Integrated analysis of transcriptome, metabolome and physiology revealed the molecular mechanisms for elevated pH-mediated-mitigation of aluminum-toxicity in Citrus sinensis leaves

•Elevated pH ameliorated Al-induced reduction of Citrus sinensis seedling growth.•Raised pH enhanced leaf ability to maintain energy and phosphate homeostasis.•Raised pH enhanced the ability to maintain cell wall and lipid metabolism stability.•Raised pH increased SM accumulation, lessened Al-induced downregulation of SMs.•Raised pH ameliorated Al-induced oxidative damage and increase of callose. The contribution of aluminum (Al)-pH-interaction-responsive metabolites and genes to Al-tolerance in Citrus leaves is still poorly understood. Seedlings of ‘Xuegan’ (Citrus sinensis) were supplied with nutrient solution at a pH of 4.0 or 3.0 and an Al concentration of 1 or 0 mM for 18 weeks. Thereafter, we investigated the impacts of Al-pH interactions on plant growth; Al concentrations in leaves and roots; and metabolome, transcriptome, and related physiological indices in leaves. Elevated pH ameliorated Al-toxicity-induced reduction of seedling (leaf) growth. Here, we screened 867 upregulated and 1041 downregulated genes, and 43 [eight primary metabolites (PMs) + 35 secondary metabolites (SMs)] and 28 downregulated (23 PMs + five SMs) in pH 3.0 + 1 mM Al-treated leaves (P3AL) vs. pH 3.0 + 0 mM Al-treated leaves (P3L); and 410 upregulated and 149 downregulated genes, and 75 upregulated (20 PMs + 55 SMs) and 32 downregulated (25 PMs + seven SMs) metabolites in pH 4.0 + 1 mM Al-treated leaves (P4AL) vs. pH 4.0 + 0 mM Al-treated leaves (P4L), implying that elevated pH ameliorated Al-toxic impacts on gene expression, but it enhanced the adaptability of metabolites to Al-stress. Further analysis suggested that raised pH-mediated-amelioration of leaf Al-stress involved the several aspects, including: (a) decreased accumulation of callose and low methylesterified pectin, increased accumulation of high methylesterified pectin, and enhanced cell wall stability; (b) less alterations of lipid metabolism and downregulation of PMs; (c) increased biosynthesis and accumulation of SMs; and (d) enhanced ability to maintain energy, phosphate and cell redox homeostasis, and less oxidative injury due to higher ability to maintain the balance between reactive oxygen species and aldehyde generation and detoxification. Some metabolic pathways such as glycolysis / gluconeogenesis and phenylpropanoid pathway; metabolites such as callose and phenolic compounds; and genes such as xyloglucan endotransglucosylase/hydrolases, purple acid phosphatases, phytochelatin synthase 3, and cysteine sy