MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle.

Abstract Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on analyzing metabolite variants between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks underlying these changes are poorly understood. In this study, we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato growth tissues and stages. In the resulting MicroTom Metabolic Network (MMN), the 540 detected metabolites and their co-expressed genes could be divided into ten distinct clusters that were based on their biological functions. Using this dataset, we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network. In addition to verifying previously well-established regulatory networks for important metabolites, we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites, such as steroidal glycoalkaloids and flavonoids. Our findings provide insight into spatio-temporal changes in tomato metabolism and generate a valuable resource for studying metabolic regulatory processes in model plants.