Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses

Transposable elements (TEs) impact genome plasticity, architecture and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defence mechanisms that can counter-balance TE expansion and spread. Closely related species can harbour drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here we describe how TEs have shaped genome evolution of the fungal wheat pathogen <em>Zymoseptoria tritici</em> and four closely related species. We compared <em>de novo</em> TE annotations and Repeat-Induced Point mutation signatures in twenty-six genomes from the <em>Zymoseptoria</em> species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The twenty-six genomes of <em>Zymoseptoria</em> species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation and with effectors in all <em>Zymoseptoria </em>species. We find that the extent of RIP-like signatures varies among <em>Z. tritici</em> genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in <em>Z. tritici</em> reflects ongoing but still moderate TE mobility.