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Lepiniec, L., Debeaujon, I., Routaboul, J. M., Baudry, A., Pourcel, L., Nesi, N., et al. (2006). Genetics and biochemistry of seed flavonoids. Annu. Rev. Plant Biol. 57, 405–430. doi:10.1146/annurev.arplant.57.032905.105252Bo Xiong *† Qin Li † Junfei Yao Zhuyuan Liu Xinxia Yang Xiaoyong Yu 1 Yuan Li Ling Liao Xun Wang Honghong Deng Mingfei Zhang Guochao Sun Zhihui Wang * Howarth, C. J., Ougham, H. J. (1993). Gene expression under temperature stress. New Phytol. 125, 1–26. doi:10.1111/j.1469-8137.1993.tb03862.x

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Rowan, D. D., Cao, M., Lin-Wang, K., Cooney, J. M., Jensen, D. J., Austin, P. T., et al. (2009). Environmental regulation of leaf colour in red 35S:PAP1 arabidopsis thaliana. New Phytol. 182, 102–115. doi:10.1111/j.1469-8137.2008.02737.x Ahmed, O. M., Hassan, M. A., Abdel-Twab, S. M., Azeem, M. N. A. (2017). Navel orange peel hydroethanolic extract, naringin and naringenin have anti-diabetic potentials in type 2 diabetic rats. Biomed. Pharmacother. 94, 197–205. doi:10.1016/j.biopha.2017.07.094 Owens, D. K., Alerding, A. B., Crosby, K. C., Bandara, A. B., Westwood, J. H., Winkel, B. S. (2008). Functional analysis of a predicted flavonol synthase gene family in arabidopsis. Plant Physiol. 147, 1046–1061. doi:10.1104/pp.108.117457The original contributions presented in the study are publicly available. This data can be found here: NCBI Sequence Read Archive (BioProject: PRJNA934884). Author contributions In GO annotation analysis, a total of 38,397 DEGs were annotated in three categories: biological process, molecular function, and cellular component categories ( Supplementary Table7). These DEGs were further divided into 47 categories based on gene function, with 722 genes related to biological processes such as signaling. TopGO analysis revealed that the most enriched molecular function terms were monooxygenase activity (GO0004497), oxidoreductase activity (GO0016705), heme binding (GO0020037), iron ion binding (GO0005506), and tetrapyrrole binding (GO0046906) ( Supplementary Figure7). The most enriched biological process terms were flavonoid metabolic process (GO0009812) and flavonoid biosynthetic process (GO0009813). The most enriched cellular component terms were chloroplast thylakoid (GO0009534) and plastid thylakoid (GO0031976). KEGG enrichment analysis identified the top 20 enriched metabolic pathways, including metabolic pathways (ko01100), biosynthesis of secondary metabolites (ko01110), MAPK signaling pathway-plant (ko04016), plant hormone signal transduction (ko04075), phenylpropanoid biosynthesis (ko00940), and flavonoid biosynthesis (ko00941) under magnesium stress ( Figure5D). These results were presented in a bubble diagram. Metabolic and gene co-expression networks in SOPs at different developmental stages Li, P., Yao, X., Zhou, Q. Q., Meng, X., Zhou, T., Gu, Q. (2022a). Citrus peel flavonoid extracts: health-beneficial bioactivities and regulation of intestinal microecology in vitro. Front. Nutr. 9. doi:10.3389/fnut.2022.888745

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Hichri, I., Barrieu, F., Bogs, J., Kappel, C., Delrot, S., Lauvergeat, V. (2011). Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. J. Exp. Bot. 62, 2465–2483. doi:10.1093/jxb/erq442 Li, H., Li, Y., Yu, J. X., Wu, T., Zhang, J., Tian, J., et al. (2020a). MdMYB8 is associated with flavonol biosynthesis via the activation of the MdFLS promoter in the fruits of malus crabapple. Horticult. Res. 7. doi:10.1038/s41438-020-0238-z The first two principal components accounted for 50.35% (PC1) and 17.79% (PC2), respectively, and the 18 samples (including 3 replicates) were classified into 6 groups based on their developmental stage along PC1. The sample positions along PC2 were influenced by magnesium stress ( Figure3B). These findings suggest that the observed differences in flavonoid profiles were related to developmental stages and magnesium stress and were consistent with the trend in total flavonoid accumulation that peaked in MS2 or MD2 ( Figures3B, C). In addition, OPLS-DA analysis was utilized to evaluate the differences between MS and MD (Q2 = 0.99) ( Supplementary Figure2). The high Q2 value (>0.9) suggested that the OPLS-DA modules were stable and reliable and that the differences in flavonoid content could be further explored. Hierarchical clustering analysis (HCA) of the flavonoid metabolite accumulation patterns among different samples showed good repeatability within the sample group ( Figures3D). In the HCA, six clusters, corresponding to the successive stages of flavonoid metabolites in SOPs for the 18 samples, were significantly separated. The results of PCA, OPLS-DA, correlation analysis, and HCA reflected large differences between samples, high similarity among the three biological replicates, and high repeatability within samples. Differentially accumulated flavonoids metabolites in SOPsYang, J. W., Wu, X., Aucapiña, C. B., Zhang, D. Y., Huang, J. Z., Hao, Z. Y., et al. (2023). NtMYB12 requires for competition between flavonol and (pro)anthocyanin biosynthesis in narcissus tazetta tepals. Mol. Horticult. 3. doi:10.1186/s43897-023-00050-7