Comprehensive transcriptome-based characterization of differentially expressed genes involved in carotenoid biosynthesis of different ripening stages of Capsicum

•The β-carotene, zeaxanthin, β-cryptoxanthin and capsanthin were the main carotenoids contents in red pepper, while it was lutein in orange chili pepper.•The differences in the regulation of CCS gene resulted in the formation of different pepper fruit colors.•Some of the F-box protein, F-box/LRR-repeat protein, zinc finger family and MADS-box family may be involved in the regulation of CCS genes.