Integrated profiling identifies miRNAs in mantle exosomes/sEVs associated with nacre pigmentation in the Akoya pearl oyster (Pinctada fucata)

Exosomes/small extracellular vesicles (sEVs) are nanoscale vesicles with a phospholipid bilayer that can transport biomolecules such as proteins, lipids, and nucleic acids between cells. They participate in intercellular communication, notably through the delivery of microRNAs (miRNAs), which are key post-transcriptional regulators of gene expression. In this study, we explored associations between miRNAs in mantle-derived exosomes/sEVs and nacre pigmentation in the Akoya pearl oyster, Pinctada fucata . We performed mRNA sequencing of mantle tissues and small RNA sequencing of mantle-derived exosomes/sEVs in two groups of individuals exhibiting different levels of yellow pigment accumulation. Differential expression analysis and miRNA–mRNA interaction predictions suggested that several pigmentation-related pathways, including cytochrome P450-mediated drug metabolism and porphyrin metabolism, were enriched among the differentially expressed genes. Furthermore, four candidate differentially expressed miRNAs in exosomes/sEVs were identified (mle-miR-124–3p, v4.1_scaf_12a_21394, lgi-miR-315, and v4.1_scaf_04a_9961), with predicted target genes such as ADAMTS18, CSMD1, and TSPAN9, which are potentially involved in pigment transport and deposition. Our findings identify candidate associations related to nacre color formation in P. fucata and suggest the potential involvement of miRNAs in exosomes/sEVs in molluscan biomineralization processes.