Fruit skin color is a critical agronomic trait determining fruit quality, but the mechanisms governing melon ( L.) fruit skin pigmentation remain inadequately characterized. We performed cytological, transcriptomic, and whole-genome bisulfite sequencing (WGBS) comparative analyses on two near-isogenic lines (NILs) at different developmental stages: the green-skinned (GS) and white-skinned (WS) melon. The enriched functions among the 536 identified differentially expressed genes (DEGs) were related to chloroplast development, pigment metabolism, and photosynthetic pathway. The genes in these pathways were downregulated in the WS line, potentially contributing to the decreased chlorophyll content and abnormal chloroplast development in WS. WGBS analysis revealed that the levels of genomic DNA methylation in WS progressively exceeded those in GS as the fruits developed. The integrated analysis of the transcriptome and methylome identified DMR-associated DEGs (, and ) involved in chlorophyll metabolism. Notably, exhibited downregulated expression and was hypermethylated in WS fruits during two developmental stages, showing a coordinated expression with the chlorophyll contents in developing WS and GS fruits. Furthermore, we identified a transcription factor gene, MELO3C011576, that was closely associated with the expression of and chlorophyll levels across three developmental stages in both NILs. We speculate that positively regulates chlorophyll biosynthesis in the two NILs, with its expression may be co-controlled by DNA methylation and transcription factors.

中文翻译：

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控制瓜类果实皮肤色素沉着的机制：转录组测序和全基因组亚硫酸氢盐测序分析的见解


果皮颜色是决定果实品质的关键农艺性状，但控制甜瓜（L.）果皮色素沉着的机制仍不充分。我们对不同发育阶段的两个近等基因系（NIL）：绿皮（GS）和白皮（WS）甜瓜进行了细胞学、转录组和全基因组亚硫酸氢盐测序（WGBS）比较分析。 536 个已鉴定的差异表达基因 (DEG) 的丰富功能与叶绿体发育、色素代谢和光合作用途径有关。这些途径中的基因在 WS 系中下调，可能导致 WS 中叶绿素含量降低和叶绿体发育异常。 WGBS 分析显示，随着果实的发育，WS 中的基因组 DNA 甲基化水平逐渐超过 GS 中的水平。转录组和甲基化组的综合分析确定了参与叶绿素代谢的 DMR 相关 DEG（和）。值得注意的是，在两个发育阶段，WS 果实中表达下调并高度甲基化，在发育中的 WS 和 GS 果实中显示出与叶绿素含量的协调表达。此外，我们还发现了一个转录因子基因 MELO3C011576，它与两个 NIL 的三个发育阶段的表达和叶绿素水平密切相关。我们推测这两个NILs中正向调节叶绿素生物合成，其表达可能受到DNA甲基化和转录因子的共同控制。