Theoretical Biology & Bioinformatics

tree of life
Michael F Seidl

Microbial Genome Evolution Team

Michael F Seidl

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Main Research Lines

Research in the Fungal Evolutionary Genomics group revolves around fungal genome evolution with three main research lines:

(i) We investigate molecular mechanisms driving genome evolution. Driven by the newest sequencing technologies, we describe genomic diversity in plant-associated fungi (Seidl et al. 2015; Shi-Kunne et al. 2018; Chavarro et al. in preparation), which is often established by transposons (Faino et al. 2016; Seidl et al. 2017). Additionally, we study how interspecific hybridizations incite genomic and transcriptomic changes and contribute to adaptation (Depotter et al. 2016, 2017).

(ii) We study chromatin and its impact on adaptive genome evolution (supported by an NWO ALW-VENI grant [2015-2018]). We recently resolved genome-wide chromatin maps revealing that specific chromatin-types associate with hypervariable genomic regions. Several research articles describing this emerging research field are in preparation (Seidl et al., Kramer et al., Cook et al.), and its impact has been discussed in multiple review articles (Seidl et al. 2016; Seidl et al. 2017a, 2017b).

(iii) We study effector diversity in pathogen populations (Kombrink et al. 2017; Gibriel et al. submitted). For instance, we recently showed that, contrary to expectations, pathogens that are subject to high stress levels (e.g. host immune responses or fungicide treatment) still reproduce sexually, which has significant impact on pathogen populations (Kema et al. 2018).

Five key publications

  • Stress and sexual reproduction affect the dynamics of the wheat pathogen effector AvrStb6 and strobilurin resistance
    Kema GHJ, Mirzadi Gohari A, Aouini L, Gibriel HAY, Ware SB, van den Bosch F, Manning- Smith R, Alonso-Chavez V, Helps J, Ben M'Barek S, Mehrabi R, Diaz-Trujillo C, Zamani E, Schouten HJ, van der Lee TAJ, Waalwijk C, de Waard MA, de Wit PJGM, Verstappen ECP, Thomma BPHJ, Meijer HJG and Seidl MF
    Nat Genet. 2018 50(3): 375-380
  • Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss
    Shi-Kunne X, Faino L, van den Berg GCM, Thomma BPHJ and Seidl MF
    Environ Microbiol. 2018 20(4): 1362-1373
  • Transposable elements direct the coevolution between plants and microbes
    Seidl MF and Thomma BPHJ
    Trends Genet. 2017 33(11): 842-851
  • Chromatin biology impacts adaptive evolution of filamentous plant pathogens
    Seidl MF, Cook DE and Thomma BPHJ
    PLoS Pathogens 2016 3(12): e1005920
  • Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen
    Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GC, Wittenberg AH and Thomma BPHJ
    Genome Res. 2016 26(8): 1091-100.