Integrated Transcriptome–Metabolome Analysis Uncovers Organ-Specific Divergence in Floral Scent Biosynthesis of Nymphaea Hybrid

Fragrance lotus (Nymphaea hybrid) is a tropical interspecific cultivar characterized by large flowers and high scent intensity, offering dual potential for ornamental commerce and natural fragrance extraction. Floral scent determines both economic value and pollinator attraction, yet the biosynthetic organs and metabolic routes remain undocumented. To fill this gap, single flowers of the high-aroma cultivar ‘Eldorado’ at full anthesis were dissected into petal (PE), stamen (ST) and pistil (PI); each organ was subjected to untargeted LC-MS/MS metabolomics and Illumina RNA-seq. Organ-specific gene–metabolite co-expression networks were constructed by pairwise integration of transcript and metabolite matrices. All three organs formed distinct clusters in principal-component space. Compared with PE, 6221, 3352 and 5891 differentially expressed genes (DEGs) together with 30, 24 and 39 differentially accumulated metabolites (DAMs) were identified in ST, PI and PE, respectively. The phenylpropanoid biosynthesis pathway (map00940) was the only route simultaneously enriched at both transcript and metabolite levels; 59 DEGs mapped to this pathway co-linearly with three scent-related DAMs. ST contained the highest concentration of scent-active volatiles; phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate-CoA ligase (4CL) and benzaldehyde reductase (BAR) were all significantly up-regulated in this organ, driving the accumulation of p-coumaric acid that is subsequently channeled into benzyl alcohol via side-chain cleavage and BAR-mediated reduction, thereby generating the characteristic fragrance of Nymphaea. This study provides the first organ-level resolution of scent biosynthesis and metabolic flux partitioning in fragrance lotus, furnishing molecular targets for directed aroma improvement and efficient natural fragrance extraction.