DSSS - Plant pathogen genome evolution in three dimensions

Filamentous plant pathogens engage in rapid co-evolutionary arms races with their hosts, thereby challenging contemporary agricultural practices. Hence, understanding the molecular processes that drive pathogen genome evolution is essential to address major societal challenges such as sustainable agriculture and food security. At Utrecht University in the Netherlands, the Microbial Genome Evolution team uses computational approaches alongside data from large-scale genomics experiments to elucidate processes that generate genome variation and study how these in turn affect genome organization, functioning, and evolution in filamentous plant pathogens.

Many filamentous plant pathogens have evolved compartmentalized genomes. In these genomes, housekeeping genes are localized in gene-rich, transposon-poor regions, while virulence-related genes are typically found in distinct genomic compartments. Recent research, including our own work, has shown that these regions are highly dynamic, characterized by an abundance of transposable elements, chromosomal rearrangements, and gene copy number and presence/absence variations. Notably, these dynamic compartments also exhibit a distinct chromatin organization compared to the rest of the genome. Despite being distributed across different chromosomes, we have recently demonstrated that these dynamic compartments physically co-localize within the nucleus. Together, these findings suggest that the interplay between the linear and the 3D genome plays a crucial role in shaping the functioning and evolution of these compartments, aiding pathogen adaptation to various host environments. In this seminar, I will discuss our recent insights into the functioning and evolution of adaptive genomic compartments in vascular wilt pathogens, which cause severe diseases in hundreds of crop species and contribute significantly to global yield losses.