DNA甲基化、代谢组和转录组分析揭示了二倍体和四倍体白菜种子表观基因组的差异。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics Pub Date : 2025-07-17 DOI:10.1016/j.ygeno.2025.111088

Chuan Meng, Xiaodong Liu, Fang Wu, Xiaochao Ma, Lei Ma, Qingfeng Wang, Mingqiu Wang

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引用次数: 0

摘要

本研究旨在阐明二倍体和四倍体白菜种子的表观基因组差异，并初步探讨四倍体种子活力降低的机制。我们综合分析了转录组、代谢组和全基因组亚硫酸盐测序（WGBS），以研究不同年份二倍体和四倍体白菜种子的基因表达、代谢物谱和DNA甲基化模式。结果表明，在所有序列背景下（CG、CHG和CHH），四倍体种子比二倍体种子表现出更低的DNA甲基化水平和更少的甲基化胞嘧啶。差异甲基化区（DMRs）主要富集于基因的上游和下游区域，二倍体种子中高甲基化区数量较多。转录组学分析显示萌发前后基因表达有显著变化，萌发后下调的基因较多。KEGG富集分析表明，差异表达基因主要参与碳水化合物代谢、氨基酸代谢和信号转导途径。代谢组学分析鉴定出1346种代谢物，其中黄酮类化合物和植物激素信号转导途径最为突出。值得注意的是，aba相关基因，包括7个ABF基因、18个PYR/PYL基因、6个SRK基因和2个PP2C基因，在二倍体和四倍体种子中表现出不同的甲基化和表达模式。这些基因在次生代谢物生物合成和植物激素信号通路中富集，表明它们可能与四倍体种子活力降低有关。总之，我们的研究提供了二倍体和四倍体白菜种子活力差异的表观遗传和转录特征的全面认识。这些发现强调了DNA甲基化和ABA信号在调节种子发育和活力中的重要性。

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DNA methylation, metabolome, and transcriptome analysis reveal epigenomic differences between diploid Chinese cabbage seeds and tetraploid Chinese cabbage seeds

This study aimed to elucidate the epigenomic differences between diploid and tetraploid Chinese cabbage seeds and preliminarily explore the mechanisms underlying the reduced seed vigor in tetraploid seeds. We comprehensively analyzed the transcriptome, metabolome, and whole-genome bisulfite sequencing (WGBS) to investigate gene expression, metabolite profiles, and DNA methylation patterns in diploid and tetraploid Chinese cabbage seeds from different years.

Results showed that tetraploid seeds exhibited lower DNA methylation levels and fewer methylated cytosines than diploid seeds across all sequence contexts (CG, CHG, and CHH). Differentially methylated regions (DMRs) were predominantly enriched in upstream and downstream regions of genes, with a higher number of hypermethylated regions in diploid seeds. Transcriptomic analysis revealed significant changes in gene expression before and after germination, with more genes downregulated post-germination. KEGG enrichment analysis indicated that differentially expressed genes were mainly involved in carbohydrate metabolism, amino acid metabolism, and signal transduction pathways. Metabolome analysis identified 1346 metabolites, with flavonoids and plant hormone signal transduction pathways being the most prominent. Notably, ABA-related genes, including seven ABF genes, 18 PYR/PYL genes, six SRK genes, and two PP2C genes, exhibited differential methylation and expression patterns between diploid and tetraploid seeds. These genes were enriched in pathways related to secondary metabolite biosynthesis and plant hormone signaling, suggesting a potential role in the reduced seed vigor of tetraploid seeds. In conclusion, our study provides a comprehensive understanding of the epigenetic and transcriptional characteristics underlying the differences in seed vigor between diploid and tetraploid Chinese cabbage seeds. The findings highlight the importance of DNA methylation and ABA signaling in regulating seed development and vigor.

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来源期刊

Genomics 生物-生物工程与应用微生物

CiteScore

9.60

自引率

2.30%

发文量

260

审稿时长

60 days

期刊介绍： Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.