Adaptive evolution of filamentous plant pathogens

Genome Evolution

We recently found that the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), possesses a highly diverse set of supernumerary mini-chromosomes that contribute to horizontal chromosome transfer and extensive structural genomic variation. In our research program, we aim to address following questions regarding plant pathogen genome evolution:

  1. How diverse are mini-chromosomes in blast fungus populations?
  2. How dynamic are mini-chromosomes?
  3. To which extent do mini-chromosomes facilitate genomic rearrangements?
  4. How are mini-chromosome emergence and maintenance regulated?
  5. What are the genomic elements and molecular mechanisms underlying mini-chromosome emergence, rearrangements, and transfer?
  6. To which extent does horizontal mini-chromosome transfer drive genome evolution?


Molecular Evolution

Pathogen virulence effectors rapidly evolve to adapt to various host plant genotypes or species. Our preliminary data suggest that genomic rearrangements (including mini-chromosome associated rearrangements) coincide with genomic regions that are rich in transposable elements and virulence effector genes. We want to understand to which extent structural genomic rearrangements contribute to increased evolutionary rates in virulence related regions in pathogen genomes. We will build on this knowledge to study the effect of these events on the molecular evolution of virulence effector proteins using both, dry and wet lab approaches, including genetics, biochemistry, biophysics, and structural biology. Ultimately, we want to understand how these mutations influence the protein structure and their interaction with plant proteins, and how these changes help pathogens to cause disease on diverse host plants.


Plant Immunity

Plants possess a highly complex immune system that includes cell-surface and intracellular immune receptors. In recent years a new concept emerged, revealing that some protein domains, that are targets for pathogen attacks, integrated in plant immune receptors. There, they act as so-called integrated domains that bait pathogen effectors into recognition, causing an immune response. We will exploit this concept and use our knowledge gained from studying pathogen effector / host target interactions to design bioengineered plant immune receptor with new and improved recognition specificities.


ERC-funded project “PANDEMIC”

Our research program has recently received funding from the European Research Council.
“PANDEMIC” is an ambitious high-risk/high-gain project to deliver an innovative pathogen-guided strategy for crop disease resistance. The wheat blast pandemic is a clear and present danger to global food security. It is caused by the blast fungus, Magnaporthe oryzae, which, after emerging in Brazil only ~35 years ago, has spread to Southeast Asia and Africa in the last 7 years. We discovered that all isolates of the pandemic wheat blast fungus belong to a single, clonal lineage. These pandemic isolates carry a supernumerary mini-chromosome (mChr) of ~2 Mb, which encodes 19 secreted virulence effector proteins and renders the pandemic lineage highly virulent. We propose that this mChr is the Achilles’ heel of the pandemic fungus. In “PANDEMIC”, we will target the mChr virulence properties by gene editing and bioengineering of plant immune receptors to target mChr-encoded effectors.


The Model System

The fungus Magnaporthe oryzae (Syn. Pyricularia oryzae) causes blast disease, one of the most devastating crop diseases worldwide, resulting in significant yield losses and making it a threat to global food security. M. oryzae can infect > 50 monocot species including rice, barley, wheat, foxtail millet and finger millet. In addition, M. oryzae has the capacity to undergo host jumps or host-range expansions, increasing its epidemic potential. In the mid 1980s, blast disease emerged on wheat in Brazil and has since spread through large parts of South America and, in recent years, South Asia and Africa. M. oryzae propagates predominantly asexually and clonal lineages dominate blast epidemics. However, sexual reproduction can be achieved under lab conditions and signatures of gene flow have been observed in natural populations. M. oryzae is the ideal model system to study plant-pathogen coevolution, using a combination of genome evolution, structural variation and molecular evolution of virulence effector genes. It has a small (~45 Mb), haploid genome, vast genomic resources are available, it is genetically tractable and culturable in vitro and in planta, and both the sexual and asexual cycle can be completed under laboratory conditions. Additionally, recent advances in long-read sequencing technologies have proven to be powerful in facilitating high-throughput analyses of structural variation. This enables us to extend our analyses to a population scale and to investigate the mechanisms of genome evolution experimentally in the lab.


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