Comprehensive analysis of microRNAs in the mantle central and mantle edge provide insights into shell formation in pearl oyster Pinctada fucata martensii

MicroRNAs (miRNAs) are a class of non-coding RNA molecules with presumed post-transcriptional regulatory activity in various biological processes. Pearl oyster Pinctada fucata martensii is one of the main species cultured for marine pearl production in China and Japan. In this study, we constructed two small RNA libraries of mantle central (MC) and mantle edge (ME) from P. f. martensii and obtained 24,175,537 and 21,593,898 clean reads, respectively. According to sequence similarity and hairpin structure prediction, 421 miRNAs of P. f. martensii (Pm-miRNA) were identified, and 93 differentially expressed miRNAs (DEMs) including 49 conserved Pm-miRNAs and 44 novel Pm-miRNAs were obtained from the MC and ME. The target genes of these DEMs were obviously enriched in neuroactive ligand-receptor interaction pathway, and et al. After the over-expression of Pm-miR-124 and Pm-miR-9a-5p in the MC by mimic injection into the muscle of P. f. martensii, nacre exhibited a disorderly growth as detected by scanning electron microscopy. The predicted target genes of Pm-miR-124 were Pm-nicotinic acetylcholine receptor alpha subunit, Pm-neuropeptide Y and Pm-chitin synthase. Meanwhile, the predicted target genes of Pm-miR-9a-5p were Pm-tumor necrosis factor receptor associated factor 2 and Pm-chitin synthase. These predicted target genes were down-regulated after the over-expression of Pm-miR-124 and Pm-miR-9a-5p. This study comprehensively analyzed the miRNAs in mantle tissues to enhance our understanding of the regulatory mechanism underlying shell formation.