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. Pepper (Capsicum annuum L.) is one of the widely cultivated vegetable crops in the world. The color formation of pepper fruit is closely related to the carotenoid composition and content. In order to understand the regulatory mechanism of red and orange pepper formation, comprehensive transcriptome and carotenoid content determination were carried out at 25, 40 and 55 days after flower. At the mature stage (55 DAF), the contents of zeaxanthin, β-cryptoxanthin, β-carotene and capsanthin in red chili pepper(R) were significantly higher than those in orange pepper (O), while the content of lutein in orange pepper(O) was higher than that in red pepper(R). Moreover, it was found that many differentially expressed genes (DEGs) were involved in the biosynthesis of carotenoids, phenylpropanoids, flavonoids and metabolism of phenylalanine. A total of 23 DEGs were found to be involved in carotenoid biosynthesis, among which β-carotene hydroxylase 1(CHYB1) and capsanthin-capsorubin synthase(CCS)were significantly different during fruit development. Further analysis showed that there were complete CCS genes in both red and orange pepper fruits. However, the expression level in orange pepper fruits was maintained at a very low level, on the contrary, the red fruits exhibited a remarkable upward trend and extremely high transcript level. Through weighted gene co-expression network analysis (WGCNA), transcription factors F-box protein SKIP23, GATA transcription factor 26, U-box domain-containing protein 52, zinc finger family FYVE/PHD-type, RING/FYVE/PHD-type and CONSTANS-LIKE 9 might be involved in the regulation of CCS gene. This study will lay a base to further analyze the regulation mechanism of carotenoid metabolism pathway in the process of pepper fruit color formation.