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.

珍珠色泽受遗传学、生物色素及有机基质的调控，是影响珍珠经济价值的重要因素。珍珠色素化的表观遗传调控机制至今仍处于理解不足的状态。在本研究中，我们收集了金唇珍珠贝（Pinctada fucata martensii）的金唇系和银唇系的鳃瓣（MP）以及鳃中央组织（MC），并采用全基因组亚硫酸氢盐测序（WGBS）技术，以探讨表观遗传因素对珍珠层颜色变异的可能影响。我们的研究结果表明，P. fucata martensii 基因组中约有2.5%的胞嘧啶被甲基化，其中CG甲基化类型最为常见。总体而言，我们在两组比较中识别出12,621个差异甲基化区域（DMRs），对应于3,471个DMR相关基因（DMGs）。这些DMGs主要富集于KEGG代谢通路，包括ABC转运蛋白、萜类骨架生物合成和脂肪酸降解等。此外，整合DMGs、DEGs及功能注释信息，我们确定了八个基因LDLR、NinaB、RDH、CYP、FADS、fn3、PU-1、KRMP作为与珍珠层色泽色素化相关的候选基因。进一步的研究证实，珍珠层中的色素为 violaxanthin。本研究结果为珍珠层色泽形成与DNA甲基化谱之间的关联提供了支持，并将有助于揭示珍珠贝P. fucata martensii中珍珠层色素化形成的表观遗传调控机制。