Abstract

Wampee ( Clausena lansium ) is an important tropical fruit cultivated in southern China, which is typically yellow in appearance. Recently, a unique purple wampee has been identified, and its composition of anthocyanins remains unknown. We hypothesized that this distinctive pigmentation results from the accumulation of specific anthocyanin compounds. In this study, we aimed to characterize its nutritional trait and elucidate anthocyanin composition and the molecular mechanism underlying purple pigmentation. Results revealed the abundance in 3 sugars, 5 organic acids, and 11 amino acids in purple wampee. To elucidate the pigmentation mechanism, we developed a sensitive and accurate ultra-performance liquid chromatography-tandem mass spectrometry method for high-throughput analysis of anthocyanins. The established method effectively detected 39 anthocyanins with a linear quantification range of 10–4000 ng/mL (R 2  ≥ 0.99178). Quantitative analysis revealed that three delphinidin-based anthocyanins (delphinidin, delphinidin 3-O-galactoside, and delphinidin 3-O-glucoside) constituted ≥89.52% of the total anthocyanin content, and were identified as the crucial pigments in purple wampee. Transcriptomic analysis of the purple wampee identified 2210 differentially expressed genes (DEGs) during ripening. K-means clustering analysis and enrichment analysis indicated that the expression of the Cl1978 gene exhibited a significant positive correlation ( P  < 0.05) with the accumulation of delphinidin-based anthocyanins. The role of this core candidate gene was further verified by qRT–PCR and Agrobacterium-mediated transient expression in tobacco leaves. Our findings confirm the hypothesis that delphinidin-based anthocyanins and the Cl1978 gene are central to the purple coloration of wampee, and provide a potential molecular marker for wampee breeding.