Metabolomics and Transcriptomics Studies of the Differential Accumulation of Flavonoids in Different Organs in Emilia sonchifolia
Emilia sonchifolia (L.) DC is a medicinal and edible herb of Asteraceae with Lingnan characteristics. Flavonoids are its core pharmacodynamic substances, but the molecular regulation mechanism of differential accumulation of flavonoids in different organs of this species is still unclear. In this study, the molecular basis of tissue-specific synthesis of flavonoids was analyzed by integrating UPLC-MS broad-target metabolome and Illumina high-throughput transcriptome with four tissues of Emilia sonchifolia: root, stem, leaf, and flower. The results showed that a total of 73 flavonoid metabolites were identified in the metabolome, including naringenin chalcone, luteolin, quercitrin, and other pharmacologically active substances. Multi-omics joint analysis showed that the floral organ was the core tissue for the synthesis and enrichment of flavonoids, and there were specific characteristic flavonoid subtypes in different tissues. A total of 211 differentially expressed genes related to the flavonoid synthesis pathway were screened by transcriptome analysis, including 16 flavonol synthases, five cinnamic acid 4-hydroxylases, and five chalcone synthases. The WGCNA and gene–metabolite association network showed that the transcription levels of key enzyme genes such as CHS, C4H, F3′H, and F3H were highly positively correlated with the accumulation of downstream flavonols. The qRT-PCR quantitative verification showed that the expression patterns of CHS1, CHI4, F3′H5, F3H, FLS4, and GT in the four tissues were highly consistent with the transcriptome sequencing results, which confirmed that the transcriptome data were reliable. For the first time, this study revealed the molecular regulatory network of tissue-specific accumulation of flavonoids in Emilia sonchifolia, and clarified that the flower organ was the optimal medicinal harvesting site of flavonoids. It provided key theoretical support for the breeding of high-efficacy Emilia sonchifolia germplasm, the development of flavonoid active ingredients, and the study of secondary metabolic evolution of Compositae plants.