Integrated analysis of metabolome and transcriptome reveals the molecular mechanism underlying different colors of Phyllanthus emblica L. fruit

The rare red Phyllanthus emblica L. fruit, with its distinctive appeal and potential nutritional profile, holds promise as an ideal material for both fresh consumption and plant-derived health food sector. Limited knowledge is available on the metabolic and molecular mechanism underlying this red phenotype. In this study, metabolic and transcriptome profiles of emblica fruits from four cultivars ranging from green to red color were analyzed. 726 differential accumulated metabolites (DAMs) were annotated with 72 critical metabolites for fruit reddening, which were primarily enriched in phenylpropanoid metabolism and flavonoid/anthocyanins biosynthesis pathways. Anthocyanin-targeted metabolome revealed that delphinidin 3-O-glucoside, cyanidin 3-O-glucoside and procyanidin B1 were key accumulated pigment substrates explaining fruit red coloration. WGCNA (Weighted Gene Co-Expression Network Analysis) identified PeCHS1 , PeF3H1 , PeDFR and PeLAR1 as hub genes responsible for diverse emblica fruit coloration among different cultivars. In addition, transient overexpression of PeCHS1 , PeF3H1 , PeDFR and PeLAR1 respectively in emblica fruits confirmed their roles in red coloration. Overall, our findings shed light on the metabolic basis and regulatory mechanism underlying the diverse emblica fruit coloration. • Metabolites and gene expression in emblica fruits with distinctive color traits were profiled. • Flavonoid/anthocyanins were the primary contributor to red color of emblica fruits. • Key anthocyanin monomers responsible for emblica fruit coloration were identified. • Overexpression of PeCHS1 , PeF3H1 , PeDFR and PeLAR1 induced red coloration in emblica fruits.