Biomineralization to fabricate diverse morphology shell is typical character of bivalve species and ectopic calcification to form is the production of defense. Long non-coding RNAs (LncRNAs) plays critical roles in multiple cellular biological processes in invertebrate and vertebrate. However, LncRNAs remain poorly understood about expression and regulation roles in bivalve biomineralization studies. In this research, we systematically identified lncRNAs that functioned in differentiated mantle regions for fabricating two phenotypes of CaCO crystal shell, along with pearl sac depositing pearls for ectopic calcification by CaCO. A total of 48,555 non-coding transcripts were obtained. 229 differentially expressed lncRNAs in mantle tissue as well as 401 differentially expressed lncRNAs in the comparison of mantle center to pearl sac were identified. By cis- and trans-regulation ways, these DELs could be involved in provisioning and metabolism such as chitin, glycosaminoglycan, ECM/shell matrix protein, Ca and HCO offering, and also affecting related signaling pathways. In addition, lncRNAs were found to crosstalk with miRNAs not only as primary competing endogenous RNAs but as the primary miRNAs. Our studies provided insight into non-coding RNA regulation of epigenetic regulation in biomineralization in bivalve species.
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