The Carcinogenic Liver Fluke, Clonorchis sinensis: New Assembly, Reannotation and Analysis of the Genome and Characterization of Tissue Transcriptomes

Abstract

Clonorchis sinensis (C. sinensis), an important food-borne parasite that inhabits the intrahepatic bile duct and causes clonorchiasis, is of interest to both the public health field and the scientific research community. To learn more about the migration, parasitism and pathogenesis of C. sinensis at the molecular level, the present study developed an upgraded genomic assembly and annotation by sequencing paired-end and mate-paired libraries. We also performed transcriptome sequence analyses on multiple C. sinensis tissues (sucker, muscle, ovary and testis). Genes encoding molecules involved in responses to stimuli and muscle-related development were abundantly expressed in the oral sucker. Compared with other species, genes encoding molecules that facilitate the recognition and transport of cholesterol were observed in high copy numbers in the genome and were highly expressed in the oral sucker. Genes encoding transporters for fatty acids, glucose, amino acids and oxygen were also highly expressed, along with other molecules involved in metabolizing these substrates. All genes involved in energy metabolism pathways, including the β-oxidation of fatty acids, the citrate cycle, oxidative phosphorylation, and fumarate reduction, were expressed in the adults. Finally, we also provide valuable insights into the mechanism underlying the process of pathogenesis by characterizing the secretome of C. sinensis. The characterization and elaborate analysis of the upgraded genome and the tissue transcriptomes not only form a detailed and fundamental C. sinensis resource but also provide novel insights into the physiology and pathogenesis of C. sinensis. We anticipate that this work will aid the development of innovative strategies for the prevention and control of clonorchiasis.

Transcriptome analysis of the adult rumen fluke Paramphistomum cervi following next generation sequencing

“…Additionally, gene encoding enzymes involved in the pathway that converts glucose to acetyl-CoA were transcribed at high levels (FPKM N 20) in P. cervi. This observation is consistent with a study showing glucose serving as an energy source in C. sinensis (van Grinsven et al, 2009;Huang et al, 2013). Given these data, how does the adult fluke obtain enough glucose in the rumen?…”

A constitutively active G protein-coupled acetylcholine receptor regulates motility of larval Schistosoma mansoni

“…Pharmacological studies carried out on the free-living flatworm Dugesia do suggest the involvement of muscarinic receptors in the control of motor function [55] and SmGAR is the first of these receptors to be characterized in a flatworm at the molecular level. Our bioinformatics analysis indicate that SmGAR shares significant homology with known GARs from nematodes as well as predicted GARs of fellow Platyhelminthes, including other trematodes and recently described tapeworm sequences [44, 45]. Interestingly, the flatworm GARs all appear to have exceptionally long il3 regions, resulting in longer protein sequences than those of nematodes or vertebrates.…”

“…Although the C. elegans GAR shares a higher percent similarity with SmGAR, the Clonorchis receptor has higher coverage (96%), even across the highly divergent il3 loop. Putative homologs of SmGAR also appear in the genomes of the cestodes Taenia solium and Echinococcus granulosus [44, 45]. Phylogenetic analysis (Fig.…”

The Opisthorchis viverrini genome provides insights into life in the bile duct

“…of humans all have eight chromosomes19. These findings indicate that the O. viverrini genome is very divergent from all other fluke genomes published to date9101113.…”