Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas

Regulation of microRNAs (miRNAs) on various biological processes has been a surprising and exciting field. Identification of miRNAs is the first step to comprehensively understand their functions. However, attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp Marsupenaeus japonicus, an economically important aquatic species. By performing an integrated analysis of transcriptomic profile from gastrula embryos of M. japonicus, 21 conserved miRNAs in M. japonicas (mja-miRNAs), belonging to 19 miRNA families, were identified and characterized. Of the 21 mja-miRNAs, 15 miRNAs were successfully verified to be predominantly expressed in gastrula stage, where they displayed dynamic expression patterns compared with those in naupliuin stage. Based on perfect or near-perfect match to target region, 120 target genes were predicted at transcriptome-wide level. Noteworthy, gene ontology (GO) classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental processes. Of the predicted miRNA-mRNA pairs, six targets were then randomly selected and experimentally validated by dual luciferase reporter assay, where three pairs were proved with potential targeting activity. Overall, to search for conserved miRNAs potentially involved in early development of M. japonicus, we combined in silico and experimental methods, which can be applied in other organisms as well. Our data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in M. japonicus.