Integrated analyses of the transcriptome and metabolome revealed the coloring mechanism of red-pericarp wampee (Clausena lansium).

Wampee (Clausena lansium), a tropical evergreen fruit from the Rutaceae family renowned for its rich nutrient profile and bioactive compounds, presents a fascinating case study in fruit coloration. However, changes in anthocyanins, and expressions of metabolism-associated genes during fruit maturation of red-pericarp wampee ('ZR') are not documented. In this study, metabolic and gene expression profiles of anthocyanin across different fruit developmental stages of red and yellow-pericarp wampees were analyzed. A total of 38 distinct anthocyanins were identified from the comparison of 'ZR3' and 'JX3' wampees and categorized into 17 differential anthocyanin metabolites (DAMs). Among these DAMs, fifteen were up-regulated in 'ZR3', while two were down-regulated compared with 'JX3'. The delphinidin 3-[6-(4-(caffeoylrhamnosyl)glucoside)] was the predominant anthocyanins in 'ZR' wampee. A total of 1135 metabolics mainly including amino acid metabolites and flavonoids were detected in the 'ZR' and 'JX' wampees. Significant differences were mainly concentrated in the biosynthesis of secondary metabolites in terms of flavonoid biosynthesis, ABC transporters, and anthocyanin biosynthesis. According to the combined analyses of qRT-PCR and transcriptome, the transcript levels of PAL1, PAL2, CHS1 and UFGT1 in 'ZR' wampee were two to eight-fold higher than those in 'JX' wampee during fruit pigmentation. Our study offers valuable insights into the mechanisms of anthocyanin accumulation in the red pericarp of wampee which is helpful to regulate fruit coloration of wampee.