Transcriptomic analysis of the mantle of Manila clam Ruditapes philippinarum reveals the molecular basis of...

Biomineralization in mollusks, particularly shell formation and repair, is a dynamic process mediated by shell matrix proteins and tightly regulated gene expression. In this study, we investigated the temporal transcriptomic profiles of mantle tissue in the Manila clam (Ruditapes philippinarum) during shell repair. Experimental shells were artificially damaged in a V-shaped pattern, and regeneration was monitored at short-term (48 h), long-term (18 d), and control group (cn) using RNA-seq and qPCR analysis. Scanning electron microscopy (SEM) revealed a sequential reconstruction of the periostracum, prismatic, and nacreous layer, reflecting the temporal organization of mineral deposition. Transcriptomic analysis identified stage-specific differentially expressed genes (350 in m48h vs cn, 163 in m18d vs cn, and 119 in m48h vs m18d) enriched in pathways associated with tyrosine metabolism, chitin biosynthesis, and extracellular matrix (ECM) regulation. Early-stage repair was characterized by rapid upregulation of Pif, Tem, and chitin-binding domain genes, facilitating the formation of organic scaffolds for CaCO₃ crystallization. In later stages, DPT downregulation and reduced ECM-related gene expression, alongside sustained Pif activity, suggest a regulatory mechanism to balance ECM assembly and mineralization. Additionally, upregulation of Pax7 and tyrosine metabolism genes indicates an integration of biomineralization processes with shell structural repair. These findings provide new insights into the molecular networks orchestrating bivalve shell regeneration and identify potential genetic targets for strengthening shell robustness in aquaculture and enhancing resilience to environmental stressors such as ocean acidification.