PhD position (M/F): Do host-parasite interactions promote horizontal gene transfer in animals?

Job Description

Thesis Subject

In metazoans, genetic information is primarily passed from parents to offspring through reproduction. However, in recent years, it has become clear that even highly distantly related metazoan lineages have exchanged DNA over the course of evolution. This is referred to as horizontal gene transfer. Although these transfers are significantly less frequent compared to prokaryotes, it is clear that they have contributed very significantly to the evolution of metazoans, either by enabling the colonization of genomic parasites such as transposable elements or through the transfer of genes with high adaptive potential. Despite the evolutionary importance of these horizontal transfers, the mechanisms and factors promoting their occurrence remain largely unknown. The objective of this thesis is to explore, through a bioinformatics approach, the hypothesis that horizontal transfers are promoted by parasitism. Indeed, it is expected that the physical proximity between the host and its parasite promotes the exchange of genetic material, either directly or indirectly, between the two organisms. The thesis will be based on the analysis of two datasets. The first consists of butterflies and their parasitoid insects, all collected within a nature reserve in Costa Rica. Ecological interactions involving parasitism have been particularly well documented by our collaborators, and we have sequenced the genomes of 227 species (95 parasitoids/132 hosts). This dataset will enable us to measure the contribution of ecological connections between species in the network to the flux of horizontal gene transfers. The second, larger dataset will consist of a sampling of publicly available genomes of parasitic metazoans and their hosts (n=592 parasite species in total). This second dataset will allow us to extend the conclusions to other animal clades (notably vertebrates as hosts) and to different types of parasitic relationships (e.g., hematophagy). We are looking for someone interested in evolutionary science, with an aptitude for bioinformatics.

Your Work Environment

The successful candidate will join the Laboratory of Biometrics and Evolutionary Biology (LBBE) located on the LyonTech La Doua university campus in Villeurbanne (https://lbbe.univ-lyon1.fr).
The thesis will be co-supervised by Julien Varaldi (Associate Professor, LBBE Laboratory, University of Lyon 1) and Clément Gilbert (DR CNRS, EGCE Laboratory, University of Paris-Saclay). Most of the analyses planned for the thesis will be conducted at the Laboratory of Biometry and Evolutionary Biology in Lyon, but several visits to the EGCE laboratory are planned to facilitate knowledge sharing.

This project is part of a broader ANR-funded project (VIRHOZFER, 2024–2029), involving several members of the LBBE (Univ. Lyon 1) and EGCE (Univ. Paris Saclay) laboratories, with whom the successful candidate will be able to collaborate as needed. All costs associated with the successful completion of the thesis (contribution to the cluster, conference attendance, publication fees) will be covered by the ANR VIRHOZFER project.

The doctoral project relies exclusively on genomic data and bioinformatics resources. Both of these elements are fully available within the host team. The computational aspect of the project will be made possible by access to the LBBE/PRABI Lyon bioinformatics cluster (25 nodes with 1,200 CPUs, including 4 “bigmem” nodes with 1 TB of RAM and ∼300 TB of beeGFS storage). The cluster is used by 150 people from the BioEnvis Research Group each year (∼5,000,000 hours of computation per year). In addition, we will have access to CC-IN2P3 for long-term data storage.

Our added benefits:
• A stimulating work environment working alongside research staff
• Professional support with in-house training within the laboratory
• The option to work from home
• A staff canteen offering lunch at an affordable price.
• Partial reimbursement of travel costs (75%)
+ a sustainable mobility allowance of up to €300 per year
• A site accessible by public transport (Tram T1 + T4 + bus)
• 44 days' annual leave / RTT per year
• Supplementary social security cover

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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