Differential expression of transposable elements through the course of a Zymoseptoria tritici infection

Transposable elements (TEs) are dynamic genetic entities that affect the expression landscape of the genome. In addition to transcription related to their own propagation, TEs can modulate the transcription of nearby genes. Genomic defences of the host genome limit the activity of TE by epigenetic silencing of TE-rich regions in the genome. In many pathogenic fungi TEs are located in close proximity to pathogenicity-related genes. Therefore, epigenetic silencing of TEs by the host genome can sometimes influence the expression of neighbouring genes through leakage. A pathogen infecting a host plant is undergoing high levels of cellular stress that is conducive to the reactivation of TEs. To study the interaction between host infection and TE mobilization, we used Zymoseptoria tritici as a model system. Z. tritici is an important pathogen of wheat with a highly dynamic genome, consisting of 18% TEs of which many are transcriptionally active. We investigated the differential expression of transposable elements in an infection of four isolates of Zymoseptoria tritici, with different infection rates and virulence profiles to characterize TE regulation. TE transcriptomes were compared at 4 different infection stages. The strains did not differ significantly in TE composition, but the TE expression profiles varied between isolates and over the course of the infection. We found a correlation between the evolutionary age of a TE and levels of derepression during infection, where younger TEs were more expressed. The reactivation of TEs and neighboring genes plays an important role in shaping the expression landscape of Z. tritici during infection.