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Identification and characterization of microRNAs in Trichinella spiralis by comparison with Brugia malayi and Caenorhabditis elegans

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Abstract

Trichinella spiralis is an important zoonotic nematode causing trichinellosis which is associated with human diseases such as malaise, anorexia, nausea, vomiting, abdominal pain, fever, diarrhea, and constipation. microRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of gene expression. The objective of the present study was to examine the miRNA expression profile of the larvae of T. spiralis by Solexa deep sequencing combined with stem-loop real-time polymerase chain reaction (PCR) analysis. T. spiralis larvae were collected from the skeletal muscle of naturally infected pigs in Henan province, China, by artificial digestion using pepsin. The specific identity of the T. spiralis larvae was confirmed by PCR amplification and subsequent sequence analysis of the internal transcribed spacer of ribosomal DNA. A total of 17,851,693 reads with 2,773,254 unique reads were obtained. Eleven conserved miRNAs from 115 unique xsmall RNAs (sRNAs) and 12 conserved miRNAs from 130 unique sRNAs were found by BLAST analysis against the known miRNAs of Caenorhabditis elegans (ftp://ftp.ncbi.nih.gov/genomes/Caenorhabditis_elegans) and Brugia malayi dataset (http://www.ncbi.nlm.nih.gov/genomeprj?Db=genomeprj&cmd=ShowDetailView&TermToSearch=9549) in miRBase, respectively. One novel miRNA with 12 precursors were identified and certified using the reference genome of B. malayi, while no novel miRNA was found when using the reference genome of C. elegans. Nucleotide bias analysis showed that the uracil was the prominent nucleotide, particularly at the 1st, 6th, 18th, and 23th positions, which were almost at the beginning, middle, and the end of the conserved miRNAs. The identification and characterization of T. spiralis miRNAs provides a new resource to study regulation of genes and their networks in T. spiralis.

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Acknowledgments

This work is supported in part by the Program for National S & T Major Program (grant no. 2008ZX10004-011, 2009ZX10004-302, 2009ZX10004-201), National Key Technology R & D Program (grant no. 2008BAI56B03), and the State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences. The experiments comply with the current laws of the country in which the experiments were performed.

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Authors and Affiliations

  1. National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People’s Republic of China

    M. X. Chen, L. Ai, S. H. Chen, Y. N. Zhang, J. Guo, Y. C. Cai, L. G. Tian, L. L. Zhang & J. X. Chen

  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, People’s Republic of China

    L. Ai, M. J. Xu & X. Q. Zhu

  3. College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, 510642, People’s Republic of China

    L. Ai

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  1. M. X. Chen
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  2. L. Ai
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  3. M. J. Xu
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  4. S. H. Chen
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  9. L. L. Zhang
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Correspondence to X. Q. Zhu or J. X. Chen.

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M. X. Chen and L. Ai contributed equally to this work.

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Chen, M.X., Ai, L., Xu, M.J. et al. Identification and characterization of microRNAs in Trichinella spiralis by comparison with Brugia malayi and Caenorhabditis elegans . Parasitol Res 109, 553–558 (2011). https://doi.org/10.1007/s00436-011-2283-x

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  • DOI: https://doi.org/10.1007/s00436-011-2283-x

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