Integrated metabolomic and transcriptomic analysis reveals the metabolic and molecular mechanisms underlying floral color patterning in Catalpa bungei

The molecular mechanisms underlying the complex floral color patterns in Catalpa bungei , which are characterized by purplish-red spots and yellow nectar guides, are not fully understood. To elucidate these mechanisms, we integrated metabolomic and transcriptomic analyses of three accessions (P, B, and W) with distinct floral phenotypes. Phenotypic and colorimetric analyses revealed that accession P exhibits dense purplish-red spots and deep orange-yellow nectar guides, which correlated with the highest a* values in petals and highest b* values in nectar guides, whereas accession W shows sparse spots and pale yellow guides, and accession B displays an intermediate phenotype. Metabolomic profiling identified 2217 metabolites, highlighting the accumulation of specific anthocyanin derivatives, such as pelargonidin-3- p -coumarylglucoside in P and various acylated anthocyanins in B. The yellow nectar guides were primarily proposed to be attributed to flavonol glycosides. Transcriptomic analysis indicated that key anthocyanin pathway genes ( e.g. , CHS , CHI , F3H , DFR , ANS , UFGT ) were significantly upregulated in P, whereas most FLS genes were downregulated. Weighted Gene Co-expression Network Analysis (WGCNA) identified eight modules ( e.g. , MEyellow, MEblue) strongly associated with color patterning, which are regulated by transcription factors ( e.g. , MYB, bHLH, WD40, bZIP) that show co-expression with modification genes such as UGT and AOMT . The expression patterns of 12 key genes were validated using qRT-PCR. This study provides the first comprehensive analysis of the metabolic and transcriptional networks controlling floral color patterning in C. bungei , proposing a synergistic regulatory mechanism and offering critical targets for molecular breeding. • Acylated anthocyanins determine purplish-red spot intensity in C. bungei accessions. • Flavonol glycosides, not carotenoids, are proposed as the primary pigments of nectar guides. • FLS isoform divergence potentially redirects flux between anthocyanin and flavonol pathways. • WGCNA reveals MYB, bHLH, WD40, bZIP, and NAC co-regulate floral pigment patterning. • First metabolo-transcriptomic study deciphers dual-pigment floral patterning in C. bungei .