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The draft genome of the carcinogenic human liver fluke Clonorchis sinensis

Xiaoyun Wang12, Wenjun Chen12, Yan Huang12, Jiufeng Sun12, Jingtao Men12, Hailiang Liu3, Fang Luo3, Lei Guo3, Xiaoli Lv12, Chuanhuan Deng12, Chenhui Zhou12, Yongxiu Fan12, Xuerong Li12, Lisi Huang12, Yue Hu12, Chi Liang12, Xuchu Hu12, Jin Xu12 and Xinbing Yu12*

Author Affiliations

1 Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, PR China

2 Key Laboratory for Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, 74 Zhongshan 2nd Road, Guangzhou, 510080, PR China

3 Guangzhou iGenomics Co., Ltd, 135 West Xingang Road, Guangzhou, 510275, PR China

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Genome Biology 2011, 12:R107  doi:10.1186/gb-2011-12-10-r107

Published: 24 October 2011

Additional files

Additional file 1:

Genome assembly and genome features of C. sinensis. Figure S1: 17-mer depth distribution of the sequencing reads. Figure S2: features of the assembled C. sinensis genome. Figure S3: distribution of heterozygosity in C. sinensis. Figure S4: protein domain analysis of C. sinensis, S. mansoni, and S. japonicum. Table S1: main features of C. sinensis genome sequencing data. Table S2: numbers of reads mapped to the assembled C. sinensis genome. Table S3: genome validation by PCR products. Table S4: genome validation by Sanger ESTs. Table S5: repeat composition of C. sinensis genome. Table S6: summary of predicted protein-coding genes by different methods. Table S7: statistics of the reliable gene set with homology, or functional annotation or putative full-length ORF support [95]. Table S8: numbers of homologous genes between the CEGMA set of 458 core eukaryotic genes and our gene models. Table S9: summary of gene families in several organisms. Table S10: summary of genes annotated by InterPro domains in several species. Table S11: summary of predicted non-coding RNA genes in the C. sinensis genome.

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Additional file 2:

Summary of C. sinensis miRNA precursors.

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Additional file 3:

Detailed information on putative syntenic blocks of C. sinensis versus S. japonicum and C. sinensis versus S. mansoni, respectively.

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Additional file 4:

Important metabolism pathways of C. sinensis. Figure S5: the glycolytic pathway of C. sinensis. All the key enzymes required for glycolysis were identified, indicating that the glycolytic pathway of C. sinensis is intact. EC numbers marked in red indicate the presence of the genes in the genome of C. sinensis. Figure S6: the Krebs cycle of C. sinensis. The Krebs cycle of C. sinensis is intact, reflected by related key enzymes present in C. sinensis genome, demonstrating that the liver fluke can generate energy from aerobic or anaerobic metabolism. EC numbers marked in red indicate the presence of the genes in the genome of C. sinensis. Figure S7: the fatty acid metabolism pathway of C. sinensis. C. sinensis can metabolize fatty acids as all required enzymes in the fatty acid metabolism pathway have been discovered. EC numbers marked in red indicate the presence of the genes in the genome of C. sinensis. Figure S8: the fatty acid biosynthesis pathway of C. sinensis. Only three enzymes in the fatty acid biosynthesis pathway were identified, indicating that C. sinensis cannot synthesize endogenous fatty acids. EC numbers marked in red indicate the presence of the genes in the genome of C. sinensis.

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Additional file 5:

Comprehensive analysis of genes involved in fatty acid biosynthesis in C. sinensis, S. japonicum and S. mansoni.

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Additional file 6:

Key molecules of C. sinenisis. Table S12: glycolysis molecules of C. sinensis. Table S13: protease molecules of C. sinensis. Table S14: kinase molecules of C. sinensis. Table S15: phosphatase molecules of C. sinensis. Table S16: tegument molecules of C. sinensis. Table S17: ES molecules of C. sinensis. Table S18: host binding molecules of C. sinensis. Table S19: sex determination molecules of C. sinensis. Table S20: CCA-related molecules of C. sinensis.

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Additional file 7:

Sources of gene sets used for comparative analysis.

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