Combined transcriptome and metabolome analysis reveal the chemical composition diversity and ferulate 5-hydroxylase mediated metabolite regulatory mechanism in Polygonatum

The active ingredients in different Polygonatum species (P-HJ) differ greatly, which causes confusion regarding their use. This study was to systematically compare the contents of the main active ingredients of different P-HJ (pharmacopoeia), as well as the types and contents of other metabolic compounds. Analyzed the mechanisms of the main active component synthesis in P-HJ and the related disease regulatory network. The microstructure, physicochemical indices, LC-MS/MS, RNA-Seq, and pharmacological network analysis were performed on Polygonatum cyrtonema Hua (CM), Polygonatum sibiricum Red. (SM), and Polygonatum kingianum Coll. et Hemsl (KM). The phenotypes and microstructures are sufficiently different to distinguish the authenticity of various species of Polygonatum. A total of 672 metabolites were identified including flavonoids, phenolic acids, and saccharides, etc. These metabolic compounds have different characteristics and accumulation patterns in the CM, SM, and KM. The active components in different germplasms had significant differences to affected the medicinal quality. Key metabolites and regulated genes were identified in flavonoid, lignin, and saccharide biosynthesis by association network analysis, including ferulate 5-hydroxylase (F5H). These key genes were verified using RT-qPCR. The subcellular localization and transgenic (gene overexpression) verification was conducted for F5H. In Polygonatum, 28 differentially accumulated metabolites (DAMs) have 156 targets and 134 related diseases by pharmacological network analysis. This study provides an important basis for the high-quality breeding of P-HJ.