Fungal Evolutionary Genomics Group Michael F Seidl
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Research Summary

Fungi are eukaryotic microorganisms with a cosmopolitan distribution. They can rapidly adapt to changing or challenging environments, and thus thrive in a variety of environmental niches. Some fungi can live as symbionts in mutualistic to parasitic interactions with other organisms. Tight interactions especially between pathogens and their hosts drive rapid adaptive genome evolution in host and pathogen populations.

The Fungal Evolutionary Genomics group uses comparative genomics approaches complemented by wet lab experiments to understand genome evolution and function, and how fungi adapt to novel or altered environments, both on short and long evolutionary timescales.

The main focus of the group is to understand the evolution of genomic architecture. For this, we exploit the newest sequencing technologies to uncover molecular mechanisms and processes that establish genetic diversity, ranging from structural variations over transposable elements to genome hybridizations. Furthermore, we study the evolution of chromatin regulatory mechanisms and resolve genome-wide chromatin maps to understand how chromatin influences genome function and evolution.

Our group is especially interested in the evolution of pathogens as they need to rapidly diversify during co-evolutionary arms race with their hosts. We focus on oomycete and fungal plant pathogens and unravel their emergence and global dissemination as well as the molecular mechanisms that foster pathogen diversity and adaptation. We are especially interested in the evolution of effector genes – the tools used by pathogens to subvert host immune systems.

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

Nick C Snelders, PostDoc⁺
Edgar Chavarro Carrero, PhD candidate^*
Martin Kramer, PhD candidate^*
Petros Skiadas, PhD candidate
David Torres Sanchez, PhD candidate
Anouk van Westerhoven , PhD candidate^*
Xin Zhang, PhD candidate
Iñigo Bañales Belaunde, MSc student
Alejendro Baars, MSc student
Danny Hancock, MSc student
Taieve Stoops, MSc student
Pim Swart, MSc student

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