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MicroRNA repertoire for functional genome research in tilapia identified by deep sequencing

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Abstract

The Nile tilapia (Oreochromis niloticus; Cichlidae) is an economically important species in aquaculture and occupies a prominent position in the aquaculture industry. MicroRNAs (miRNAs) are a class of noncoding RNAs that post-transcriptionally regulate gene expression involved in diverse biological and metabolic processes. To increase the repertoire of miRNAs characterized in tilapia, we used the Illumina/Solexa sequencing technology to sequence a small RNA library using pooled RNA sample isolated from the different developmental stages of tilapia. Bioinformatic analyses suggest that 197 conserved and 27 novel miRNAs are expressed in tilapia. Sequence alignments indicate that all tested miRNAs and miRNAs* are highly conserved across many species. In addition, we characterized the tissue expression patterns of five miRNAs using real-time quantitative PCR. We found that miR-1/206, miR-7/9, and miR-122 is abundantly expressed in muscle, brain, and liver, respectively, implying a potential role in the regulation of tissue differentiation or the maintenance of tissue identity. Overall, our results expand the number of tilapia miRNAs, and the discovery of miRNAs in tilapia genome contributes to a better understanding the role of miRNAs in regulating diverse biological processes.

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Acknowledgments

This work was supported by Shanghai Educational Development Foundation (Grant No. 12CG56 to B.Y.), the Specialized Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20123104120005 to B.Y.), and China Agriculture Research System (Grant No.CARS-49-4B to J.-L.Z.).

Conflict of interest

The authors have declared that no competing interests exist.

Author information

Authors and Affiliations

  1. Key Laboratory of Freshwater Fisheries Germplasm Resource, Ministry of Agriculture, SHOU, Shanghai, 201306, China

    Biao Yan & Jin-Liang Zhao

  2. College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China

    Biao Yan, Chang-Dong Zhu, Jin-Tao Guo & Jin-Liang Zhao

  3. College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China

    Zhen-Hua Wang

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  1. Biao Yan
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  2. Zhen-Hua Wang
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  3. Chang-Dong Zhu
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  4. Jin-Tao Guo
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  5. Jin-Liang Zhao
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Corresponding authors

Correspondence to Biao Yan or Jin-Liang Zhao.

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Biao Yan and Zhen-Hua Wang have contributed equally to this work.

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Yan, B., Wang, ZH., Zhu, CD. et al. MicroRNA repertoire for functional genome research in tilapia identified by deep sequencing. Mol Biol Rep 41, 4953–4963 (2014). https://doi.org/10.1007/s11033-014-3361-9

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  • DOI: https://doi.org/10.1007/s11033-014-3361-9

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