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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 flavonoid biosynthetic 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 (CNO) fruit at four development stages were used to identify the key genes and TFs for carotenoids and flavonoids accumulation.    Results  In this study, 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 days after florescence (DAF). 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 1-deoxy-D-xylulose-5-phosphate synthase ( DXS1 ), deoxyxylulose 5-phosphate reductoisomerase ( DXR ), geranylgeranyl diphosphate synthase ( GGPPS2 ), phytoene synthase ( PSY1 ) and lycopene β-cyclase ( LCYB ) 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 phenylalanine ammonia-lyase ( PAL-1  and  PAL-4 ), 4-Coumarate-CoA ligase ( 4CL-2  and  4CL-5 ), chalcone synthase ( CHS-1 ) and chalcone isomerase ( CHI ) promoters, respectively. Furthermore, both sets of 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 24 TFs were postulated as co-regulators in both pathways directly, which might play important roles in carotenoids and flavonoids accumulation in CNO fruit.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02808-3.

bmc plant biology

Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel Orange