Fungi and oomycetes include deep and diverse lineages of eukaryotic plant pathogens. The last 10 years have seen the sequencing of the genomes of a multitude of species of these so-called filamentous plant pathogens. Already, fundamental concepts have emerged. Filamentous plant pathogen genomes tend to harbor large repertoires of genes encoding virulence effectors that modulate host plant processes. Effector genes are not randomly distributed across the genomes but tend to be associated with compartments enriched in repetitive sequences and transposable elements. These findings have led to the “two-speed genome” model in which filamentous pathogen genomes have a bipartite architecture with gene sparse, repeat rich compartments serving as a cradle for adaptive evolution. Here, we review this concept and discuss how plant pathogens are great model systems to study evolutionary adaptations at multiple time scales. We will also introduce the next phase of research on this topic.
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