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

<div><p><em>Clonorchis sinensis (C. sinensis)</em>, 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 <em>C. sinensis</em> 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 <em>C. sinensis</em> 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 <em>C. sinensis</em>. The characterization and elaborate analysis of the upgraded genome and the tissue transcriptomes not only form a detailed and fundamental <em>C. sinensis</em> resource but also provide novel insights into the physiology and pathogenesis of <em>C. sinensis</em>. We anticipate that this work will aid the development of innovative strategies for the prevention and control of clonorchiasis.</p>