Theoretical Biology & Bioinformatics

tree of life
Michael F Seidl

Microbial Genome Evolution Team

Michael F Seidl

Home | Publications (PubMed) | CV

Research Summary

Eukaryotic microbes such as fungi and oomycetes can rapidly evolve and adapt to their environments. The Microbial Genome Evolution Team is part of the chair group Bioinformatics at Utrecht University. We use computational methods as well as data from large-scale genomics experiments to unravel processes that generate genome variation (e.g., chromosomal rearrangements or transposable elements) and how these in turn affect genome organization (e.g., the 3D genome), function (e.g., gene regulation and expression), and evolution of eukaryotic microbes.

We use multiple microbial systems in our research, but historically we focussed on fungal and oomycete plant pathogens that engage in co-evolutionary arms races with their hosts. These rapid arms races enable us to study evolutionary processes on short timescales and leave detectable ‘footprints’ that can range from the genome organisation to gene content and gene regulation. For instance, we are interested in identifying and studying processes that generate structural variation and uncovering how this variation intersects with the 3D genome and gene regulation, on short and long evolutionary timescales. In the post-genomic era, genomics approaches (e.g., long read sequencing or chromosome conformation capture followed by sequencing) and advances in bioinformatic methodologies (e.g., pan-genomes or artificial intelligence) now enable us to study microbial genomes and their diversity at population, species, and environmental scale.

The research in the Microbial Genome Evolution Team revolves around three broad themes:

  • We investigate molecular processes that drive microbe genome evolution
  • We study chromatin and its impact on microbial genome function and evolution
  • We uncover the diversity, evolution, and function of proteins – so called effectors - that mediate pathogen-host interaction

Insights into the molecular processes that contribute and constrain genomes on different scales are essential to better understand how eucaryotic microbes evolve. Studying the co-evolutionary arms races between pathogens and their hosts provides an intriguing framework to better understand how evolution has tweaked pathogen genomes to realize pathogenicity and symbiosis, which is essential to address grant societal challenges such as sustainable agriculture and food security.

Five key publications

  • Sexual reproduction contributes to the evolution of resistance-breaking isolates of the spinach pathogen Peronospora effusa.
    Skiadas P, Klein J, Quiroz-Monnens T, Elberse J, de Jonge R, Van den Ackerveken G, Seidl MF
    Environ Microbiol. 2022 24(3):1622-1637
  • Transposable elements contribute to genome dynamics and gene expression variation in the fungal plant pathogen Verticillium dahliae.
    Torres DE, Thomma BPHJ, Seidl MF
    Genome Biol Evol. 2021 13(7):evab135
  • An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation.
    Snelders NC, Petti GC, van den Berg GCM, Seidl MF, Thomma BPHJ
    Proc Natl Acad Sci USA. 2021 7;118(49): e2110968118
  • The interspecific fungal hybrid Verticillium longisporum displays subgenome-specific gene expression.
    Depotter JRL, van Beveren F, Rodriguez-Moreno L, Kramer HM, Chavarro Carrero EA, Fiorin GL, van den Berg GCM, Wood TA, Thomma BPHJ, Seidl MF
    mBio. 2021 12(4):e0149621
  • Repetitive elements contribute to the diversity and evolution of centromeres in the fungal genus Verticillium.
    Seidl MF, Kramer HM, Cook DE, Fiorin GL, van den Berg G, Faino L, Thomma BPHJ
    mBio 2020 11 (5), e01714-20

Team

Michael F Seidl, Principal Investigator

Edgar Chavarro Carrero, PhD candidate+
Petros Skiadas, PhD candidate
David Torres Sanchez, PhD candidate
Anouk van Westerhoven , PhD candidate*
Xin Zhang, PhD candidate
Chuanqi Gao, MSc student
Iseult Leahy, MSc student
Alvaro Ropero Lopez, MSc student
Shotaro Hato, MSc student
Luis Aznar Palop, MSc student

*joint projects with Wageningen University & Research, the Netherlands
+joint project with University of Cologne, Germany