Post-Doctoral Research in Comparative Fungal Genomics and …, Zürich (Kreis 11)

The newly established Plant Disease Dynamics group at ETH Zurich is looking to recruit a fungal genome biologist interested in how transposons shape the structure and function of plant pathogen genomes. We seek someone with prior experience in 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 partner with experts in biochemistry and cell biology. The goal is to build a collaborative interdisciplinary team that uses population genomics to support the development and 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 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 position focuses on the plant‑pathogenic fungi Bipolaris sorokiniana, Parastagonospora nodorum and Pyrenophora tritici‑repentis, all carrying the fungal virulence gene ToxA, nested inside a smaller passenger transposon called ToxTA. This transposon has been captured independently bytwo 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.

We will synthesize all available information from natural fungal isolates—including over 300 publicly accessible genomes and several dozen long‑read assemblies from the lab’s internal collection—to build hypotheses for which genetic features are essential for horizontal transfer.

Job description

Generate new long‑read Nanopore assemblies from the lab’s long‑term culture collection

Assemble, annotate and quality‑assess all existing 30+ long‑read genome assemblies

Mine available public genomes for TEs of interest

Establish reproducible Snakemake/Nextflow pipelines to support the lab’s long‑term research interests

Proactively manage the lab’s genomic data resources

Supervise and mentor PhD and Master’s 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 commitment to reproducibility 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 undergraduate and master’s research students

A desire to establish an independent research area with support/mentorship from Prof. McDonald

We offer

A dynamic and exciting research environment in a newly established ETH group

Access to state‑of‑the‑art central facilities at ETH Zurich

Core budgetary support for consumables and IT infrastructure

Integration into the wider plant pathology research network spanning Prof. McDonald’s career across four continents (USA, Switzerland, Australia, UK)

An inclusive and supportive team that values diversity

Flexible working hours and partial home office if desired

We value diversity and sustainability In line with ETH Zurich’s values, the institution 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 staff and students are respected. The ETH Zurich Equal Opportunities and Diversity policy ensures afair and open environment that allows everyone to grow and flourish. Sustainability is a core value; we are consistently working towards a climate‑neutral future.

Curious? So are we.

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