Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
Biotechnol Adv. 2018 Jul-Aug;36(4):894-904. doi: 10.1016/j.biotechadv.2018.02.008. Epub 2018 Feb 15.
Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations.
华支睾吸虫（Opisthorchiidae 科）是一种重要的食源性病原体，对中国、越南、韩国和俄罗斯远东地区约 3500 万人造成重大的社会经济影响。在人类中，感染华支睾吸虫会导致华支睾吸虫病，这是一种复杂的肝胆疾病，可诱发胆管癌（CCA），即胆管的恶性癌症。了解该疾病的流行病学的核心是了解该寄生虫种群内和种群间的遗传变异。尽管大多数已发表的分子研究似乎表明华支睾吸虫代表一个单一物种，但华支睾吸虫内的核型变异和相关的后睾科吸虫（Opisthorchis viverrini）中的隐种证据强调了研究和比较地理上不同的华支睾吸虫分离株的基因和基因组的重要性。最近，我们对来自韩国的华支睾吸虫分离株的核基因组进行了测序、组装和特征描述，并使用为比较基因组草图组装及其基因注释而建立的生物信息学工作流程，将其与该物种的中国分离株的已发表的基因组草图进行了比较。我们发现，韩国和中国华支睾吸虫基因组支架的 50.6%和 51.3%分别是同线性的。在对齐的同线性块内，基因组具有高度的核苷酸同一性（99.1%），并编码 15 个可能参与多种生物学过程的可变蛋白。在这里，我们综述了使用基因组草图进行比较基因组分析以量化同一物种分离株之间遗传变异的当前技术挑战。我们使用克服这些挑战的工作流程，报告了来自韩国的高质量华支睾吸虫基因组草图和比较基因组分析，作为未来研究华支睾吸虫种群遗传结构的基础，并讨论了这些探索的生物技术意义。
