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

作     者：濮龙军 王晶 王玉 左建伟 郭华荣 PU Longjun;WANG Jing;WANG Yu;ZUO Jianwei;GUO Huarong

作者机构：Ministry of Education Key Laboratory of Marine Genetics and Breeding College of Marine Life Sciences Ocean University of China Institute of Evolution and Marine Biodiversity Ocean University of China 

出 版 物：《Journal of Oceanology and Limnology》 (海洋湖沼学报（英文）)

年 卷 期：2018年第36卷第3期

页      面：853-869页

核心收录：

学科分类：0710[理学-生物学] 090801[农学-水产养殖] 0908[农学-水产] 07[理学] 0707[理学-海洋科学] 09[农学] 0815[工学-水利工程] 0903[农学-农业资源与环境] 0713[理学-生态学] 

基　　金：Supported by the National Natural Science Foundation of China(Nos.31172391,31472274) the Fundamental Research Funds for Central Universities(No.201762003) the Scholarship Foundation for Excellent Scientists of Shandong Province(No.BS2011SW054) the National HighTech R&D Program of China(863 Program)(No.2012AA10A402) the Open Funds of Institute of Biodiversity and Evolution,Ocean University of China(No.201362017) 

主　　题：碱基数据 对虾 生态系统 生物学 

摘      要：Study on shrimp miRNAs was limited and just 7 mature miRNA sequences of Marsupenaeus japonicus are deposited in mir Base 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 confi rmed 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.