria. The online version contains supplementary material available at 10.1186/s12864-022-08927-5.
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