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Journal of Oceanology and Limnology

, Volume 36, Issue 3, pp 853–869 | Cite as

Computational identification and characterization of microRNAs and their targets in Penaeus monodon

  • Longjun Pu (濮龙军)
  • Jing Wang (王晶)
  • Yu Wang (王玉)
  • Jianwei Zuo (左建伟)
  • Huarong Guo (郭华荣)
Article
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Abstract

Study on shrimp miRNAs was limited and just 7 mature miRNA sequences of Marsupenaeus japonicus are deposited in mirBase database. In this study, miRNAs and their target gene candidates were computationally identified from shrimp Penaeu s monodon and then experimentally validated. Using 39 908 expressed sequence tags (ESTs) and 21 124 genome survey sequences (GSSs) of P. monodon (pmo) as reference dataset, a comprehensive approach based on inter-species homolog search was employed to investigate the candidate miRNAs (i.e. pmo-miRNA). A total of eight miRNAs belonging to 7 families were computationally identified and five out of them were subsequently validated by PCR and sequencing. Of these, pmo-miR-4961a, pmo-miR-4961b, pmo-miR-4979 and pmo-miR-3819 were first identified from shrimps. Both the mature pmo-miRNAs and the corresponding precursors were conserved among different species. Based on perfect or near-perfect match to the target region, the target gene candidates of pmomiRNAs were predicted from 10 331 mRNA sequences of P. monodon. A total of 20 genes were predicted as the targets of pmo-miR-4961a, pmo-miR-4961b, pmo-miR-4979 and pmo-miR-6492. Experimental validation by dual luciferase reporter assay confirmed the targeting between 3 pmo-miRNAs and one or two of their target genes, especially the pmo-miR-4979 which could significantly down-regulate the expression of target gene (JR226772). This study updates the miRNAs and their targets in P. monodon and lays a solid foundation for future RNAi study.

Keyword

microRNA shrimp Penaeus monodon target genes 

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Notes

Acknowledgement

We thank Dr. Jerame Hui (School of Life Science, Chinese University of Hong Kong, China) for kindly providing the reporter plasmid of psiCHECK-2.

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Copyright information

© Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Longjun Pu (濮龙军)
    • 1
  • Jing Wang (王晶)
    • 1
  • Yu Wang (王玉)
    • 1
  • Jianwei Zuo (左建伟)
    • 1
  • Huarong Guo (郭华荣)
    • 1
    • 2
  1. 1.Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
  2. 2.Institute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina

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