Chromosome-level genome assembly, reannotation and decoding of a Trichomonas vaginalis clinical isolate from Shiyan, Central China

Decoding Infection and Transmission Pub Date : 2024-01-01 DOI:10.1016/j.dcit.2024.100023

Yanqing Zhao , Yinjie Lian , Wei Guan , Peng Wu , Shuguo Yang , Jian Li

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Abstract

Introduction

Trichomonas vaginalis trophozoite is a pathogen that causes trichomoniasis, the most common neglected sexually transmitted disease. The reference genome of T. vaginalis is derived from the G3 strain. Although many strains are widely present in China, no genomic information is available for relevant studies.

Methods

Clinical T. vaginalis isolates were collected, cultured and sequenced via the next-generation Illumina, SMRT DNA sequencing platform and chromosome conformation capture (Hi-C) technologies.

Results

The present assembled TV-THS1 genome, spanning 185.45 Mb, was comprised of 934 contigs with a contig N50 length of 467.79 kb anchored to six pseudochromosomes, accounting for more than 88 % of the assembled genome (164.56 Mb). The genome included 24,691 protein-coding genes, 24,376 of which (98.72 %) were functionally interpreted. A total of 131.74 Mb (71.03 %) of the assembled sequences were identified as repetitive sequences, and 5302 corresponding genes were annotated in Maverick elements. Compared with the published T. vaginalis G3 reference genome, substantial differences have been revealed. Comparative genome analysis revealed that genes related to expansion during evolution mainly participated in cell adhesion and the biosynthesis of specialized metabolites, such as those involved in binding and catalytic activity.

Conclusions

A chromosome-level reference T. vaginalis TV-THS1 genome was obtained, providing comprehensive insight into T. vaginalis evolution and the molecular mechanisms of T. vaginalis pathogenicity. This work offers valuable data for pathogen-host interaction analysis, clinical diagnosis, treatment and prevention of trichomoniasis.

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华中十堰阴道毛滴虫临床分离株的染色体级基因组组装、重新注释和解码

导言阴道毛滴虫滋养体是一种导致滴虫病的病原体，是最常见的被忽视的性传播疾病。阴道毛滴虫的参考基因组来自 G3 株。方法通过新一代Illumina、SMRT DNA测序平台和染色体构象捕获（Hi-C）技术对临床阴道球菌分离株进行收集、培养和测序。结果目前组装的 TV-THS1 基因组跨度为 185.45 Mb，由 934 个等位基因组成，等位基因 N50 长度为 467.79 kb，锚定在 6 个假染色体上，占组装基因组（164.56 Mb）的 88% 以上。基因组包括 24,691 个蛋白质编码基因，其中 24,376 个（98.72 %）有功能解释。共有 131.74 Mb（71.03 %）的组装序列被鉴定为重复序列，5302 个相应基因被注释为 Maverick 元素。与已发表的阴道球菌 G3 参考基因组相比，发现了巨大的差异。结论获得了染色体组水平的阴道球菌TV-THS1参考基因组，为阴道球菌的进化和致病分子机制提供了全面的信息。这项工作为滴虫病的病原体-宿主相互作用分析、临床诊断、治疗和预防提供了宝贵的数据。

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Decoding Infection and Transmission

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