Image_2_Increased histone H3 acetylation inhibit the inflammatory response and activate the serum immunity of Pearl oyster Pinctada fucata martensii.tif

To produce cultured pearls, a mantle graft with a nucleus is transplanted into a host pearl oyster, this process is called “transplantation”. The immune response of pearl oyster after transplantation is a major factor that leads to nucleus rejection and death. Butyrate is a histone deacetylase (HDAC) inhibitor which can inhibit the deacetylation process of histones and effectively reduce the inflammatory response. To clarify the function of histone acetylation in immune response after transplantation, butyrate (10 mmol/L) was used for the treatment of pearl oysters before transplantation. Results showed that the proportion of histone H3 acetylation of the hemocytes was significantly increased after butyrate treatment before transplantation (BH group) compared with the control group at 6–24 h. Transcriptome analysis showed that butyrate treatment activated the “lysosome”, inhibited cell migration and cell proliferation at 6 and 12 h, respectively, and activated the intracellular immune recognition response of pearl oyster at 24 h after transplantation. The apoptosis detection revealed no significant difference in the proportion of apoptotic cells between the control and BH group. Moreover, butyrate treatment increased the activity of some immune-related enzymes in the serum of pearl oyster after transplantation.</p

Image_1_Increased histone H3 acetylation inhibit the inflammatory response and activate the serum immunity of Pearl oyster Pinctada fucata martensii.tif

To produce cultured pearls, a mantle graft with a nucleus is transplanted into a host pearl oyster, this process is called “transplantation”. The immune response of pearl oyster after transplantation is a major factor that leads to nucleus rejection and death. Butyrate is a histone deacetylase (HDAC) inhibitor which can inhibit the deacetylation process of histones and effectively reduce the inflammatory response. To clarify the function of histone acetylation in immune response after transplantation, butyrate (10 mmol/L) was used for the treatment of pearl oysters before transplantation. Results showed that the proportion of histone H3 acetylation of the hemocytes was significantly increased after butyrate treatment before transplantation (BH group) compared with the control group at 6–24 h. Transcriptome analysis showed that butyrate treatment activated the “lysosome”, inhibited cell migration and cell proliferation at 6 and 12 h, respectively, and activated the intracellular immune recognition response of pearl oyster at 24 h after transplantation. The apoptosis detection revealed no significant difference in the proportion of apoptotic cells between the control and BH group. Moreover, butyrate treatment increased the activity of some immune-related enzymes in the serum of pearl oyster after transplantation.</p

Correlation analysis between <i>PfmPif97-like</i> expression and growth traits of <i>P</i>. <i>f</i>. <i>martensii</i>.

Correlation analysis between PfmPif97-like expression and growth traits of P. f. martensii.</p

Additional file 7: of Developmental characteristics of pearl oyster Pinctada fucata martensii: insight into key molecular events related to shell formation, settlement and metamorphosis

The ecdysone receptors and the Nvds in bivalves. a. The ecdysone receptors in mollusk species. b, the expression pattern of Ecr at different development stages in C. gigas. E, egg; TC, two cells; FC, four cells; EM, early morula; M, morula; B, blastula; RM, rotary movement; FS, free swimming;EG, early gastrula stage; G, gastrula; T1, trochophore 1; T2, trochophore 2; T3,trochophore 3; T4, trochophore 4; T5, trochophore 5; ED1, early D-larva 1; ED2, early D-larva 2; D1, D-larva 1; D2, D-larva 2; D3, D-larva 3; D4, D-larva 4; D5, D-larva 5; D6, D-larva 6; D7, D-larva 7; EU1, early umbo larva 1; EU2, early umbo larva 2; U1, umbo larva 1; U2, umbo larva 2; U3, umbo larva 3; U4, umbo larva 4; U5, umbo larva 5; U6, umbo larva 6; LU1, later umbo larva 1; LU2, later umbo larva 2; P1, pediveliger 1; P2, pediveliger 2; S, spat; and J, juvenile. c. the expression pattern of Nvd at different development stages in P. f. martensii and C. gigas. Egg, egg; Fe, fertilized egg; B, blastula; G, gastrula; ET, early trochophore; T, trochophore; D, D-stage larvae; DF, D-stage larvae before feeding; EU, early umbo larvae; EL, eyed larvae; S, spat; J, juveniles. (PDF 772 kb

Nucleotide and amino acid sequence of <i>PfmPif97-like</i>.

