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Genome-wide discovery of novel and conserved microRNAs in white shrimp (Litopenaeus vannamei)

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Abstract

Of late years, a large amount of conserved and species-specific microRNAs (miRNAs) have been performed on identification from species which are economically important but lack a full genome sequence. In this study, Solexa deep sequencing and cross-species miRNA microarray were used to detect miRNAs in white shrimp. We identified 239 conserved miRNAs, 14 miRNA* sequences and 20 novel miRNAs by bioinformatics analysis from 7,561,406 high-quality reads representing 325,370 distinct sequences. The all 20 novel miRNAs were species-specific in white shrimp and not homologous in other species. Using the conserved miRNAs from the miRBase database as a query set to search for homologs from shrimp expressed sequence tags (ESTs), 32 conserved computationally predicted miRNAs were discovered in shrimp. In addition, using microarray analysis in the shrimp fed with Panax ginseng polysaccharide complex, 151 conserved miRNAs were identified, 18 of which were significant up-expression, while 49 miRNAs were significant down-expression. In particular, qRT-PCR analysis was also performed for nine miRNAs in three shrimp tissues such as muscle, gill and hepatopancreas. Results showed that these miRNAs expression are tissue specific. Combining results of the three methods, we detected 20 novel and 394 conserved miRNAs. Verification with quantitative reverse transcription (qRT-PCR) and Northern blot showed a high confidentiality of data. The study provides the first comprehensive specific miRNA profile of white shrimp, which includes useful information for future investigations into the function of miRNAs in regulation of shrimp development and immunology.

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Abbreviations

miRNAs:

MicroRNAs

ESTs:

Expressed sequence tags

qRT-PCR:

Quantitative real-time PCR

miRNP:

miRNA ribonucleoprotein complex

NCBI:

The National Center for Biotechnology Information

snRNAs:

Small nuclear RNAs

snoRNAs:

Small nucleolar RNAs

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Acknowledgments

This study was supported by grants from the Chinese Key Basic Plan (No. 2011CB944200), and the Natural Science Foundation of Guangdong province (S2013010013215).

Conflicts of interest

The authors report no conflicts of interest with this study.

Author information

Authors and Affiliations

  1. Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China

    Qian-Yun Xi, Yuan-Mei Wang, Xiao Cheng, Qi-En Qi, Gang Shu, Song-Bo Wang, Li-Na Wang, Ping Gao, Xiao-Tong Zhu, Qing-Yan Jiang, Yong-Liang Zhang & Li Liu

  2. College of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China

    Yuan-Yan Xiong

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  1. Qian-Yun Xi
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  2. Yuan-Yan Xiong
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  4. Xiao Cheng
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  6. Gang Shu
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  12. Yong-Liang Zhang
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  13. Li Liu
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Corresponding authors

Correspondence to Yong-Liang Zhang or Li Liu.

Additional information

Qian-Yun Xi, Yuan-Yan Xiong and Yuan-Mei Wang: co-first authors and also contributed equally to this study.

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Xi, QY., Xiong, YY., Wang, YM. et al. Genome-wide discovery of novel and conserved microRNAs in white shrimp (Litopenaeus vannamei). Mol Biol Rep 42, 61–69 (2015). https://doi.org/10.1007/s11033-014-3740-2

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  • DOI: https://doi.org/10.1007/s11033-014-3740-2

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