Theoretical Biology & Bioinformatics

tree of life
Michael F Seidl

Fungal Evolutionary Genomics Group

Michael F Seidl

Home | Publications (PubMed) | CV

Research Summary

The fungal kingdom contains unicellular as well as multicellular organisms. Fungi have a cosmopolitan distribution and thrive in a variety of environmental niches. They are able to rapidly adapt to changing and challenging environments, and thus have been exploited for decades in food production and biotechnology. Additionally, some fungi also live as symbionts in mutualistic to parasitic interactions with other organisms. The research of the Fungal Evolutionary Genomics group aims to understand the molecular mechanisms contribute to fungal (genome) evolution, and how these changes translate to the capacity of fungi to adapt to novel or altered environments, both on short and long evolutionary time-scales.

Main research lines

Research in our group revolves around fungal genome evolution. We study diverse fungal systems and utilize bioinformatics approaches that exploit diverse large-scale genomics as well as transcriptomics data. Most of our research combines a wet-lab experimental component and extensive bioinformatics, and can be summarized in three complementary research lines:

(i) Adaptation to novel or changing environments is typically mediated by genetic variability, which is caused by a plethora of mechanisms including meiotic and mitotic recombination, genome rearrangements, gene duplications or losses, and horizontal gene transfer. We investigate molecular mechanisms driving fungal genome evolution, which is facilated by the newest sequencing technologies (Seidl et al. 2015; Faino et al. 2015; Shi-Kunne et al. 2018; Shi-Kunne et al. 2019). In particular, we focus on the roles of transposable elements in generating genetic diversity (Faino et al. 2016; Seidl et al. 2017). Additionally, we study the changes in the number and organization of the chromosomal sets within a cell. For example, we study how interspecific hybridizations incite genomic and transcriptomic changes and contribute to adaptation (Depotter et al. 2016, 2017).

(ii) The genetic material within a nucleus is organized by chromatin, a complex of DNA and (histone) proteins. Chromatin can dynamically influence DNA accessibility with profound impact on genome regulation and evolution. We study the evolution of chromatin-regulatory mechanisms, and how chromatin influences on genome regulation and adaptive genome evolution. The latter was supported by an NWO ALW-VENI grant [2015-2018] and the emerging link between chromatin and genome evolution has been discussed in multiple review articles (Seidl et al. 2016; Seidl et al. 2017a, 2017b). We study how chromatin controls the expression of genes and pathways with important functions in medicine, industry and agriculture, and how these regulatory mechanisms evolve. Moreover, we recently resolved genome-wide chromatin maps in multiple plant pathogens revealing that specific chromatin-types associate with hypervariable genomic regions, which might be linked to their adaptation to the host immune system.

(iii) Rapid adaptation is particularly apparent in the tight symbiosis between pathogens and their hosts: While hosts evolved mechanisms to detect and restrain pathogens, pathogens evolved means, often secreted effector proteins, to disguise themselves or suppress host responses. Our goal is to elucidate the evolution of plant pathogens and to unravel molecular mechanisms that foster their diversification during the co-evolutionary arms race with their hosts. In particular, we study mechanisms contributing to effector diversity in pathogen populations (see e.g. Kombrink et al. 2017; Shi-Kunne et al. 2019). Additionally, we recently demonstrated that, contrary to expectations, pathogens that are subject to high stress levels (e.g. host immune responses or fungicide treatment) can still reproduce sexually, which has significant impact on pathogen populations, epidemiology, and disease managment (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.

Team

Michael F Seidl, Principal Investigator
David Torres Sanchez, PhD student, Wageningen Univerisity & Research, supervision with Prof. Thomma
Edgar Chavarro Carrero, PhD student, Wageningen Univeristy & Research, supervision with Prof. Thomma
Sander Rodenburg, PhD student, Wageningen Univeristy & Research, supervision with Prof. de Ridder & Prof. Govers
Martin Kramer, PhD student, Wageningen Univeristy & Research, supervision with Prof. Thomma
Xin Zhang, MSc student