Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of B. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in B. napus might be partially regulated by MET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed Brassica polyploids.

中文翻译：

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DNA 修复和核苷酸代谢相关基因在天然和合成多倍体 (Brassica napus L.) 中表现出不同的 CHG 甲基化模式

多倍化在被子植物物种的进化中起着至关重要的作用。几乎所有新形成的多倍体都会遇到遗传或表观遗传的不稳定性。然而，导致合成多倍体基因组不稳定性的分子机制尚未明确阐明。在这里，我们对天然和合成的多倍体油菜籽进行了全面的转录组和甲基组分析（油菜）。我们的研究结果表明，在不同基因组环境（基因、转座子区域和重复区域）中，合成油菜的 CHG 甲基化水平显着低于天然油菜。天然多倍体和合成多倍体之间的 CHG-DMRs 的总数和长度远大于 CG-DMRs 和 CHH-DMRs，与这些 CHG-DMRs 重叠的基因在 DNA 损伤修复和核苷酸代谢途径中显着富集。这些结果表明 CHG 甲基化可能比 CG 和 CHH 甲基化更敏感地调节多倍体基因组的稳定性。油菜. 此外，许多参与 DNA 损伤修复、核苷酸代谢和细胞周期控制的基因在天然油菜籽和合成油菜籽之间存在显着差异表达。我们的研究结果强调，与 DNA 修复和核苷酸代谢相关的基因在天然和合成多倍体之间显示出不同的 CHG 甲基化模式，并揭示了多倍体植物的基因组不稳定性与 DNA 甲基化缺陷和 DNA 修复系统失调之间的潜在联系。此外，还发现 CHG 甲基化的维持油菜可能受到部分监管MET1. 我们的研究为多倍体植物的建立和进化提供了新的见解，并为提高新形成的基因组稳定性提供了潜在的思路芸苔属多倍体。