Abstract
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 defense mechanisms that can counter-balance TE expansion and spread. Closely related species can harbor 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 Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and repeat-induced point mutation signatures in 26 genomes from the Zymoseptoria 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 26 genomes of Zymoseptoria 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 Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.
Highlights
Transposable elements (TEs), DNA elements that can replicate through transposition are ubiquitous in eukaryotic genomes
We addressed the following questions: (i) How do TE distributions and insertion ages impact genome architecture and plasticity? (ii) Does TE content correlate with gene presence/absence variation among genomes? (iii) What is the extent of variation in repeat-induced point (RIP) among genomes? To answer these questions, we annotated the TE content of each of the 26 genomes de novo and analyzed TE landscapes within and among genomes
Transposable elements content varies in the genomes of the Zymoseptoria species-complex
Summary
Transposable elements (TEs), DNA elements that can replicate through transposition (i.e., independently of the host DNA replication machinery) are ubiquitous in eukaryotic genomes. TEs are categorized into two classes, retrotransposons (class I) and DNA transposons (class II), based on their mechanism of transposition (Wicker et al 2007). TEs can be autonomous (e.g., LTRs and TIRs) or nonautonomous (e.g., SINEs and MITEs). The latter relies on the replication machinery of autonomous TEs to transpose (Wicker et al 2007). TEs engage in a co-evolutionary arms race dynamic with the host genome (Biemont 2010; Castanera et al 2016)
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