Elsevier

Genomics

Volume 113, Issue 3, May 2021, Pages 1605-1615
Genomics

Original Article
High-quality reference genome for Clonorchis sinensis

https://doi.org/10.1016/j.ygeno.2021.03.001Get rights and content
Under a Creative Commons license
open access

Highlights

  • First chromosome-level assembly of a liver fluke parasite.

  • We resolve genome fragmentation in a draft genome utilising advanced DNA sequencing and informatic approaches.

  • This reference genome provides a key genomic resource for molecular investigations of Clonorchis sinensis and clonorchiasis.

Abstract

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.

Keywords

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

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