Metabolomics and transcriptomics analyses provide insights into the dynamic of metabolites and the molecular mechanisms of natural pigment formation of different color-transition types of red Pepper (Capsicum)

• Shared/unique metabolites were identified in 3 color-transition types of red peppers. • Some beneficial metabolites to humans accumulate more in young pepper pericarp. • Potential regulatory genes of anthocyanins were identified in pepper pericarp. • Potential regulatory genes of capsanthin were identified that target CCS in pepper. • Valuable references were provided for fully utilizing pepper's beneficial substances. Pepper is highly popular as a vegetable, spice, and natural red pigment material. However, little is known about metabolite accumulation dynamics in red pepper pericarp, which limits the full utilization of nutrients at different stages of pepper pericarp development. Moreover, few regulatory genes responsible for natural pigment flavonoids and carotenoids biosynthesis were reported in peppers, resulting in a constrained understanding of the molecular mechanisms that contribute to their formation. Here, we identified 1429 metabolites for the first time during the development and ripening processes of three color-transition types of red peppers (white/purple/green transition to red, respectively), by widely-targeted and carotenoid-targeted metabolomics analysis. Metabolites’ weighted gene co-expression network analysis (mWGCNA) was performed to analyze the accumulation patterns of metabolites in widely-targeted metabolomics. Among them, 290 flavonoids and 68 carotenoids were identified, revealing the material basis of the natural purple color and red color peppers. The formation of the purple color in '5' is crucially dependent on delphinidin-3-O-(2′''-O-p-coumaroyl) rutinoside-5-O-glucoside and delphinidin-3-O-(2′''-O-p-coumaroyl) rutinoside-7-O-glucoside, especially the former, while capsanthin plays a crucial role in the appearance of the red color in peppers. Integrating transcriptome and metabolome data for WGCNA, potential regulatory genes MYB113, TT8, TT8 - like, TTG1 , and BRF for anthocyanins biosynthesis, and DIVARICATA1, MADS - RIN, AGL9 - like , and Y subunit for capsanthin biosynthesis were identified. Our research is crucial for maximizing the edible and industrial application of pepper. The identified potential regulatory genes for anthocyanins and capsanthin provide a reference for an in-depth study of natural pigment biosynthetic mechanisms in pepper.