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 the analysis of metabolite differences between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie 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 tissues and growth stages. In the resulting MicroTom Metabolic Network, the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters 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 insights into spatio-temporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants.

番茄（番茄）是全球主要的园艺作物，已经成为代谢研究的杰出典范。尽管许多研究工作都集中在分析品种和物种之间的代谢差异，但人们对番茄生长周期中代谢变化的动力学以及这些变化背后的调控网络知之甚少。在这项研究中，我们整合了高分辨率的时空代谢组和转录组数据，系统地探索了20个主要番茄组织和生长阶段的代谢态势。在最终的MicroTom代谢网络中，根据其生物学功能，可以将540种检测到的代谢物及其共表达的基因分为10个不同的簇。使用此数据集，我们绘制了整个番茄生长周期中发生的主要代谢变化的全球地图，并解剖了基本的调控网络。除了验证以前建立的重要代谢物调控网络外，我们还发现了新的转录因子，可调控重要的次生代谢物的生物合成，例如甾体类生物碱和类黄酮。我们的发现提供了对番茄代谢时空变化的见解，并为研究模型植物的代谢调控过程提供了宝贵的资源。我们发现了新的转录因子，可调节重要的次生代谢产物的生物合成，例如甾体糖类生物碱和类黄酮。我们的发现提供了对番茄代谢时空变化的见解，并为研究模型植物的代谢调控过程提供了宝贵的资源。我们发现了新的转录因子，可调节重要的次生代谢产物的生物合成，例如甾体糖类生物碱和类黄酮。我们的发现提供了对番茄代谢时空变化的见解，并为研究模型植物的代谢调控过程提供了宝贵的资源。