Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi.
Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi.
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DOI：
10.1371/journal.pntd.0006566
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发表时间：
2018-06
影响因子：
3.8
通讯作者：
Salje J
中科院分区：
文献类型：
--
作者：
Batty EM;Chaemchuen S;Blacksell S;Richards AL;Paris D;Bowden R;Chan C;Lachumanan R;Day N;Donnelly P;Chen S;Salje J
恙虫病东方体是一种临床上重要但被忽视的立克次体科专性细胞内细菌病原体，可导致可能危及生命的人类疾病恙虫病。与许多专性细胞内细菌的基因组减少相反，东方体的早期遗传研究揭示了迄今为止测序的最重复的细菌基因组之一。移动的元件的急剧扩张阻碍了使用短读段测序方法生成完整基因组序列的努力，因此很少有对这种被忽视的物种的比较基因组学的研究。我们报告了新的高质量的基因组O。使用PacBio单分子长读段测序生成的六种毒株的恙虫病病毒：Karp、Kato、Gilliam、TA 686、UT 76和UT 176。在比较基因组学分析这些菌株连同现有的参考基因组从池田和Boryong株，我们确定了一个相对较小的核心基因组的657个基因，分为核心基因岛和重复区域分开，并使用核心基因来推断第一个全基因组同源性Orientia。多个东方体基因组的完整组装验证了最初的建议，即这些是显着的生物体。与大多数其他立克次体科相比，它们具有更大的基因组，具有广泛的重复元件扩增和菌株之间的大量染色体重排。在基因水平上，东方体有一组相对较小的普遍保守的基因，类似于其他专性细胞内细菌，基因组大小的相对扩张可以通过基因复制和重复扩增来解释。我们的研究证明了长读段测序在研究复杂的细菌基因组和细菌基因组变异中的实用性。恙虫病东方体是一种专性细胞内细菌病原体，是人类疾病恙虫病的病原体。这种媒介传播的细菌感染如果不迅速用适当的抗生素治疗，可能危及生命。东方病在亚洲大部分地区流行，估计每年至少感染100万人。O.恙虫病的基因组非常不寻常。它的长度为2.1 Mbp，几乎是大多数其他专性细胞内细菌基因组大小的两倍，这些细菌在适应细胞内生活方式时经历了广泛的基因组减少。东方体相对扩展的基因组是由丰富的重复DNA元件解释的。事实上，东方体的基因组是迄今为止报道的最高度重复的细菌基因组。因此，很难使用短读段测序技术产生东方体的完整基因组组装体。在目前的报告中，作者使用太平洋生物科学公司的长读测序技术生成了不同O.恙虫病。通过比较这些基因组，作者表明，基因组内的基因排序几乎没有共线性，即使在密切相关的菌株之间也是如此。这种同线性的缺乏表明，在这个物种中经常发生大规模的染色体重排事件，尽管其潜在的机制还没有被证明。这里报告的基因组序列和分析将有利于那些从事这种临床上重要但被忽视的细菌物种生物学各个方面的工作的人。
Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species. We report new high-quality genomes of O. tsutsugamushi, generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene islands and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny of Orientia. Complete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have larger genomes compared with most other Rickettsiaceae, with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation. Orientia tsutsugamushi is an obligate intracellular bacterial pathogen, and the causative agent of the human disease scrub typhus. This vector-borne bacterial infection can be life-threatening if not treated rapidly with appropriate antibiotics. Orientia is endemic across large parts of Asia and is estimated to infect at least one million people per year. O. tsutsugamushi has a highly unusual genome. At 2.1 Mbp in length, it is almost double the size of most other obligate intracellular bacterial genomes, which have undergone extensive genome reduction in their adaptation to the intracellular lifestyle. The comparatively expanded genome of Orientia is accounted for by an abundance of repeated DNA elements. Indeed, the genome of Orientia is the most highly repeated bacterial genome reported to date. As a consequence of this, it has been difficult to generate complete genome assemblies of Orientia using short-read sequencing technologies. In the current report, the authors use Pacific Biosciences long-read sequencing to generate six complete genomes of diverse strains of O. tsutsugamushi. By comparing these genomes, the authors show that there is very little colinearity in the ordering of genes within the genome, even between closely related strains. This lack of synteny suggests that there have been frequent events of massive chromosomal rearrangement in this species, although the underlying mechanisms for this have not been shown. The genome sequences and analysis reported here will benefit those working on various aspects of the biology of this clinically important but neglected bacterial species.
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Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
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作者：
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通讯作者：
Day, Nicholas P. J.
影响因子：
2.1
作者：
Enatsu, T;Urakami, HL;Tamura, A
通讯作者：
Tamura, A
影响因子：
3.8
作者：
Giengkam, Suparat;Blakes, Alex;Salje, Jeanne
通讯作者：
Salje, Jeanne