Expression of ClPAP and ClPSY1 in watermelon correlates with chromoplast differentiation, carotenoid accumulation, and flesh color formation

•The carotenoid compositions of different flesh color watermelon were analyzed by LC-MS/MS.•Chromoplast differentiation was correlated with the accumulation of carotenoids.•The schematic diagram of chromoplast differentiation with different flesh color was inferred in watermelon.•ClPSY1 and ClPAP may play an important role in carotenoid generation and storage.