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In molluscs, shell matrix proteins are associated with biomineralization, a biologically controlled process that involves nucleation and growth of calcium carbonate crystals. Identification and characterization of shell matrix proteins are important for better understanding of the adaptive radiation of a large variety of molluscs. We searched the draft genome sequence of the pearl oyster Pinctada fucata and annotated 30 different kinds of shell matrix proteins. Of these, we could identified Perlucin, ependymin-related protein and SPARC as common genes shared by bivalves and gastropods; however, most gastropod shell matrix proteins were not found in the P. fucata genome. Glycinerich proteins were conserved in the genus Pinctada. Another important finding with regard to these annotated genes was that numerous shell matrix proteins are encoded by more than one gene; e.g., three ACCBP-like proteins, three CaLPs, five chitin synthase-like proteins, two N16 proteins (pearlins), 10 N19 proteins, two nacreins, four Pifs, nine shematrins, two prismalin-14 proteins, and 21 tyrosinases. This diversity of shell matrix proteins may be implicated in the morphological diversity of mollusc shells. The annotated genes reported here can be searched in P. fucata gene models version 1.1 and genome assembly version 1.0 ( http://marinegenomics.oist.jp/pinctada_fucata ). These genes should provide a useful resource for studies of the genetic basis of biomineralization and evaluation of the role of shell matrix proteins as an evolutionary toolkit among the molluscs.

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 © 2012. Published by Elsevier B.V.)