Unraveling the regulatory mechanism of petal spot formation in Rhododendron rivulare by integrated transcriptome and metabolome analysis

• Integrated multi-omics reveals anthocyanin-driven spot formation in Rhododendron rivulare. • Eighty-four anthocyanins are identified, with twelve key pigments defining spot-specific coloration. • Transcriptome uncovers 13,570 DEGs and 2293 conserved regulators strongly correlated with pigmentation. • A coordinated module of structural genes and transcriptional activators (e.g., RsMYB1) is characterized. • Anatomical and colorimetric evidence supports a metabolism-dependent, non-structural model for spot patterning.