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

• Skiadas P, Riera Vidal S, Dommisse J, Mendel MN, Elberse J, van den Ackerveken G, de Jonge R, Seidl MF (2024) Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew. PLoS Genetics pgen.1011452

• van Westerhoven AC, Dijkstra J, Aznar Palop JL, Wissink K, Bell J, Kema  GHJ , Seidl MF (2024) Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen. mBio11;15(12):e0275824

• 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 

• Snelders NC, Petti GC, van den Berg GCM, Seidl MF, Thomma BPHJ (2021) An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation. Proceedings of the National Academy of Sciences USA. 7;118(49): e2110968118

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

Team members

Dr. Paula Gómez-Zapata, Postdoc¹

Sibbe Bakker, Research assistant

Josje Romeijn, PhD candidate
Petros Skiadas, PhD candidate 
David Giron Villalobos, PhD candidate
Anouk van Westerhoven, PhD candidate²

Lorenzo Caranti, MSc student
Bas Odekerken, MSc student

¹joint project with Swedish University of Agricultural Sciences, Sweden 
²joint projects with Wageningen University & Research, the Netherlands