BACKGROUND The genus Borrelia comprises spirochaetal bacteria maintained in natural transmission cycles by tick vectors and vertebrate reservoir hosts. The main groups are represented by a species complex including the causative agents of Lyme borreliosis and relapsing fever group Borrelia. Borrelia miyamotoi belongs to the relapsing fever group of spirochetes and forms distinct populations in North America, Asia, and Europe. As all Borrelia species B. miyamotoi possess an unusual and complex genome consisting of a linear chromosome and a number of linear and circular plasmids. The species is considered an emerging human pathogen and an increasing number of human cases are being described in the Northern hemisphere. The aim of this study was to produce a high quality reference genome that will facilitate future studies into genetic differences between different populations and the genome plasticity of B. miyamotoi. RESULTS We used multiple available sequencing methods, including Pacific Bioscience single-molecule real-time technology (SMRT) and Oxford Nanopore technology (ONT) supplemented with highly accurate Illumina sequences, to explore the suitability for whole genome assembly of the Russian B. miyamotoi isolate, Izh-4. Plasmids were typed according to their potential plasmid partitioning genes (PF32, 49, 50, 57/62). Comparing and combining results of both long-read (SMRT and ONT) and short-read methods (Illumina), we determined that the genome of the isolate Izh-4 consisted of one linear chromosome, 12 linear and two circular plasmids. Whilst the majority of plasmids had corresponding contigs in the Asian B. miyamotoi isolate FR64b, there were only four that matched plasmids of the North American isolate CT13-2396, indicating differences between B. miyamotoi populations. Several plasmids, e.g. lp41, lp29, lp23, and lp24, were found to carry variable major proteins. Amongst those were variable large proteins (Vlp) subtype Vlp-α, Vlp-γ, Vlp-δ and also Vlp-β. Phylogenetic analysis of common plasmids types showed the uniqueness in Russian/Asian isolates of B. miyamotoi compared to other isolates. CONCLUSIONS We here describe the genome of a Russian B. miyamotoi clinical isolate, providing a solid basis for future comparative genomics of B. miyamotoi isolates. This will be a great impetus for further basic, molecular and epidemiological research on this emerging tick-borne pathogen.

中文翻译：

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宫果疏螺旋体分离物Izh-4的全基因组测序：复杂细菌基因组的参考。

背景技术疏螺旋体属包括由tick虫载体和脊椎动物水库宿主以自然传播周期维持的螺旋体细菌。主要群体以物种复合体为代表，其中包括莱姆病（Lyme borreliosis）病原体和复发性发热组伯雷利亚（Borrelia）。宫本疏螺旋体属于螺旋体的复发性发烧组，在北美，亚洲和欧洲形成不同的种群。由于所有的疏螺旋体种，宫本芽孢杆菌都具有不寻常且复杂的基因组，该基因组由线性染色体以及许多线性和环状质粒组成。该物种被认为是一种新兴的人类病原体，北半球正在描述越来越多的人类病例。这项研究的目的是产生高质量的参考基因组，这将有助于将来对不同种群之间的遗传差异以及宫本芽孢杆菌的基因组可塑性进行研究。结果我们使用了多种可用的测序方法，包括太平洋生物科学单分子实时技术（SMRT）和牛津纳米孔技术（ONT）并补充了高精度的Illumina序列，以探索俄罗斯宫本B.分离株全基因组装配的适用性，Izh-4。根据其潜在的质粒分配基因（PF32、49、50、57 / 62）对质粒进行分型。比较长读法（SMRT和ONT）和短读法（Illumina）的结果，我们确定了分离株Izh-4的基因组由一个线性染色体，12个线性和两个环状质粒组成。尽管大多数质粒在亚洲宫本芽孢杆菌分离株FR64b中具有相应的重叠群，但只有四个与北美分离株CT13-2396的质粒匹配，表明宫本芽孢杆菌种群之间存在差异。发现几种质粒，例如lp41，lp29，lp23和lp24携带可变的主要蛋白。其中包括可变大蛋白（Vlp）亚型Vlp-α，Vlp-γ，Vlp-δ以及Vlp-β。常见质粒类型的系统进化分析表明，与其他分离株相比，宫本芽孢杆菌在俄罗斯/亚洲分离株中具有独特性。结论我们在此描述了俄罗斯宫本氏菌临床分离株的基因组，为将来宫本氏菌分离株的比较基因组学提供了坚实的基础。这将是对该新兴tick传播病原体进行进一步基础，分子和流行病学研究的强大动力。