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. 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. 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.

中文翻译：

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综合转录组学和代谢组学分析揭示了“卡拉卡拉”脐橙中类胡萝卜素和类黄酮生物合成的转录调控网络

类胡萝卜素和类黄酮是植物中重要的次生代谢产物，具有多种生物活性，对人体健康有益。尽管编码类胡萝卜素和类黄酮生物合成酶的基因已得到很好的表征，但与通路基因相关的转录调控机制仍有待研究。在本研究中，使用处于四个发育阶段的“Cara cara”脐橙 (CNO) 果实来鉴定类胡萝卜素和黄酮类化合物积累的关键基因和 TF。在这项研究中，CNO 被用于通过代谢组学和转录组学分析的组合来研究类胡萝卜素和类黄酮的特征。发现主要类胡萝卜素番茄红素积累的重要阶段是在花期 (DAF) 后 120 天。五种胡萝卜素生成基因的转录本与番茄红素含量高度相关，预计 16、40、48、24 和 18 个转录因子 (TF) 可能与 1-脱氧-D-木酮糖-5-磷酸合酶 (DXS1)、脱氧木酮糖结合分别是 5-磷酸还原异构酶 (DXR)、香叶基香叶基二磷酸合酶 (GGPPS2)、八氢番茄红素合酶 (PSY1) 和番茄红素 β-环化酶 (LCYB) 启动子。Narirutin 是早期果肉中含量最多的黄酮类化合物，60 DAF 是黄酮类物质积累的最重要阶段，17、22、14、25、24 和 16 TFs 可能与苯丙氨酸解氨酶（PAL- 1 和 PAL-4)、4-香豆酸-CoA 连接酶（4CL-2 和 4CL-5）、查尔酮合酶 (CHS-1) 和查尔酮异构酶 (CHI) 启动子。此外，两组 15 个候选 TF 可能调节至少三个关键基因，并有助于 CNO 果实中类胡萝卜素/类黄酮的积累。最后，提出了通路基因和 TF 之间调控网络的分层模型。总的来说，我们的结果表明 DXS1、DXR、GGPPS2、PSY1 和 LCYB 基因是类胡萝卜素积累最重要的基因，而 PAL-1、PAL-4、4CL-2、4CL-5、CHS-1 和 CHI 是类黄酮生物合成的最重要基因. 共有 24 个 TF 被假定为直接在这两种途径中的共调节剂，它们可能在 CNO 果实中类胡萝卜素和黄酮类化合物的积累中起重要作用。PSY1 和 LCYB 基因是类胡萝卜素积累最重要的基因，而 PAL-1、PAL-4、4CL-2、4CL-5、CHS-1 和 CHI 是类黄酮生物合成的最重要基因。共有 24 个 TF 被假定为直接在这两种途径中的共调节剂，它们可能在 CNO 果实中类胡萝卜素和黄酮类化合物的积累中起重要作用。PSY1 和 LCYB 基因是类胡萝卜素积累最重要的基因，而 PAL-1、PAL-4、4CL-2、4CL-5、CHS-1 和 CHI 是类黄酮生物合成的最重要基因。共有 24 个 TF 被假定为直接在这两种途径中的共调节剂，它们可能在 CNO 果实中类胡萝卜素和黄酮类化合物的积累中起重要作用。