项目介绍

2024年5月5日

Function

Are you looking for a PhD position focusing on the interplay between insects and their microbiomes? Are you a bioinformatician who wants to develop and apply computational methods for microbiome analysis and virus discovery using sequencing data sets? Then this PhD vacancy might be of interest to you.

Like all organisms, insects have a native microbiome, including bacteria, fungi, and insect viruses. Many insects also serve as vectors to transmit viruses among animals or plants and the insect microbiome potentially influences this virus transmission. Therefore, the focus of insect virus research expanded from individual virus-host systems to metagenomics, i.e., bulk sequencing the genetic content of environmental samples without the need for prior virus isolation.

In this project, we will study whiteflies, a diverse group of agriculturally important insects that feed on plants and can transmit a variety of plant viruses. Whiteflies pose a severe threat to many plant crops, both in greenhouses and open fields. The management of this pest currently relies on insecticides; however, most whitefly species have already developed insecticide resistance. Biological control based on microorganisms is a promising tool; however, this requires fundamental understanding of the microbiome of whiteflies and its impact on virus transmission.

In this PhD project, you will contribute to developing bioinformatics approaches for microbiome analyses in insects, with a focus on the virome. You will discover the microbiome players and reconstruct virus genomes from metagenomics sequencing data of individual whiteflies. You will then associate this information with additional meta-data (such as geographic location and host plant) and, additionally, zoom in on the co-occurrence of different microorganisms in individual whiteflies to reveal possible synergistic or antagonistic effects. This project will thus contribute to understanding the factors that shape the viromes of insects.

You will integrate data from public sources, from international collaborations and from individual insects to be sampled in the Netherlands. Beyond the scientific and potential application merits, you will build a network for your future career both within and outside Wageningen University.

Function Requirements

• a successfully completed MSc degree in bioinformatics or a related field
• demonstrable experience in high-throughput sequencing data analysis and comparative genomics;
• proficiency in programming (e.g., python);
• affinity with virology, ecology, and molecular evolution;
• enthusiasm for working in close collaborations with experimental biologists;
• a proactive attitude and teamwork skills and are committed to obtaining a PhD;
• a very good level of oral and written English. You are required to show a certification of English skills. For more information about the required level please take a look at this link.

Contactinformation

For more information about this function, please contact Astrid Bryon (staff member of the WU Laboratory of Virology; astrid.bryon@wur.nl) and Anne Kupczok (staff member of the WU Bioinformatics Group; anne.kupczok@wur.nl) by e-mail. Applications are only accepted using the apply button on the vacancy page.

For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.

General information about the Bioinformatics Group can be found on https://wur.eu/BIF. General information about the Laboratory of Virology can be found on https://wur.eu/VIR.