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High-quality reference genome for Clonorchis sinensis 收藏

Clonorchis Sinensis的高质量参考基因组

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作者

Andreas J.Stroehlein[a];LiinaKinkar[a];TaoWang[a];Woon-MokSohn[b];Bill C.H.Chang[a];ParwinderKaur[c];DavidWeisz[d];OlgaDudchenko[d][e];Erez LiebermanAiden[c][d][e][f];Pasi K.Korhonen[a];Robin B.Gasser[a]

作者单位

[a]aDepartment of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, AustraliaDepartment of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia[b]bDepartment of Parasitology and Institute of Health Sciences, School of Medicine, Gyeongsang National University, Jinju, Republic of KoreaDepartment of Parasitology and Institute of Health Sciences, School of Medicine, Gyeongsang National University, Jinju, Republic of Korea[c]cUWA School of Agriculture and Environment, Faculty of Science, University of Western Australia, Perth, Western Australia 6009, AustraliaUWA School of Agriculture and Environment, Faculty of Science, University of Western Australia, Perth, Western Australia 6009, Australia[d]dThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USAThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA[e]eCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005, USACenter for Theoretical Biological Physics, Rice University, Houston TX 77005, USA[f]fShanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, ChinaShanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China

关键词

Chinese liver fluke;Clonorchis sinensis;Third-generation sequencing;Advanced bioinformatics;Reference genome;

关键词译文

中国肝霉菌; Clonorchis Sinensis;第三代测序;晚期生物信息学;参考基因组;

发布日期

1 May 2021

DOI

10.1016/j.ygeno.2021.03.001

来源信息

Genomics ISSN：0888-7543, 2021年, 113卷, 3期

摘要

The Chinese liver fluke, Clonorchis sinensis, causes the disease clonorchiasis, affecting ~35 million people in regions of China, Vietnam, Korea and the Russian Far East. Chronic clonorchiasis causes cholangitis and can induce a malignant cancer, called cholangiocarcinoma, in the biliary system. Control in endemic regions is challenging, and often relies largely on chemotherapy with one anthelmintic, called praziquantel. Routine treatment carries a significant risk of inducing resistance to this anthelmintic in the fluke, such that the discovery of new interventions is considered important. It is hoped that the use of molecular technologies will assist this endeavour by enabling the identification of drug or vaccine targets involved in crucial biological processes and/or pathways in the parasite. Although draft genomes of C. sinensis have been published, their assemblies are fragmented. In the present study, we tackle this genome fragmentation issue by utilising, in an integrated way, advanced (second- and third-generation) DNA sequencing and informatic approaches to build a high-quality reference genome for C. sinensis, with chromosome-level contiguity and curated gene models. This substantially-enhanced genome provides a resource that could accelerate fundamental and applied molecular investigations of C. sinensis, clonorchiasis and/or cholangiocarcinoma, and assist in the discovery of new interventions against what is a highly significant, but neglected disease-complex.

摘要译文

中国肝博士，Clonorchis Sinensis导致疾病克拿大病，影响了中国，越南，韩国和俄罗斯远东地区的3500万人。慢性克隆罗基病导致胆管炎，可以诱导胆管系统中的恶性癌症，称为胆管癌。流行区域的控制是挑战性的，并且通常很大程度上依靠化疗与一种叫吡喹酮的一个αsthelmintic。常规治疗具有在侥幸中对这种疾病造成这种抗性的显着风险，使得新干预的发现被认为是重要的。希望使用分子技术的使用将通过能够鉴定寄生虫中关键的生物方法和/或途径中涉及的药物或疫苗靶标的来帮助这种努力。虽然C. Sinensis草案已发表，但它们的组件是碎片化的。在本研究中，我们通过以综合的方式，先进（第二代和第三代）DNA测序和信息方法来解决这种基因组碎片问题，以构建C. Sinensis的高质量参考基因组，具有染色体水平邻缘和愈合基因模型。这种基本上增强的基因组提供了可以加速C. sinensis，Clonorchiaisis和/或胆管癌的基本和应用分子调查的资源，并协助发现对患有强度重要但被忽视的疾病复杂的新干预措施。