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, function, 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:
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.
For an overview of the diverse work we do, please see these recent key publications
Dr. Paula Gómez-Zapata1
Dogukan Bayraktar, MSc student
Alvaro Ropero Lopez, MSc student
Luis Aznar Palop, MSc student
Kyran Wissing, MSc student
1joint project with Swedish University of Agricultural Sciences, Sweden
2joint project with University of Cologne, Germany
3joint projects with Wageningen University & Research, the Netherlands