Adaptation in fungal pathogens attacking crops procedes often at speeds that easily overwhelm our ability to identify resistant cultivars and develop new antifungals. Understanding the molecular basis of adaptation becomes critical to define more sustainable containment strategies. Here, I will show how studying variation in pathogen populations enables to make inferences about the route of adaptation and future trajectories. We combine analyses of complete genome sequences with data on genome-wide transcription and phenotypic trait variation. I will highlight how some of the most dynamic regions in the genome make significant contributions to rapid pathogen adaptation.
