Open Positions

PhD position in evolutionary genomics of pathogens at the ETH Zurich

Modern agriculture relies on effective control of pathogens. The continent-scale homogenisation of crop varieties and the heavy reliance on a small set of fungicides has greatly increased risks to global food security. The speed of pathogen adaptation to new crop varieties is directly related to the extent of mono-cultures. The genomic revolution fundamentally altered the field of pathogen research. The establishment of reference genome sequences for a large number of pathogenic fungi and bacteria provided extensive catalogues of the genomic and functional characteristics of pathogens. The comparison of different pathogen genomes revealed similar strategies for host exploitation. However, the evolutionary history of effectors or host specific toxins remains largely obscured by the fact that these genes seem to arise rapidly and share little sequence similarity.

The next phase in the genomic revolution will be the sequencing of very large numbers of isolates within one species. Mycosphaerella graminicola (synonym Zymoseptoria tritici) is a major pathogen of wheat that incurs up to 30% yield loss during outbreaks and has a well documented evolutionary history. The pathogen emerged from wild progenitor species found on wild grasses in the Fertile Crescent. M. graminicola carries an extensive set of accessory chromosomes (chromosomes not found in all members of a species). Accessory chromosomes likely provide a cradle for adaptive evolution in pathogens. Despite the high-quality genomic resources, very few genes involved in host virulence and climate adaptation are known.

We aim to identify the various selective pressures that acted on the genome by analyzing 120 genomes from four different populations covering the geographic range and the phenotypic diversity of the species. We will use genome-scale comparisons to document fundamental mechanisms shaping the evolution of gene and chromosomal structure. This project will be at the interface of genome and evolutionary biology, as well as agricultural sciences.

This project is best suited for a biologist (MSc or Honors BSc) with a strong interest both in evolutionary biology and the analysis of genomic sequences. Experience in bioinformatics, statistics (e.g. R) and/or programming is a plus but not a requirement. A strong motivation to learn these techniques and a willingness to work in a team will be important.

You will be supervised jointly by Dr. Daniel Croll and Prof. Bruce McDonald at the Institute for Integrative Biology at the ETH Zurich. You will have access to a state of the art user laboratory (Genetic Diversity Centre), next-generation sequencing center (at the D-BSSE) and high-performance computing resources (BRUTUS). The workplace is located in the center of Zurich and provides a wealth of opportunities to interact with other students.

For further information, please contact: daniel.croll@usys.ethz.ch

For your application, please send a pdf containing both a statement of your research interests (1 page) and a CV (2 pages) including addresses and phone numbers of two academic references to daniel.croll@usys.ethz.ch.