Plant specialized metabolites provide a promising but underexplored resource for drug development and agrochemicals. Yet, structural complexity and downstream modifications of plant metabolites pose challenges for biosynthetic pathway elucidation. Therefore, automated pathway annotation across plant species, and discovery efforts based on comparative omics-based approaches both require the development of similarity metrics accounting for the complexity of plant genome architecture. To this end, integration of genomics, transcriptomics, and metabolomics data resources will be needed. However, paired omics datasets covering multiple taxonomic orders are largely unavailable.

Here, we present a paired metabolomics (untargeted Liquid Chromatography Mass-Spectrometry) and transcriptomics (RNAseq) dataset for 10 species representing two lineages within the Brassicaceae family, with publicly available genome assemblies of corresponding genotypes, and selected accounting for whole genome duplication events. Gene expression and abundance of metabolite features and mass shifts were captured in a time-series across two tissues under four conditions, using phytohormone treatments with jasmonic acid, salicylic acid, and abscisic acid to mimic biotic and abiotic stresses in a standardized experimental design. Curation of this paired omics dataset was based on established metadata ontologies, to facilitate public data integration. Ultimately, the establishment of orthologous pathway modules across related species exploited plant taxonomy, gene co-expression and metabolite abundance, in combination with genomic organization (i.e., gene synteny).

The resulting insights into biosynthetic pathway evolution are expected to support natural product discovery in plants and provide new groundwork for synthetic biology and targeted plant breeding strategies. In addition, the design of this paired omics data resource was developed in accordance with FAIR data guidelines, promoting its reuse, interoperability, and integration across the broader plant sciences community.