Post-Doctoral Research in Comparative Fungal Genomics and Transposon Diversity

100%, Zurich, fixed-term

The newly established Plant Disease Dynamics group at the ETH Zurich is looking to recruit a fungal genome biologist interested in the ways in which transposons shape the structure and function of plant pathogen genomes. We are looking for someone with prior experience in either fungal or transposon comparative genomics, who can explore the diversity and evolution of Starship transposons and the genes and transposons they carry within plant infecting fungal species.

This position forms one pillar of a three-pillared research project, where you will be partnered with other experts in biochemistry and cell biology. The goal is to build a collaborative interdisciplinary team that uses population genomics to support the development an implementation of working experimental transposon models in the lab.

Project background

Horizontal gene transfer (HGT) enables the spread of pathogenicity genes between microbes and can therefore drive the emergence of novel diseases. In pathogenic fungi, an emerging global threat to both humans and our crops, the mechanisms that facilitate HGT remain unknown. Recent work has uncovered a novel group of giant transposons called Starships, which have moved virulence, metal tolerance and other fitness associated genes horizontally between fungal species. This post-doctoral positions is focused on the plant pathogenic fungi, Bipolaris sorokiniana, Parastagonospora nodorum and Pyrenophora tritici-repentis that all carry the fungal virulence gene ToxA, which is nested inside a smaller passenger transposon called ToxTA. This transposon has been captured independently by two different Starship transposons, Sanctuary and Horizon with evidence of other captures in other fungal species. We seek to understand the evolutionary history and horizontal transfer of the ToxTA transposon in natural populations of all fungal species in which it is found. This includes over 300 publicly accessible genomes as well as several dozen long-read assemblies from the lab’s internal collection. This position aims to synthesise all available information from these natural fungal isolates to build hypotheses for which genetic features are essential for horizontal transfer.

Job description

• Generate new long-read Nanopore assemblies from the labs long-term culture collection
• Assemble, annotate and quality assess all existing 30+ long-read genome assemblies
• Mine availalbe public genomes for TEs of interest
• Establish reproducible Snakemake/Nextflow pipelines to support the labs long-term research interests
• Proactively manage the labs genomic data resources
• Supervise and mentor PhD and Masters students in comparative fungal genomics
• Assist in the delivery of lectures or seminars for the Plant Disease Dynamics group
• Write and publish peer-reviewed manuscripts
• Apply for funding to develop research independence

The initial contract duration is two years, with the possibility of extension.

Profile

• A PhD in comparative genomics or transposon biology, preferably of fungal species or other Eukaryotes
• Evidence of research excellence through peer-reviewed publications
• Evidence of comittment to reproducibity in bioinformatics through the use of Code Repositories
• Evidence of ability and experience in handling large DNA datasets
• A strong desire to contribute to teaching of both Undergraduate and Masters Research Students
• A desire to establish an independent research area with support/mentorship from Prof. McDonald

Workplace

We offer

• A dynamic and exciting research environment in a newly established ETH group
• Access to state-of-the-art central facilites at the ETH Zurich
• Core budgetary support for consumables and IT infastructure
• Integration into the wider plant pathology research network spanning Prof. McDonald’s career accross four continents (USA, Switzerland, Australia, UK)
• An inclusive and supportive team that values diversity
• Flexible working hours and partial home office if desired

Working, teaching and research at ETH Zurich

We value diversity and sustainability

In line with our values , ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open environment that allows everyone to grow and flourish. Sustainability is a core value for us - we are consistently working towards a climate-neutral future .

Curious? So are we.

We look forward to receiving your online application with the following documents:

• Moviation Letter, stating clearly your reason for applying and qualifications
• A 500 word statement on independent reasearch interests
• CV
• Code repository website (GitHub or other)
• At least two reference letters

Questions regarding the position should be directed to Prof. Megan McDonald at megan.mcdonald@ usys.ethz.ch (no applications).

The review of applications will start at the end of April.

Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered.

We would like to point out that the pre-selection is carried out by the responsible recruiters and not by artificial intelligence.

Apply online now

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