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

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

机构地区：[1]Ministry of Education Key Laboratory of Marine Genetics and Breeding,College of Marine Life Sciences,Ocean University of China,Qingdao 266003,China [2]Institute of Evolution and Marine Biodiversity,Ocean University of China,Qingdao 266003,China

出　　处：《Journal of Oceanology and Limnology》2018年第3期853-869,共17页海洋湖沼学报（英文）

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)

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.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.

关 键 词：microRNA shrimp PENAEUS MONODON target genes 

分 类 号：S968.226[农业科学—水产养殖] X171[农业科学—水产科学]