PhD student in evolutionary genomics of symbiotic bacteria and their hosts

The Department of Cell and Molecular Biology is organized into seven research programmes which all focus on different areas of cell and molecular biology: Computational Biology and Bioinformatics, Microbiology and Immunology, Molecular Biology, Molecular Biophysics, Molecular Evolution, Molecular Systems Biology and Structural Biology. The scientific basis of what we do lies in biology, but our research overlaps with other areas such as medicine, computer science, mathematics, chemistry, engineering sciences and physics. In total, we have over 200 staff and ~60 Ph.D. students. Please read more about the department’s work at https://icm.uu.se.

This PhD position will be placed in Lisa Klasson’s research group in the Molecular Evolution program. https://www.icm.uu.se/molecular-evolution/klasson-lab/

Project description
The project aims to study how symbiotic interactions between bacteria and animal hosts affect both partners’ genetic material and evolution. Our model system is the endosymbiotic bacterium Wolbachia in different Drosophila species, primarily from the willistoni group.

Wolbachia is often called one of the world’s most successful infections since it can be found in a large variety of invertebrates and is estimated to infect over 60% of all insect species on Earth. It is maternally transmitted, occurs in both facultative and obligate host interactions and can be everything from beneficial to pathogenic for the host. However, Wolbachia is best known as a facultative infection that interferes with host reproduction to increase the fitness of infected females and thereby its transmission success.

In the Drosophila willistoni group, most species are infected with highly similar Wolbachia strains that vary in their interaction with the host in several ways, for example, being obligate or facultative for the host, able to manipulate reproduction or not and having high or low infection levels. Using mostly large-scale sequencing of both Drosophila and Wolbachia genomes and performing comparative genomics, the goal is to determine the genetic factors in both Wolbachia and Drosophila that determine this variability in host-symbiont interaction and to elucidate the evolutionary events that took place to create it.

Duties
The work will mostly consist of bioinformatic analyses of sequence data from different species of the Drosophila willistoni group. Such work can include, for example, de novo assembly of sequence data, genome annotation, phylogenetic analyses and comparative genomics. To a lesser extent, the work might also include handling Drosophila and using standard molecular lab techniques such as DNA extractions and PCR.

The Ph.D. student shall primarily focus on postgraduate studies, but other duties related to teaching and administrative work may be involved, up to a maximum of 20 % of the time. Information about doctoral education, eligibility requirements and admission rules can be found on the faculty website, http://www. teknat.uu.se/utbildning/utbildning-pa-forskarniva/.

Requirements
To meet the entry requirements for doctoral studies, you must

• hold a Master’s (second-cycle) degree in bioinformatics, evolutionary biology, molecular biology, or another subject that the employer considers to be equivalent, or
• have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.

The applicant must have a good ability to work independently as well as in a group. A prerequisite is good written and oral skills in English, as the work takes place in an international environment. To work creatively, goal-oriented and structured are central abilities during a doctoral education and will therefore be given special consideration.

Additional qualifications
Previous experience of working with sequence data and bioinformatic analyses as well as familiarity with work in a Linux/Unix environment and a scripting language such as Python, R or Perl is highly desirable. Previous experience working with standard molecular biology techniques like DNA extractions and PCR and handling Drosophila or other insects is also meriting.

The application
Your application is preferably written in English and must include:

• A personal letter where you describe yourself, your research interest, your experiences and why you are interested in the position (max. 2 pages).
• A CV containing your education and other qualifications that are relevant to the position.
• A copy of your diploma(s) and your degree thesis.
• Contact information of two reference persons. 

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date as soon as possible or as agreed. Placement: Uppsala

For further information about the position, please contact: Lisa Klasson, lisa.klasson@icm.uu.se, tel. 018-471 6403

Please submit your application by 27 May 2024, UFV-PA 2024/1444.

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