Multi‐Omics Landscape to Reveal the Discrepancy in the Accumulation of Flavonoids in <i>Artemisia argyi</i> Across Multiple Growth Stages

Flavonoids are a major component of Artemisia argyi and play a crucial role in its pharmacological properties. However, the molecular mechanisms underlying flavonoid biosynthesis in A. argyi remain unclear. To address this, transcriptome and quantitative metabolome analyses were conducted across five developmental stages of A. argyi. In total, 85 flavonoid compounds were identified across these different stages. Differentially expressed candidate genes and metabolites involved in flavonoid biosynthesis were also identified. Differentially accumulated flavonoid metabolites (DFMs) were observed among the 10 comparison groups, with 29 DFMs identified from the five developmental stages of A. argyi leaves. The biosynthesis process identified 38 differentially expressed genes (DEGs) from seven gene families. Furthermore, 26 DEGs exhibited a significant correlation with the levels of seven active flavonoid metabolites, as revealed by weighted gene co-expression network analysis. These DEGs included eight HCT genes, six CHI genes, two CHS genes, three CCoAOMT genes, two F3'H genes, two C4H genes, two CYP98A genes, and one F3H gene. Based on preliminary analysis, HCT1 may be associated with accumulating hispidulin and jaceosidin. This study investigated the relationship between differential gene expression and flavonoid accumulation using an integrated transcriptomic and metabolomic approach, providing valuable insights into the mechanisms of flavonoid biosynthesis and quality formation in A. argyi.