Untargeted metabolomic dataset of leaves from twenty-four accessions of wild and cultivated tomato plants

Tomato ( Solanum lycopersicum var. lycopersicum ), one of the most important crops worldwide, has a complex domestication history that began in Latin America, region hosting also fourteen wild relative species and subspecies. Domestication and subsequent breeding efforts have led to the development of the modern cultivated tomato, prized for its agronomic performance and economic value. However, this process also resulted in a substantial erosion of genetic and metabolic diversity, potentially limiting the plant’s adaptive capacity and resilience to environmental stresses. Previous comparative studies between domesticated tomato cultivars and wild relative species have underscored the evolutionary shifts in various plant traits associated with biotic stress. Yet, most of these studies relied on a limited number of wild accessions, reflecting a general tendency to underestimate their genetic and metabolic diversity. In this study, we sought to characterize both intra- and inter-specific metabolic diversity in tomato and its wild relatives. Using Liquid Chromatography High Resolution Mass Spectrometry (LC-HRMS) analysis, we profiled the chemical composition of hydro-methanolic leaf extracts from twenty-four accessions representing five Solanum species and subspecies, each with distinct natural histories and domestication levels. This dataset provides a comprehensive overview of leaf metabolic diversity across cultivated and wild tomato species, offering insights into the evolutionary and ecological forces shaping specialized metabolism within the tomato clade. It is available at https://doi.org/10.57745/QM0BOR .