Integrated mRNA and Small RNA Sequencing Reveals Regulatory Expression of Larval Metamorphosis of the Razor Clam.

The razor clam, Sinonovacula constricta, is an important economic marine shellfish, and its larval development involves obvious morphological and physiological changes. MicroRNA plays a key role in the physiological changes of the organism through regulating targeted mRNA. This study performed miRNA-mRNA sequencing for eight different developmental stages of S. constricta using Illumina sequencing. A total of 2156 miRNAs were obtained, including 2069 known miRNAs and 87 novel miRNAs. In addition, target genes were predicted for key miRNAs differentially expressed between adjacent development samples by integrating the mRNA transcriptome. Further analysis revealed that the differentially expressed genes were enriched in complement activation, alternative pathways, translation, and negative regulation of monocyte molecular protein-1 production. KEGG pathway annotation showed significant enrichment in the regulation of the ribosome, phagosome, tuberculosis and fluid shear stress, and atherosclerosis. Ten mRNAs and ten miRNAs that are related to larval metamorphosis were identified using real-time PCR. Furthermore, the double luciferase experiment validated the negative regulatory relationship between miR-133 and peroxisome proliferator-activated receptor-γ (PPAR-γ). These results indicated that the target genes regulated by these differentially expressed miRNAs may play an important regulatory role in the metamorphosis development of S. constricta.