Spatiotemporal methylome remodeling during fiber differentiation in Gossypium hirsutum.

IF 3.7 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

BMC Genomics Pub Date : 2025-10-09 DOI:10.1186/s12864-025-12116-5

Zhipeng Yu, Haijuan Cao, Xiaolian Xiong, Shuhan Wen, Xia Huang, Ying Jin, Junkang Rong, Mingquan Ding

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Abstract

Whole-genome methylome analysis reveals DNA methylation dynamics during upland cotton (Gossypium hirsutum) fiber development. DNA methylation levels initially increased and then decreased from -3 days post-anthesis (DPA) to 5 DPA, with a significant rise during the rapid elongation stage (5 DPA to 14 DPA), particularly in CHH methylation levels. Integrated transcriptome analysis links elevated DNA methylation to reduced demethylase gene expression (DME, ROS1, DML3). DNA methylation remodeling modulates fiber development through coordinated regulation of lipid metabolism, DNA replication, phosphatidylinositol signaling system and hormonal signaling pathways. Several key transcription factors, such as TCP14, HD1, HOX3, and MYB25-like, showed a strong correlation with DMRs, suggesting their regulation by DNA methylation. Furthermore, Multi-omics integration posits that DNA methylation may regulate genes related to fiber development, particularly those related to fatty acid biosynthesis and metabolism, ultimately influencing upland cotton fiber development. Analysis of genes highly correlated with changes in differentially methylated regions (DMRs) indicates DNA methylation can modulate the expression of KCS family genes, including KCS13, as well as KCRL1, thereby participating in the fatty acid elongation pathway.

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棉纤维分化过程中的时空甲基组重构。

全基因组甲基组分析揭示了陆地棉花纤维发育过程中的DNA甲基化动力学。DNA甲基化水平在花后3天至5天先上升后下降，在快速伸长期（5天至14天）显著上升，尤其是CHH甲基化水平。整合转录组分析将DNA甲基化升高与去甲基化酶基因表达降低（DME, ROS1, DML3）联系起来。DNA甲基化重塑通过协调调节脂质代谢、DNA复制、磷脂酰肌醇信号系统和激素信号通路来调节纤维的发育。几个关键转录因子，如TCP14、HD1、HOX3和MYB25-like，与DMRs有很强的相关性，表明它们受到DNA甲基化的调控。此外，多组学整合认为DNA甲基化可能调控与纤维发育相关的基因，特别是与脂肪酸生物合成和代谢相关的基因，最终影响陆地棉纤维的发育。对差异甲基化区（DMRs）变化高度相关基因的分析表明，DNA甲基化可以调节KCS家族基因的表达，包括KCS13和KCRL1，从而参与脂肪酸延伸途径。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

BMC Genomics 生物-生物工程与应用微生物

CiteScore

7.40

自引率

4.50%

发文量

769

审稿时长

6.4 months

期刊介绍： BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.