PhD fellowship in Fungal Genomics21

We are seeking a candidate to fill a fully funded PhD position for a period of 3 years in the Applied Evolutionary Ecology research group led by Henrik H. De Fine Licht at the The Department of Plant and Environmental Sciences, University of Copenhagen, Denmark.

Start date is (expected to be) 1st September, 2024, or as soon as possible thereafter.

The project
The PhD project will be part of newly established research project on genome plasticity of root-associated insect-pathogenic fungi funded by the Novo Nordisk Foundation.

Fungi in the genus Metarhizium show remarkable diversity between species in terms of host range and capacity for plant-root colonization. There is also ample diversity within species among isolates in pathogenic capacity, toxin production, and nutritional growth characteristics. Recently the presence of multiple accessory chromosomes among isolates of Metarhizium has been discovered. Accessory chromosomes are entire chromosomes with telomeres that are present in some individuals but not in others. These chromosomes contain hundreds of genes but their effect on the phenotype of these fungi is unknown (Further scientific background information can for example be found in Habig et. al. 2024, PNAS, 121:e2316284121). The project aims to investigate the phenotypic effect of accessory chromosomes, and whether they influence the pathogenic host range and/or the symbiotic effect in the plant rhizosphere along the mutualistic-pathogenic continuum. The project is a collaboration with Michael Habig at Kiel University, Germany, and while the phd-student will be based at University of Copenhagen a longer stay in Kiel during the PhD is expected.

Who are we looking for?
We are looking for a committed and enthusiastic graduate student to work with root-symbiotic insect-pathogenic fungal genomics, evolution and ecology. The project will explore gene expression profiles and phenotyping of fungal isolates with/without specific accessory chromosomes. The successful PhD student will thus obtain competences within experimental mycology, fungal genomics and transcriptomics, applied bioinformatics, insect and plant fungal bioassays. We are looking for candidates with experience in any or all of the following areas: Fungal pathogen biology, mycological techniques, fungal genetics/genomics, molecular genetic laboratory techniques, and computational analysis of genomic sequence data (programming, e.g. Perl, Python, Bash, R; genome/transcriptome assembly; comparative genomics etc.). Most importantly, the successful candidate is enthusiastic, have a good grasp of molecular biology and is interested in host-pathogen evolution.

Our group and research- and what do we offer?
In the Applied Evolutionary Ecology research group we study how antagonistic (pathogenic) and beneficial (mutualistic) fungal symbionts are shaped by host ecology and evolution, how ecological and evolutionary factors determine the species-range partners interact with, and how new species interactions are established, for example through partner-shifts. We mainly use molecular and applied bioinformatics coupled with experimental work. Our work is fundamental in nature, but of applied significance for example for biological control, plant-microbe interactions in agriculture, and pathogen host shifts. Our research focuses on co-evolution in mutualistic and parasitic interactions, and we are particularly interested in the underlying genetic factors that influence the evolutionary processes of adaptation and govern the outcome of species interactions. More information can be found on the webpage https://sites.google.com/site/henrikdefinelicht.

The Applied Evolutionary Ecology group is a part of the Section for Organismal Biology, Department of Plant and Environmental Sciences, Faculty of SCIENCE, University of Copenhagen. We are located in Copenhagen.

We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include modern laboratories and various insect, plant, and microbiology rearing facilities as well as computational resources.

Principal supervisor is Associate Professor Henrik H. De Fine Licht, Department of Plant and Environmental Sciences, Section for Organismal Biology, Email:[email protected], Direct Phone: (+45) 35320097.

The PhD programme

A three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

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Getting into a position on the regular PhD programme

Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. Biology, Biotechnology, or similar. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programme

• Carry through an independent research project under supervision

• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

We are looking for the following qualifications:

• Professional qualifications relevant to the PhD project
• Relevant work experience
• Interest in joining an international research environment and interdisciplinary research
• Curious mind-set with a strong interest in fungal genomics
• A proven record of excellent English speaking, reading, and writing skills

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Application and Assessment Procedure
Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

• Cover letter stating research interests and reasons for applying to this specific position (max. two pages)
• Curriculum vitae including information about your education, experience, publications (if any), language skills and other skills relevant for the position
• Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
• Full contact details (name, address, e-mail, telephone numbers and addresses of 2 professional references).

Application deadline:
The deadline for applications is 21st April 2024, 23:59 GMT +2.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

Interviews with selected candidates are expected to be held in the period 23 may till 31 May 2024.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.