Elucidating and exploring specialised plant metabolism through a pangenomic and pantranscriptomic lens

Specialised metabolism is an important factor in how plants cope with biotic and, to a lesser extent, abiotic stress. Current approaches to identify and study the genes involved in such metabolic pathways mainly leverage genomic and transcriptomic datasets of plants, in order to improve our understanding of plant resilience. Even though modern sequencing techniques have provided access to high-quality reference genome or transcriptome datasets, sequencing costs have for a long time forced a restriction to a selected reference accession. However, individual plants within a population often exhibit substantial differences in metabolic profiles, sometimes even leading to completely different chemotypes. This generated an urgent need to transition from single-reference accessions to the wider diversity of plant populations or even beyond the species level. Thanks to decreasing costs and improved reliability of sequencing techniques, this is now possible through pangenomic or pantranscriptomic approaches. In this review, we provide an introduction into the current state of the fields of pangenomics and pantranscriptomics and highlight recent examples on how these approaches have been used to elucidate and investigate specialised metabolic pathways in plants. We also provide an overview of database resources that might be useful for researchers in the field. Lastly, we present a critical summary and discussion of limitations and trends that are important for future innovations. With these developments in mind, we anticipate that pangenomics and pantranscriptomics will play a crucial role in exploring and harnessing the diversity of plant specialised metabolism beyond single individuals.