[BBC] PhD position in plant virus bioinformatics

[Kupczok, Anne]

Dear colleagues,

The Evolutionary (Meta-)genomics group in the Bioinformatics Group at Wageningen University invites applications for a bioinformatics PhD student in ‘Virus diversity and evolution in natural plant ecosystems’.

You might share our view that wild plant communities might act as viral reservoirs that are also connected to agricultural plants. Since viruses can spill over from natural to agricultural systems, it is highly relevant to characterize virus diversity in wild plants. Plant virus genomes are highly diverse and evolve rapidly. To know which role plant viruses play in shaping natural plant communities, we must characterize their biodiversity and evolution.

You might be familiar with the phenomenon that plant virus infections are often asymptomatic, i.e., they do not cause overt disease, and can even be beneficial for the host. Recently, plant virus research expanded from the study of individual virus-host systems into characterizing global diversity using metagenomics, i.e., sequencing the genetic content of environmental samples without the need for prior virus isolation. Metagenomics led to the surprising observation that virus infections are ubiquitous, that there is a high incidence of mixed infection, and that most plant viruses identified in crops also occur in wild plants. There is growing evidence that viruses can impact plant ecosystems, which calls for a reappraisal of the role of viruses in natural ecosystems and accentuates the need to understand virus genomes and their function and evolution.

The aim of this project is to develop bioinformatics methods to analyze plant virus metagenome data that has been sampled from wild plants in the Netherlands. This (and potentially your) project will contribute to understanding plant virus diversity and evolution in natural Dutch ecosystems. You will contribute to developing bioinformatics methods to discover and reconstruct virus genomes from high-throughput plant virus sequencing data and to analyze ecological and evolutionary properties of these viruses. To this end, we aim to analyze the effect of host range and mixed infections on intra-host diversity and estimate how recombination and selection impact virus genome evolution.

Beyond the scientific and potentially application merits, you will build a wide network for your future career both within and outside Wageningen University.

The research is embedded within the chair group of Bioinformatics at Wageningen University which is led by Prof. Dick de Ridder (https://www.bioinformatics.nl/). You will be supervised by Dr. Anne Kupczok (https://annecmg.github.io/). The research will be carried out in close collaboration with Dr. Mark Zwart at the Netherlands Institute of Ecology (NIOO-KNAW) (https://nioo.knaw.nl/nl/employees/mark-zwart). The position is for four years and funded by the graduate school Experimental Plant Sciences (https://www.graduateschool-eps.info/).


We ask
•       a successfully completed MSc degree in bioinformatics or a related field;
•       excellent background in high-throughput sequencing analysis and comparative genomics;
•       affinity with ecology, evolution, and population genomics;
•       interest in close collaborations with experimental biologists and ability to work effectively as a team member and to carry out individual research;
•       very good level of oral and written English.

Please find all details and instructions how to apply here: https://www.wur.nl/en/vacancy/PhD-position-Virus-diversity-and-evolution-in-natural-plant-ecosystems-2.htm

For enquiries regarding the position and research topic, please contact Anne Kupczok: anne.kupczok at wur.nl<mailto:anne.kupczok at wur.nl>

--
Dr. Anne Kupczok
Assistant Professor
Bioinformatics, Department of Plant Sciences, Wageningen University


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