We are looking for an enthusiastic molecular biologist, interested in plants and plant diseases who would like to perform cutting-edge fundamental research on downy mildews, an agriculturally important group of pathogens. Downy mildews are obligate biotrophic oomycetes that cause severe foliage blights on many crops including the targeted vegetable crop here, spinach. Downy mildews adapt at a stunning pace and rapidly break new resistance traits requiring new strategies for resistance breeding. For this, pathogen informed approaches are highly demanded. Understanding the tools, weapons, and strategies that pathogens use for infection provides a strong basis for developing/selecting resistance mechanisms that effectively protect the plant. Identifying all effectors - the tools used by the pathogens to support host infection - and unravelling their activities gives a clear profile of the pathogen. We aim to develop this innovation for the spinach downy mildew Peronospora effusa by using state-of-the-art genome analyses methods, bioinformatics, and functional assays. This is where you come in. You will work at the intersection of bioinformatical identification and functional characterization of pathogen effectors, and accordingly you will contribute to the development of a functional genomics platform to assess effector contribution to pathogen virulence and disease.
Your PhD research will be conducted in the Plant-Microbe Interactions group of Dr Ronnie de Jonge and Prof Guido van den Ackerveken and in close collaboration with the Theoretical Biology & Bioinformatics group of Dr Michael Seidl at Utrecht University. Your PhD project will be part of the Topsector AF&TU project "Understanding the evolution of downy mildew virulence for knowledge-driven resistance breeding of spinach", lead by Prof van den Ackerveken and supported by four vegetable breeding companies. In this project, you will work closely together with a bioinformatics PhD student. A selection of ongoing research lines across the groups includes broadly host-microbe interactions studying pathogens and plants, microbial genomics, fungal genome evolution, genome organization, microbiome analyses, experimental evolution, and cell-type specific gene expression profiling.
Recent key publications:
- de Jonge et al. (2018) "Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum", Proc Natl Acad Sci USA 115:E5459-E5466
- Thines et al. (2020) "The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters", Mol Plant-Microbe Interact MPMI-07-19-0211-R
- Klein et al. (2020) "Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering". PLoS ONE 15:e0225808
- Seidl and van den Ackerveken (2019) "Activity and phylogenetics of the broadly occurring family of microbial Nep1-like proteins" Annu Rev Phytopathol 25:367-386
- Kema et al. (2018) "Stress and sexual reproduction affect the dynamics of the wheat pathogen effector AvrStb6 and strobilurin resistance" Nat Genet 50:375-380
- Depotter et al. 2019 "Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation" Mol Ecol 15:3482-3495