The amino acid sequences are shown below the nucleotide sequence. The amino acid sequence with the black bold font is signal peptide and with gray background is VWA domain. The underlined amino acid sequences are two ChtBD2 domains. The nucleotide with a frame represents the start and stop codons. The sequence before ATG is the 5′UTR region. The sequence after TAA is the 3′UTR region.</p

Pfm-miR-9b-5p targeting <i>PfmPif97-like</i> 3′UTR.

A1 and A2: The target site obtained by using miranda and RNAhybrid. B: Results of dual-luciferase assay in 293T cells. The relative expression of Pfm-miR-9b-5p in the central zone of mantle (C1) and the mantle edge (C2) after injecting Pfm-miR-9b-5p mimics. The relative expression of Pfm-Pif97-like in the mantle pallial (C3) and the mantle edge (C4) after injecting Pfm-miR-9b-5p mimics. D1 and D2 SEM image of nacre layer after injecting Pfm-miR-9b-5p mimics; D3 and D4: SEM images of nacre layer after injecting N. C. mimics; D5 and D6: SEM images of prismatic layer after injecting Pfm-miR-9b-5p mimics; D7 and D8: SEM image of prismatic layer after injecting N. C. mimics. “a” and “*” represents a significant difference (P .05); “b” represents no significant difference. The white line in the image indicates the scale.</p

Additional file 1: of Developmental characteristics of pearl oyster Pinctada fucata martensii: insight into key molecular events related to shell formation, settlement and metamorphosis

Kegg enrichment of differentially expressed genes in P. f. martensii (XLSX 19 kb

DataSheet1_DNA Methylation Analyses Unveil a Regulatory Landscape in the Formation of Nacre Color in Pearl Oyster Pinctada fucata martensii.xlsx

Pearl color is regulated by genetics, biological pigments, and organic matrices and an important factor that influences the pearl economic value. The epigenetic regulation mechanism underlying pearl pigmentation remains poorly understood. In this study, we collected the mantle pallial (MP) and mantle central (MC) of the golden-lipped strain, and MP of the silver-lipped strain of pearl oyster Pinctada fucata martensii. The whole-genome bisulfite sequencing (WGBS) technology was employed to investigate the possible implication of epigenetic factors regulating nacre color variation. Our results revealed approximately 2.5% of the cytosines in the genome of the P. fucata martensii were methylated, with the CG methylation type was in most abundance. Overall, we identified 12, 621 differentially methylated regions (DMRs) corresponding to 3,471 DMR-associated genes (DMGs) between the two comparison groups. These DMGs were principally enriched into KEGG metabolic pathways including ABC transporters, Terpenoid backbone biosynthesis, and fatty acid degradation. In addition, integrating information about DMGs, DEGs, and function annotation indicated eight genes LDLR, NinaB, RDH, CYP, FADS, fn3, PU-1, KRMP as the candidate genes related to pigmentation of nacre color. A further study proved that the pigment in nacre is violaxanthin. The results of our study provide the support that there is an association between nacre color formation and DNA methylation profiles and will help to reveal the epigenetic regulation of nacre pigmentation formation in pearl oyster P. fucata martensii.</p

Additional file 2: of Developmental characteristics of pearl oyster Pinctada fucata martensii: insight into key molecular events related to shell formation, settlement and metamorphosis

Gene Ontology enrichment of differentially expressed genes in P. f. martensii (XLSX 22 kb

Additional file 5: of Developmental characteristics of pearl oyster Pinctada fucata martensii: insight into key molecular events related to shell formation, settlement and metamorphosis

Differentially expressed genes between early trochophore and trochophore stage involved in osteoclast differentiation in P. f. martensii. The red color represented the upregulation at trochophore stage, the green color represented the downregulation at trochophore stage. The yellow color represented the absence genes in P. f. martensii. (PDF 135 kb