Identification and characterization of miRNA and their predicted functions in the larval development of pearl oyster Pinctada fucata

An important economic shellfish, the pearl oyster, Pinctada fucata, and its larvae are an ideal model for studying of larval development molecular mechanisms in invertebrates. Larval development directly affects the yield and quality of pearl oyster breeding. Increasing evidence suggests that microRNAs (miRNAs) play important roles in development, but knowledge of miRNA expression effects on P. fucata early development remains limited. In this study, the miRNA and mRNA transcriptomics were analyzed via Illumina RNA sequencing in seven different P. fucata developmental stages. A total of 329 miRNAs, encompassing 87 known miRNAs and 242 novel miRNAs, and 33,550 unigenes, including 26,333 known genes and 7,217 predicted new genes, were identified in these stages. Cluster analysis showed that the number of miRNAs with significant differences was the largest between fertilized eggs and trochophores. In addition, the integrated mRNA transcriptome was used to predict target genes for key miRNAs differentially expressed between adjacent developmental stages. Using the Gene Ontology (GO) annotation, 100 different expressed genes (DEGs) and 95 different expressed miRNAs (DEMs) were identified as part of larval development regulation. Real-time PCR was used to identify 8 mRNAs and 3 miRNAs related to larval development. The present findings could be helpful for further clarifying the regulation mechanisms of invertebrate larval development.