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Abstract: The molluscan shell is a composite of inorganic crystals comprising calcium carbonate and a minute amount of organic matrix. The organic matrix (OM) is intimately involved in every step of shell formation and has consequently received much attention in recent years. However, most of the deposited information has resulted from cDNA analysis, with little analysis of the genome, including the presence and effects of polymorphic genes encoding OM proteins. The current study aimed to clarify the genome structure of the N16 gene from the Japanese pearl oyster, Pinctada fucata, with particular reference to polymorphisms. The N16 gene was analyzed using PCR and DNA sequencing. 23 polymorphic variants were identified from 28 individuals. The variants were analyzed for their relationship to shell formation. All the variations detected by genomic PCR appeared in the cDNAs, implying that all the polymorphisms were transcribed and translated into N16 proteins. Additional genome analysis revealed at least two N16 genes, which were sequentially positioned, each of them comprising four exons and three introns. Further analyses of the transcriptional regulation and function of the N16 genes may provide new insights into their role in molluscan biomineralization. [Copyright &y& Elsevier]