DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from Pinctada fucata martensii. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from P. f. martensii via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of P. f. martensii and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation.

中文翻译：

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珍珠牡蛎Pinctada fucata martensii的地幔边缘和地幔中央全基因组DNA甲基化分析。

DNA甲基化是一种表观遗传修饰，可在不改变DNA序列的情况下改变基因表达并介导某些表型可塑性的情况。在这项研究中，我们从Pinctada fucata martensii中鉴定了六个DNA甲基转移酶（DNMT）基因和两个甲基-CpG结合域蛋白2（MBD2）基因。我们还分析了P.f.的地幔边缘（ME）和地幔中央（MC）的全基因组DNA甲基化水平。马滕西通过甲基化免疫沉淀测序（MeDIP-Seq）。结果显示，ME和MC均具有1.22亿次读取，并且分别具有58,702和55,721个峰。获得的基因元件和重复序列的甲基化模式表明，编码蛋白质的基因，特别是内含子和编码外显子（CDSs）的甲基化比珍珠贝基因组中的其他基因组元件更频繁。我们将甲基化数据与P.f.的ME和MC的RNA-seq数据结合在一起。马滕西并且发现启动子，CDS和内含子甲基化水平与基因表达水平呈正相关，除了最高的基因表达水平。我们还确定了313个差异甲基化基因（DMG），并注释了其中的212个。这些DMG显着丰富了30种途径，例如氨基酸和蛋白质代谢，能量代谢，类萜合成以及免疫相关途径。这项研究全面分析了与生物矿化有关的组织的甲基化，并有助于增进我们对壳形成的调控机制的了解。