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Introduction: Polyploidy is a widespread phenomenon in nature and is thought to play a major role in the evolution of flowering plants. Additionally, polyploidization produces novel phenotypes that through plant breeding have enhanced the production of biomass and improved the stress tolerance of major economic crops. However, the effect of polyploidization on plant metabolism is still unclear. Objectives: In order to test whether there are common metabolic responses following genome doubling, we performed a comparative metabolomic analysis of mature leaves from doubled diploids and the corresponding diploids of red tangerine ( Citrus reticulata Blanco), trifoliate orange ( Poncirus trifoliata L. Raf.) and precocious trifoliate orange ( P. trifoliata). Methods: Non-targeted and targeted metabolic profiling of mature leaves from three doubled diploids and their diploid controls were performed by using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS). Results: About 11-34% of the detected metabolic features differentially accumulated in the doubled diploids, mostly by less than fivefold. The levels of primary metabolites tended to increase in the doubled diploids. Concentrations of tricarboxylic acid cycle intermediates-citric acid, malic acid, fumaric acid and succinic acid, enhanced in all of the doubled diploids. The levels of secondary metabolites, including phenylpropanoids and terpenoids, tended to decrease in the doubled diploids. This is consistent with the lower C/N ratios in the doubled diploids. Conclusions: Polyploidization had a significant but relatively limited influence on the accumulation of metabolites in these citrus species. We conclude that primary metabolism takes priority over secondary metabolism in doubled diploid plants to relieve the 'genomic stress' encountered during the early stages of genome doubling, probably to promote vitality and growth. [ABSTRACT FROM AUTHOR]