title: 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.
authors: Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China.
authors: Yan
authors: Y
authors: Huang
authors: Wenjun
authors: W
authors: Chen
authors: Xiaoyun
authors: X
authors: Wang
authors: Hailiang
authors: H
authors: Liu
authors: Yangyi
authors: Y
authors: Chen
authors: Lei
authors: L
authors: Guo
authors: Fang
authors: F
authors: Luo
authors: Jiufeng
authors: J
authors: Sun
authors: Qiang
authors: Q
authors: Mao
authors: Pei
authors: P
authors: Liang
authors: Zhizhi
authors: Z
authors: Xie
authors: Chenhui
authors: C
authors: Zhou
authors: Yanli
authors: Y
authors: Tian
authors: Xiaoli
authors: X
authors: Lv
authors: Lisi
authors: L
authors: Huang
authors: Juanjuan
authors: J
authors: Zhou
authors: Yue
authors: Y
authors: Hu
authors: Ran
authors: R
authors: Li
authors: Fan
authors: F
authors: Zhang
authors: Huali
authors: H
authors: Lei
authors: Wenfang
authors: W
authors: Li
authors: Xuchu
authors: X
authors: Hu
authors: Chi
authors: C
authors: Liang
authors: Jin
authors: J
authors: Xu
authors: Xuerong
authors: X
authors: Li
authors: Xinbing
authors: X
authors: Yu
mesh_terms: D000818:Animals; D002471:Cell Transformation, Neoplastic; D003003:Clonorchiasis / Q000469:parasitology; D003004:Clonorchis sinensis / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D016000:Cluster Analysis; D004734:Energy Metabolism; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D018503:Genome, Protozoan; D006801:Humans; D008099:Liver / Q000469:parasitology*; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D009928:Organ Specificity / Q000235:genetics; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D015800:Protozoan Proteins
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