Genome rearrangements in asexual fungi facilitate adaptive evolution

Pathogens constantly co-evolve with their hosts to maintain a high level of virulence and to avoid recognition by the immune system. To quickly adapt to changing environments, many pathogens developed flexible genomes with a high number of transposable elements (TE). Sexual propagating and recombining species with large-population sizes together with ectopic recombination mediated by TEs provide powerful mechanisms to generate novel or altered effectors maintaining a high level of virulence.

In contrast, asexual pathogens reproduce clonally and consequently do not sexually recombine. Therefore, they were thought to be limited in their genetic variability. However, electrophoretic karyotyping in asexual fungi indicated common chromosomal rearrangements that might contribute to their adaptation. Recently, de Jonge and colleagues provide the first compelling evidence for this hypothesis. The asexual fungi Verticillium dahliae displays remarkable chromosomal rearrangements establishing lineage-specific regions that harbor genes encoding secreted proteins involved in pathogenicity. Genomic rearrangement could therefore be a general mechanism to facilitate adaptive evolution.

Even though V. dahliae contains only few TEs, these are suspected to mediate the observed chromosomal rearrangements. However, TEs are only one of few factors that influence chromosomal integrity. DNA methylation, repeat induced point mutations (RIP), DNA repair pathways and mitotic checkpoint are just few of the components involved in DNA integrity, (suppression of) recombination or TE activity.

We therefore study chromosomal rearrangements using two complementary approaches: (i) next-generation sequencing allows us to rapidly sequence genomes of closely related species and strains of V. dahliae to assess the prevalence of genomic rearmaments in these asexual fungi. Moreover, we assess how epigenetics, in particular DNA methylation, influence the chromosomal stability in V. dahliae under in vivo conditions. (ii) we use a large-scale phylogenomic approach to study the constitution and evolution of central components of pathways involved in the maintenance of genome integrity in V. dahliae and other plant pathogenic fungi. These complementary approaches will allow us to assess the prevalence and provide first evidence for the underlying mechanisms for chromosomal rearrangements as well as genome integrity in asexual fungi.