Key message

Several hypomethylated sites within the Karma region of EgDEF1 and hotspot regions in chromosomes 1, 2, 3, and 5 may be associated with mantling.

Abstract

One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the “mantled” phenotype that can lead to reduced yields. This clonal abnormality is an epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC₃-poor genes) were increasingly methylated towards their 3′ region, while GC₃-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5′ UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling.

中文翻译：

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克隆繁殖油棕的 DNA 甲基化变化。

关键信息

例如DEF1的Karma区域内的几个低甲基化位点和染色体 1、2、3 和 5 中的热点区域可能与套膜有关。

抽象的

油棕业面临的主要挑战之一是果实异常，例如可导致产量下降的“覆盖”表型。这种克隆异常是一种表观遗传现象，与 Eg DEF1基因内的转座因子的低甲基化有关。为了了解克隆中的表观基因组变化，将克隆油棕的甲基化组与幼苗衍生油棕的甲基化组进行了比较。分析来自幼苗、正常和覆盖克隆的全基因组亚硫酸氢盐测序数据，以确定和比较上下文特异性 DNA 甲基化组。在幼苗中，编码区和调节区通常是低甲基化的，而内含子和重复区是广泛甲基化的。位于密码子第三位的鸟嘌呤和胞嘧啶数量较少的基因（GC ₃贫基因）的 3' 区域甲基化程度越来越高，而富含 GC ₃的基因保持去甲基化，类似于其他真核物种的模式。预测的启动子区域通常在幼苗中低甲基化。在克隆中，CG、CHG 和 CHH 甲基化水平通常在功能重要区域（如启动子、5' UTR 和编码区）中降低。尽管在克隆基因组中发现随机区域低甲基化，但某些热点区域的低甲基化可能与克隆覆盖表型有关。因此，我们的研究结果表明，例如DEF1的Karma中的其他低甲基化 CHG 位点和染色体 1、2、3 和 5 中的低甲基化热点区域与套膜有关。