Putative Synergetic Genes Involved in the Syntheses of Carotenoids and Flavonoids in 'Cara cara' Navel Orange as Revealed by Integrated Transcriptome and Metabolomics Analysis

Abstract Background Carotenoids and flavonoids are important secondary metabolites in plants, which exert multiple bioactivities and benefits to human health. Although the genes that encode carotenogenesis and flavonoids enzymes are well characterized, the transcriptional regulatory mechanisms that are related to the pathway genes remain to be investigated. In this study, Cara cara navel orange fruit at four development stages were used to identify the key genes and TFs for carotenoids and flavonoids accumulation. Results In this study, Cara cara navel orange (CNO) was used to investigate the profiles of carotenoids and flavonoids by a combination of metabolomic and transcriptomic analyses. The important stage for the accumulation of the major carotenoid, lycopene was found to be at 120 DAF (days after florescence). The transcripts of five carotenogenesis genes were highly correlated with lycopene contents, and 16, 40, 48, 24 and 18 transcription factors (TFs) were predicted to potentially bind their promoters, respectively. Narirutin was the most abundant flavonoid in the flesh at the early stages, 60 DAF was the most important stage for the accumulation of flavonoids, and 17, 22, 14, 25, 24 and 16 TFs could potentially bind their promoters, respectively. Furthermore, 15/15 candidate TFs might regulate at least three key genes and contribute to carotenoids/flavonoids accumulation in CNO fruit. Finally, a hierarchical model for the regulatory network among the pathway genes and TFs was proposed. Conclusions Collectively, our results suggest that DXS1, DXR, GGPPS2, PSY1 and LCYB genes were the most important genes for carotenoids accumulation, while PAL-1, PAL-4, 4CL-2, 4CL-5, CHS-1 and CHI for flavonoids biosynthesis. A total of 34 TFs were postulated as co-regulators in both pathways directly or indirectly, which might play important roles in carotenoids and flavonoids accumulation in CNO fruit.