Microbial Genome Evolution Team

Synopsis

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 and how these in turn affect genome organization, functioning, 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 genome organisation to gene content or gene regulation. For instance, we are interested in identifying and studying processes that generate structural variation and uncovering how this intersects with the 3D genome organization 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:

1. We investigate molecular processes that drive microbe genome evolution

2. We study chromatin and its impact on microbial genome function and evolution

3. 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 grand societal challenges such as sustainable agriculture and food security.

For an overview of the diverse work we do, please see these recent key publications

• Romeijn J, Bañales I, Seidl MF (2025) Extensive horizontal transfer of transposable elements shapes fungal mobilomes. Current Biology 5:S0960-9822(25)01480-0
   
• Skiadas P, Mendel MN, Elberse J, van den Ackerveken G, de Jonge R, Seidl MF (2026) Pangenome graph analysis reveals evolution of resistance breaking in spinach downy mildew. PLoS Biology 24(1):e3003596 
   
• Sato Y, Bex R, van den Berg GCM, Santhanam P, Höfte M, Seidl MF, Thomma BPHJ (2025) Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution. Nature Communication 24;16(1):6806
   
• van Westerhoven AC, Fokkens L, Wissink K, Kema GHJ, Rep M, Seidl MF (2025) Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen. Nuclei Acid Research, Genomics & Bioinformatics 7(2):lqaf034
   
• van Westerhoven AC, Aguilera-Galvez C, Nakasato-Tagami G, Shi-Kunne X, Martinez de la Parte E, Chavarro-Carrero E, Meijer HJG, Feurtey A, Maryani N, Ordóñez N, Schneiders H, Nijbroek K, Wittenberg AHJ, Hofstede R, García-Bastidas F, Sørensen A, Swennen R, Drenth A, Stukenbrock EH, Kema GHJ, Seidl MF (2024) Segmental duplications drive the evolution of accessory regions in a major crop pathogen. New Phytologist 242(2):610-625 
   
• Torres DE, Kramer HM, Tracanna V, Fiorin GL, Cook DE, Seidl MF, Thomma BPHJ (2024) Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen. Nature Communications 24;15(1):1701 
   

For a complete overview of the publications, please see Publications or Pubmed.

Team members

Sergio Alías-Segura, visiting PhD candidate (Universidad Complutense de Madrid, Spain)
Jasper Bell, PhD candidate
Valerie Buijs, PhD candidate²
Melanie Mendel, PhD candidate¹
Josje Romeijn, PhD candidate
Petros Skiadas, PhD candidate 
David Giron Villalobos, PhD candidate

Bas Odekerken, MSc student
Lőrinc Kóródi, MSc student

Frida Kaske, BSc student
Selena Valenkamp, BSc student

¹joint project with Ronnie de Jonge and Guido van den Ackerveken

²joint project with Pedro Crous

Previous team members:

Paula Gomez-Zapata (Postdoc), Nick Snelders (Postdoc), Anouk van Westerhoven (PhD candidate, graduated 2025), Xin Zhang (PhD candidate, graduated 2024), Edgar Chavarro-Carrero (PhD candidate, graduated 2024), David Torres (PhD candidate, graduated 2023), Martin Kramer (PhD candidate, graduated 2022), Sander Rodenburg (PhD candidate, graduated 2020), Hesham Gibriel (PhD candidate, graduated 2019), Xiaoqian Shi-Kunne (PhD candidate, graduated 2019), Jasper Depotter (PhD candidate, graduated 2018), Nadia Ordonez-Roman (PhD candidate, graduated 2018), and Sibbe Bakker (Research assistant)