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A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes

机译:杂种参考引导的从头组装方法产生环孢菌线粒体基因组

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摘要

Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mitochondrial genome assembly to be used as a reference genome by applying bioinformatic analyses. Using this reference genome, three new mitochondrial genome assemblies were built starting with metagenomic reads generated by sequencing DNA extracted from oocysts present in stool samples from cyclosporiasis patients. Nucleotide variants were identified in the new and other publicly available genomes in comparison with the mitochondrial reference genome. A consolidated workflow, presented here, to generate new mitochondrion genomes using our reference-guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, and in their application for subtyping C. cayetanensis strains during foodborne outbreak investigations.
机译:cayetanensis Cyclospora cayetanensis是一种球虫寄生虫,与全球范围内的大规模和复杂的食源性暴发有关。使用传统的流行病学方法,将食源性暴发期间的环孢子虫病患者的样本与可疑的受污染食物联系起来,一直是一个挑战。为了解决这个问题,基于潜在的基因组标记进行菌株水平鉴定的新方法的开发一直是食品安全研究界的首要任务。缺乏以高置信度鉴定核苷酸和结构变体的参考基因组,限制了在暴发调查期间使用测序数据进行来源追踪的应用。在这项工作中,我们通过应用生物信息学分析确定了高分辨率,精心策划的公共线粒体基因组装配体的质量,以用作参考基因组。使用该参考基因组,从宏基因组读取开始,构建了三个新的线粒体基因组组件,该宏基因组读取通过对从孢子虫病患者粪便样品中存在的卵囊中提取的DNA进行测序而产生。与线粒体参考基因组相比,在新的和其他公共可用的基因组中鉴定出了核苷酸变体。使用我们的参考指导的从头装配方法,在这里提出的合并的工作流程,以生成新的线粒体基因组,可能对促进其他线粒体序列的产生以及在食源性暴发调查期间将其应用于C. cayetanensis菌株的应用很有帮助。

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