Research

We study fungal biodiversity in an evolutionary and molecular context. A main goal of our research is to understand the underlying molecular mechanism of species divergence and adaptive evolution in fungal plant pathogens.

 

Comparative population genomics

Adaptive evolution: To compare and contrast evolutionary processes in different ecosystems we have collected population genomics datasets from three pathogen species. The three species are very closely related however one species Zymoseptoria tritici (synonym Mycosphaerella graminicola) has adapted and specialized to an agricultural host while the two other species occur on grass hosts in natural ecosystems. We apply evolutionary predictions to identify footprints of natural selection in the genomes and use coalescence models to study the divergence of pathogen species in the different environments.

Hybrid speciation: The closest know relative of Z. tritici, Z. pseudotritici, originated by a very recent homoploid hybridization event (within the last 5-600 years). Z. pseudotritici is today a widespread pathogen at the center of origin of this group of plant pathogens, the Middle East. Our initial genome study of the hybrid species has included five genomes, which allowed us to describe overall genome patterns in new species. We are currently sequencing additional 25 genomes of Z. pseudotritici to perform a more fine scale characterization of genome evolution in such a new hybrid species.


“Host specialization” and “speciation” gene

We have used evolutionary predictions to identify genes, which have evolved under positive selection during the divergence of the pathogen species. We hypothesize that these genes are involved in either host adaptation or in speciation. To investigate the functional role and importance of these genes we use molecular and experimental approaches. The fungal species can be genetically modified using Agrobacterium mediated transformation and we can either delete or replace genes of interest. To compare phenotypes of mutant and wild type lineages we use a set of different host species. We are mainly assessing the effect of gene deletion/replacement on virulence of the fungal strain. However a goal is to also develop an assay were we could study the importance of the genes in the process of speciation.

 

Evolution at the level of gene regulation

Next to the accumulation of adaptive mutations, the fungal pathogens also have also diverged at the level of gene regulation. We aim to characterize evolution at the level of transcription by comparing large scale RNAseq datasets from multiple combinations of pathogen and host species. This allows us to identify genes in the pathogen that are differently induced in different host environments. We hypothesize that these genes play a role in host specificity.