Distinct modes of sequence evolution and epigenetic modifications underpin the origins of Starship-mediated variation in Pyricularia fungal plant pathogens

Fungal pathogens display remarkable variation in genome content and organization that directly impacts their survival and host interactions. Although numerous models have been proposed to explain the origins of this variation, they generally fail to explain or predict the mechanisms that generate the genome variation observed in natural populations. Starships are a recently discovered group of giant fungal transposons that carry dozens of genes as cargo and horizontally transfer both within and between species. Here, we identify the features of a newly defined "Starship compartment" in the major fungal plant pathogen Pyricularia oryzae. We test the hypothesis that the Starship compartment makes distinct contributions to fungal genome evolution by explicitly comparing its transferability, mutability, and epigenetic modifications with those of the canonical core and accessory compartments. To enable this, we developed an updated and user-friendly version of the annotation tool stargraph for the comprehensive annotation of Starships and Starship-like regions. Using this approach, we identified two distinct families of Starships and related Starship-like regions in P. oryzae that differ in their activity, impacts on genome organization, modes of sequence evolution, and epigenetic modifications. Elements from the more active family exhibit higher rates of structural variation than all other genomic compartments in the predominantly clonal isolates infecting rice. Both families of Starships encode specific suites of known effector sequences that contribute to plant disease and Starship activity accounts for avirulence gene turnover, which suggests that evolutionary change within the Starship compartment may subsequently impact the evolution of plant-fungal interactions. Starships from the more active family have repeatedly transferred across the Pyricularia genus and tend to be depleted in heterochromatic histone modifications and repeat-induced point mutations. However, contrasting histone modification profiles in this family suggests a genomic conflict between silencing or maintaining Starship activity. Our findings demonstrate that variation in the mode of sequence diversification and epigenetic modification within the Starship compartment underpins the impacts of these giant transposons on fungal genome evolution. We argue for the explicit consideration of not only the Starship compartment but of element-specific dynamics when investigating the evolution of host-fungal interactions.