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Open Access Research article

Identification and characterization of microRNAs in Clonorchis sinensis of human health significance

Min-Jun Xu12, Quan Liu3, Alasdair J Nisbet4, Xian-Quan Cai5, Chao Yan1, Rui-Qing Lin1, Zi-Guo Yuan1, Hui-Qun Song12, Xian-Hui He1 and Xing-Quan Zhu126*

Author Affiliations

1 Department of Parasitology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China

2 State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu Province 730046, PR China

3 Laboratory of Parasitology, Veterinary Institute, AMMS, 1068 Qinglong Road, Changchun 130062, PR China

4 Parasitology Division, Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK

5 Zhongshan Entry-Exit Inspection and Quarantine Bureau, Zhongshan, Guangdong Province 528403, PR China

6 College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province 650201, PR China

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BMC Genomics 2010, 11:521  doi:10.1186/1471-2164-11-521

Published: 28 September 2010

Abstract

Background

Clonorchis sinensis is a zoonotic parasite causing clonorchiasis-associated human disease such as biliary calculi, cholecystitis, liver cirrhosis, and it is currently classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules which are essential for the complex life cycles of parasites and are involved in parasitic infections. To identify and characterize miRNAs expressed in adult C. sinensis residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing and bioinformatic predictions with stem-loop real-time PCR analysis.

Results

Here we report the use of this approach to identify and clone 6 new and 62,512 conserved C. sinensis miRNAs which belonged to 284 families. There was strong bias on families, family members and sequence nucleotides in C. sinensis. Uracil was the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and end of conserved miRNAs. There was no significant "seed region" at the first and ninth positions which were commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of C. sinensis were still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There were two miRNA strategies in C. sinensis for its parasitic life: keeping a large category of miRNA families of different animals and keeping stringent conserved seed regions with high active innovation in other places of miRNAs mainly in the middle and the end, which were perfect for the parasite to perform its complex life style and for host changes.

Conclusions

The present study represented the first large scale characterization of C. sinensis miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as miRNA studies of other related species such as Opisthorchis viverrini and Opisthorchis felineus of human and animal health significance.