High-Accuracy Long-Read Sequencing of Mycobacterium tuberculosis PSNK363 Isolated From the Democratic People's Republic of Korea.

IF 2.6 4区 医学 Q3 INFECTIOUS DISEASES
Thi-Binh Dang, Nackmoon Sung, Kyunghyun Lim, Soyoung Lee, Jaehyun Jeon, Sanghoon Jheon
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Abstract

Long-read sequencing is a valuable technique for high-precision genome analysis. Despite the widespread use of the Mycobacterium tuberculosis H37Rv genome sequence as a reference for genetic variation analysis, its suitability for comparing clinical strains is limited. Therefore, we constructed the first known whole genome of a clinical M. tuberculosis strain, PSNK363, isolated from the Democratic People's Republic of Korea, using high-quality high-fidelity (HiFi) read sequencing and compared its genetic variations to those of H37Rv. PSNK363 was cultured to obtain genomic DNA, which was subjected to de novo whole-genome assembly using PacBio Sequel II with long-read HiFi sequencing. The sequences were compared to the reference genome H37Rv. HiFi long-read sequencing of M. tuberculosis PSNK363, with an accuracy of 99.99%, revealed a single circular chromosome of 4,422,110 bp, which is 10,578 bp longer than the H37Rv chromosome. The assembly had an average G + C content of 65.6%, 4079 protein-coding sequences, 53 tRNA genes, and 3 rRNA genes. Most genes (72.7%) were assigned as putative functions, whereas the remaining 27.3% were annotated as hypothetical. Comparison with H37Rv revealed a large inversion in the PSNK363 genome, which contains most of the deletion and insertion variants. M. tuberculosis PSNK363 had a longer genome sequence, more protein-coding genes, and a larger inversion region than H37Rv. High-accuracy whole-genome sequencing of PSNK363 holds the potential for enriching virulence databases and identifying informative loci for drug resistance analysis in M. tuberculosis isolates in the Democratic People's Republic of Korea.

朝鲜结核分枝杆菌PSNK363的高准确度长读序列分析
长读测序是一种有价值的高精度基因组分析技术。尽管广泛使用结核分枝杆菌H37Rv基因组序列作为遗传变异分析的参考,但其在临床菌株比较中的适用性有限。因此,我们利用高质量高保真(HiFi)测序技术构建了从朝鲜民主主义人民共和国分离出来的临床结核分枝杆菌PSNK363的全基因组,并将其与H37Rv的遗传变异进行了比较。培养PSNK363获得基因组DNA,使用PacBio Sequel II进行从头全基因组组装,并进行长读段HiFi测序。将序列与参考基因组H37Rv进行比较。结核分枝杆菌PSNK363的HiFi长读测序准确率为99.99%,结果显示,结核分枝杆菌PSNK363的单环状染色体长度为4422110 bp,比H37Rv染色体长10578 bp。该装配体平均G + C含量为65.6%,蛋白编码序列4079个,tRNA基因53个,rRNA基因3个。大多数基因(72.7%)被指定为假定功能,而其余27.3%被注释为假设功能。与H37Rv比较发现PSNK363基因组存在较大的反转,其中包含大部分缺失和插入变异。结核分枝杆菌PSNK363基因组序列较H37Rv长,编码蛋白基因较多,倒置区较大。PSNK363的高精度全基因组测序具有丰富毒力数据库和鉴定信息位点的潜力,可用于朝鲜民主主义人民共和国结核分枝杆菌分离株的耐药性分析。
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来源期刊
CiteScore
4.30
自引率
0.00%
发文量
108
审稿时长
>12 weeks
期刊介绍: Canadian Journal of Infectious Diseases and Medical Microbiology is a peer-reviewed, Open Access journal that publishes original research articles, review articles, and clinical studies related to infectious diseases of bacterial, viral and parasitic origin. The journal welcomes articles describing research on pathogenesis, epidemiology of infection, diagnosis and treatment, antibiotics and resistance, and immunology.
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