Integrated Transcriptomic and Metabolomic Analysis Revealed Regulatory Mechanisms on Flavonoids Biosynthesis in the Skin of Passion Fruit (Passiflora spp.)

Passion fruit is one of the most famous fruit crops in tropical and subtropical regions due to its high edible, medicinal, and ornamental value. Flavonoids, a class of plant secondary metabolites, have important health-related roles. In this study, a total of 151 flavonoid metabolites were identified, of which 25 key metabolites may be the main contributors to the purple phenotype. Using RNA sequencing, 11,180 differentially expressed genes (DEGs) were identified. Among these, 48 flavonoid biosynthesis genes (PAL, 4CL, C4H, CHS, CHI, F3H, DFR, ANS, and UFGT) and 123 transcription factors were identified. Furthermore, 12 distinct modules were identified through weighted gene coexpression network analysis, of which the brown module displays a robust positive correlation with numerous flavonoid metabolites. Overexpression of PeMYB114 significantly promoted flavonoids accumulation in tobacco leaves. Our study provided a key candidate gene for molecular breeding to improve color traits in passion fruit.