Eva H. Stukenbrock
Recombination rate variation and recombination hot spots in fungal plant pathogens
Abstract: We study a species complex of plant pathogenic fungi including the wheat pathogen
Zymoseptoria tritici (synonym Mycosphaerella graminicola). Speciation of Z. tritici was associated with
wheat domestication and dates back to 10-12000 ya. Several closely related species of Z. tritici exist in
natural grasslands in the Middle East. We have taken a comparative population genomics approach to
study the underlying evolutionary processes that drive adaptive evolution of Zymoseptoria in managed and
natural ecosystems. We have previously shown a strong impact of natural selection in genome evolution of
Zymoseptoria spp. Interestingly; speciation of the wheat pathogen Z. tritici has not entailed a loss of
variation in spite of strong directional selection in the homogenous agro-ecosystem where it has evolved.
Recombination may play a crucial role in the generation and maintenance of genetic variation in Z. tritici.
To study and compare recombination patterns in Z. tritici and its close relative Z. ardabiliae we used a
coalescent based method and population genomic dataset including full genomes of 29 fungal individuals
and 1.1 and 0.8 million SNPs in the two species respectively. We show that recombination rate varies
considerably across the genome of the two Zymoseptoria species and the data supports a model where
recombination occurs in hotspots. Consistent with a higher effective population size in Z. tritici we also
estimate a considerably higher recombination rate (computed as rho = 4.Ne.r, where r is the per generation
recombination rate). Intra-genic recombination rates exceed inter-genic recombination rates in Z. tritici and
a high proportion of genes co-localize with recombination hot spots. While recombination maps of Z. tritici
and Z. ardabiliae are correlated, we find evidence for regions with highly divergent recombination patterns
between the two species. These two fined-scaled recombination maps are a unique tool to understand the
role of recombination during recent speciation and host specialization of the wheat pathogen Z. tritici.