Fig. 2

Microstructures and proteomes of the Crassotrea nippona shell. Shell layers: prismatic layer (PL), foliated layer (FL), chalky layer (CL), nacre layer (NL). a SEM micrographs of the microstructures of the prismatic, foliated, and chalky layers of the C. nippona shell. b Number of proteins identified from the prismatic, foliated, and chalky layers. c Circos diagram of seven representative molluscan shell proteomes (the E-value cut-off of BLASTP is 1e − 20); with the shell of farmed C. nippona on the left. Different color showed the sequences of SMPs in different molluscs and their proteins pairs with SMPs of C. nippona. Percentages and proportions in brackets indicate the number of SMPs having similarities between C. nippona and the other six molluscs. The solid circles above the species names represent that the shells contain calcite, while the hollow circles indicate the shells contain aragonite. d Upset plot comparing the protein domains identified from the shell proteomes of seven molluscs. The bar chart indicates the number of functional domains conserved among shell microstructure(s) or the whole shell of specie(s). The colored dots below histograms indicate the presence of the domains in shells of the molluscs. Domains only detected in the C. gigas shell and the chalky layer of C. nippona shell are indicated in orange. Domains shared by all shell layers across seven molluscs are colored in green. The complete results are shown in supplementary figure S11 (Additional file 1). e Expression of SMPs with domains specifically detected in C. gigas and the chalky layer of C. nippona in six tissues of C. nippona. Tissues: adductor muscle (AM), digestive gland (D), gill (G), hemolymph (H), mantle edge (ME), central mantle (MC). The number after the abbreviation of tissue represents biologically independent individuals (N = 3). f Spatial expression patterns of three SMPs with domains specific for chalky layers in the mantle tissue of C. nippona. The protein domain structures of genes are shown in the supplementary figure S12 (Additional file 1). Full view (left) and partial enlargement (right) show positive cells stained in blue by in situ hybridization of each gene, respectively. White arrows symbolize the end of the gene expression region. Mantle folds: outer fold (OF), middle fold (MF), inner fold (IF) (scale bars: 200 µm)