DataSheet1_Integration of Transcriptome and Methylome Analyses Provides Insight Into the Pathway of Floral Scent Biosynthesis in Prunus mume.docx

DNA methylation is a common epigenetic modification involved in regulating many biological processes. However, the epigenetic mechanisms involved in the formation of floral scent have rarely been reported within a famous traditional ornamental plant Prunus mume emitting pleasant fragrance in China. By combining whole-genome bisulfite sequencing and RNA-seq, we determined the global change in DNA methylation and expression levels of genes involved in the biosynthesis of floral scent in four different flowering stages of P. mume. During flowering, the methylation status in the “CHH” sequence context (with H representing A, T, or C) in the promoter regions of genes showed the most significant change. Enrichment analysis showed that the differentially methylated genes (DMGs) were widely involved in eight pathways known to be related to floral scent biosynthesis. As the key biosynthesis pathway of the dominant volatile fragrance of P. mume, the phenylpropane biosynthesis pathway contained the most differentially expressed genes (DEGs) and DMGs. We detected 97 DMGs participated in the most biosynthetic steps of the phenylpropane biosynthesis pathway. Furthermore, among the previously identified genes encoding key enzymes in the biosynthesis of the floral scent of P. mume, 47 candidate genes showed an expression pattern matching the release of floral fragrances and 22 of them were differentially methylated during flowering. Some of these DMGs may or have already been proven to play an important role in biosynthesis of the key floral scent components of P. mume, such as PmCFAT1a/1c, PmBEAT36/37, PmPAL2, PmPAAS3, PmBAR8/9/10, and PmCNL1/3/5/6/14/17/20. In conclusion, our results for the first time revealed that DNA methylation is widely involved in the biosynthesis of floral scent and may play critical roles in regulating the floral scent biosynthesis of P. mume. This study provided insights into floral scent metabolism for molecular breeding.

DNA甲基化（DNA methylation）是一类常见的表观遗传修饰，参与调控诸多生物学进程。然而，在中国著名传统观赏植物、可释放宜人花香的梅（Prunus mume）中，参与花香形成的表观遗传机制却鲜有报道。本研究结合全基因组亚硫酸氢盐测序（whole-genome bisulfite sequencing）与RNA-seq，分析了梅四个不同开花阶段的全基因组DNA甲基化全局变化，以及花香生物合成相关基因的表达水平。开花过程中，基因启动子区域内“CHH”序列背景（其中H代表A、T或C）的甲基化状态变化最为显著。富集分析结果显示，差异甲基化基因（differentially methylated genes, DMGs）广泛参与8条已知与花香生物合成相关的通路。作为梅优势挥发性香气的关键生物合成途径，苯丙烷生物合成途径包含的差异表达基因（differentially expressed genes, DEGs）与DMGs数量最多。本研究共检测到97个DMGs参与苯丙烷生物合成途径的绝大多数步骤。此外，在先前已鉴定的梅花香生物合成关键酶编码基因中，有47个候选基因的表达模式与花香释放节律相匹配，其中22个在开花过程中发生了甲基化差异。部分此类差异甲基化基因已被证实或可能在梅关键花香组分的生物合成中发挥重要作用，例如PmCFAT1a/1c、PmBEAT36/37、PmPAL2、PmPAAS3、PmBAR8/9/10以及PmCNL1/3/5/6/14/17/20。综上，本研究首次揭示DNA甲基化广泛参与花香生物合成过程，并可能在调控梅的花香生物合成中发挥关键作用。本研究为花香代谢的分子育种提供了新的见解。