An integrative analysis of transcriptome and proteome provides new insights into carotenoid biosynthesis and regulation in sweet orange fruits

► An integrative analysis of transcriptome and proteome was used to study the molecular basis of a red-flesh citrus mutant. ► A set of genes/proteins associated with carotenoid biosynthesis and the regulation were identified. ► Some intriguing genes/proteins were previously unrecognized related with the formation of red-flesh trait. ► Different expression patterns were found between the Cara Cara and another red-flesh sweet orange Hong Anliu.