Integrated Transcriptomic and Metabolomic Profiling Reveals Developmental Reprogramming of Flavonoid Biosynthesis in Styphnolobium japonicum Flowers.

Styphnolobium japonicum is valued for its flavonoid-rich flowers, yet the developmental regulation of these metabolites remains unclear. Here, we integrated transcriptomic and metabolomic analyzes across four floral stages to reveal dynamic changes in flavonoid biosynthesis. Flavonoids emerged as the predominant metabolites, showing distinct stage-specific accumulation. Early stages showed high expression of CHS and F3H, with naringenin and eriodictyol as dominant metabolites. Mid-development maintained FLS-driven flavonol production, yielding quercetin and kaempferol derivatives. Late stages exhibited coordinated upregulation of CYP93C and HIDH, driving isoflavone (genistein) enrichment, alongside ANS and F3GT upregulation, enhancing anthocyanin glycosylation. Weighted gene co-expression and KEGG enrichment analyzes further supported a temporal reprogramming from primary metabolism to specialized bioactive compound production. Coordinated gene-metabolite patterns highlighted a temporal reprogramming from primary metabolism to targeted bioactive compound production. This study provides molecular insight into flavonoid biosynthesis during floral development and offers a framework for metabolic enhancement in S. japonicum.