Tapping the potential of plant specialized metabolic diversity through integrative omics

The diversity of plant secondary metabolites provides a promising yet unexplored resource for the development of novel drugs and agrochemicals. Structural complexity and downstream modifications in plant secondary metabolism evolved dynamically in response to biotic and abiotic stressors. The emergence of next-generation sequencing techniques accelerated developments in automated pathway discovery. In plants, genomic organization of biosynthetic pathway modules has evolved to a higher level of complexity compared to bacteria and fungi. Specifically, formation of biosynthetic gene clusters is a less common phenomenon in plant evolution, and genome duplications and polyploidy result in complex gene regulatory networks and functional redundancy. Hence, automated pathway annotation across plant species, as well as discovery efforts based on comparative approaches 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 datasets for gene expression, and corresponding plant metabolite profiles are unavailable for important crop species. Here, I will develop a phylogenetic metric in combination with a co-expression metric for the identification of orthologous pathway modules across crop species and wild relatives in the Brassicaceae family. The metrics will be tested and validated on generated paired expression and metabolic profile datasets for eight _Brassicaceous_ species under biotic stress conditions. Ultimately, I will reconstruct the ancestral states of biosynthetic pathway modules, to assess conservation of specialized metabolism with respect to whole genome duplication events. The resulting insights and predictions on biosynthetic pathway evolution will accelerate natural product discovery and provide new resources for synthetic biology and targeted plant breeding strategies.