Integrated transcriptomic analysis and anthocyanin profiling identify a PcNAC68–PcAAT1 module associated with red-stem pigmentation in cultivated Polygonatum cyrtonema

The metabolites and regulatory mechanisms associated with contrasting stem coloration in Polygonatum cyrtonema remain incompletely understood. We compared red- and green-stem landraces at three matched developmental stages to distinguish persistent pigmentation-associated differences from stage-specific variation. Targeted LC–MS/MS profiling identified 27, 25, and 23 differentially accumulated metabolites, respectively, including 16 anthocyanins shared across stages. Five shared anthocyanins were supported by corresponding authentic-standard measurements, whereas 11 were putatively annotated through database matching and their reported amounts were treated as semi-quantitative estimates. Four red-stem-enriched signals were putatively assigned to coumaroylated petunidin or malvidin glycosides. Transcriptomic analysis prioritized the candidate acyltransferase gene PcAAT1 , whose transient expression in Nicotiana benthamiana increased total anthocyanins approximately sixfold. Silencing PcAAT1 in P. cyrtonema reduced purple stem coloration and total anthocyanin content. PcNAC68 activated the PcAAT1 promoter and recognized a CATGTG-containing region in yeast and in vitro. Silencing PcNAC68 in native plants reduced PcAAT1 transcript levels and anthocyanin content. These results support a PcNAC68 – PcAAT1 regulatory relationship contributing to pigmentation. PcAAT1 catalytic specificity remains to be established.