Description du sujet de thèse

This project aims to assess the contribution of viruses as vectors of horizontal gene transfer (HGT) between insects. This type of transfer is defined as the movement of DNA between organisms by means other than reproduction. We will focus on HGT involving transposable elements (HTT), the most frequent type of transfer among eukaryotes, and concentrate our efforts on insects, a group in which HTTs are particularly widespread.

The first part of the project will experimentally measure the frequency of virus-to-host HTTs in butterflies and Drosophila species infected with one, two, or three viruses (a baculovirus, an iridovirus, and a domesticated virus from a parasitoid wasp).

In the second part, we will perform large-scale bioinformatic screenings of HTTs among insects and test whether the number of HTTs between species can be explained by the presence of viruses. This will be carried out using a subset of field samples from the SymbioCode database, hosted by the LBBE laboratory (University of Lyon 1), in which the viral flora will be characterized using PoolSeq on multiple individuals from each insect species.

Overall, this project, which combines experimental and comparative genomic approaches, will provide new insights into the mechanistic aspects of HTTs. It will also help determine whether viruses have played a role in shaping the distribution of HTTs among insects.

Activities:
- Handling of insects and infection of insects with multiple viruses, virus purification and DNA extraction
- Characterization of horizontal transfers of transposable elements from insect hosts to viruses (short-read high-throughput sequencing and bioinformatic analyses)
- Detection of transposable elements integrated into the somatic and germline genomes of insects infected by viruses carrying TEs from other insects (PCR, vectorette PCR, Sanger sequencing, short- and/or long-read sequencing)
- Sequencing and assembly of insect genomes
- Annotation of transposable elements and viruses in assembled genomes (bioinformatic analyses)
- Inference and counting of horizontal transfer events between insects and statistical testing of a potential link between HGT rates and virus sharing

Expected Skills:
- Master's degree (MSc) in evolutionary biology and/or bioinformatics and/or virology
- Strong interest in evolutionary genomics
- Good command of spoken and written English
- Programming and statistical skills are desirable (training during the PhD is possible)

Contexte de travail

This is a 3-year PhD position that is part of the broader ANR-funded project VIRHOZFER (2024–2029), involving several members from the EGCE and LBBE laboratories (Univ. Lyon 1), with whom the candidate will be able to interact as needed. All experimental work will be funded by the VIRHOZFER ANR project.

The PhD will be co-supervised by Clément Gilbert (CNRS Researcher, HDR, EGCE laboratory, Univ. Paris-Saclay) and Julien Varaldi (Associate Professor, HDR, LBBE laboratory, Univ. Lyon 1). Most of the planned experiments and analyses will be carried out at the EGCE laboratory, but several research stays at the LBBE laboratory are expected.

Two free-living viruses (a baculovirus [AcMNPV] and an iridovirus [IIV6]) and one domesticated virus (the bracovirus of the parasitoid wasp Cotesia typhae) are available at the EGCE laboratory. EGCE also maintains live colonies of several dozen Drosophila species, one butterfly species, and one parasitoid wasp species, all of which can be used for the single and multiple infections planned in the project.

All individuals of butterfly species that will be sequenced in pools for the second research objective are available and preserved in ethanol at -20°C in the LBBE laboratory.

The recruited PhD student will receive training in both bioinformatics and laboratory best practices from the supervisors and at least two technical staff members at EGCE. They will be expected to present their work regularly to members of the LBBE and EGCE laboratories, as well as at meetings of the GDR 3546 "Transposable Elements" research group.

The recruited candidate will work in an optimal professional environment, with their own workspace and research equipment. As the working environment is international, a good command of English is highly desirable.