Eukaryotic microbes such as fungi and oomycetes can rapidly evolve and adapt to their environments. The Microbial Genome Evolution Team is part of the chair group Bioinformatics at Utrecht University. We use computational methods as well as data from large-scale genomics experiments to unravel processes that generate genome variation (e.g., chromosomal rearrangements or transposable elements) and how these in turn affect genome organization (e.g., the 3D genome), function (e.g., gene regulation and expression), and evolution of eukaryotic microbes.