Description du sujet de thèse

Insect parasitoids lay their eggs in the bodies of other arthropods, mainly insects, and are therefore the main natural regulators of insect populations, including pests. In the vast majority of cases, their development ends with the death of their hosts. Among the extraordinary diversity of parasitoids found in the order Hymenoptera, we know that 3 monophyletic clades of wasps have domesticated viruses, enabling them to protect their offspring from the immune response of their hosts. This phenomenon is made possible by the fact that these viruses 'domesticated' by the wasp are injected into the host and enable the wasp's genes to be integrated into the host, thereby manipulating host physiology from the inside! The current literature indicates that these wasp segments can integrate not only the DNA of somatic tissues but also the DNA of germinal tissues of attacked hosts, with some even becoming fixed within certain host species, despite the fact that parasitized hosts usually die. However, the actual flow of wasp genes passed on during evolution from parasitoid wasps to their hosts is not known. Nor do we know to what extent they contribute or have contributed to the fitness of these 'recipient' species. Nor is it known whether other cases of virus domestication, beyond the three currently known, have occurred in the wide diversity of hymenopteran parasitoids. The thesis project aims at answering these questions, based on a bioinformatics analysis of the 7125 insect genome assemblies currently available, including 437 Hymenoptera with a parasitoid lifestyle.
We are seeking a highly motivated student interested in evolutionary biology and with bioinformatics skills.

Contexte de travail

The new recruit will join the Biométrie et Biologie Evolutive (LBBE) laboratory on the LyonTech La Doua university campus in Villeurbanne (https://lbbe.univ-lyon1.fr).
The thesis will be co-supervised by Julien Varaldi (MCF HDR, LBBE laboratory, Univ. Lyon 1) and Clément Gilbert (DR CNRS, EGCE laboratory, Univ. Paris-Saclay). Most of the analyses in the thesis will be carried out in the Biometrics and Evolutionary Biology laboratory in Lyon, but several visits to the EGCE laboratory are planned in order to facilitate the sharing of knowledge.
This project is part of a larger funded ANR project (VIRHOZFER, 2024 - 2029), involving several members of the LBBE (Univ. Lyon1) and EGCE (Univ. Paris-Saclay) laboratories, with whom the candidate will be able to interact as required. All costs associated with the successful completion of the thesis (contribution to the cluster, participation in conferences, publication costs) will be covered by the ANR VIRHOZFER project.
The PhD project relies exclusively on genomics data and bioinformatics resources. Both are fully available in the host team. The computational part of the project will be possible thanks to the access to the LBBE/PRABI Lyon bioinformatic cluster (25 nodes for 1200 cpu, including 4 nodes "bigmem" with 1 To of RAM and ∼300 To of beeGFS storage). The cluster is used by 150 people from the FR BioEnvis every year (∼5000000 h calculations (on per year). Additionally, we will have access to the (CC-IN2P3) for long-term storage of the data.
Our little extras :
- A stimulating work environment in contact with research staff
- Professional support with in-house training
- The possibility of teleworking
- A company restaurant where you can have lunch at an attractive price.
- Partial reimbursement of travel expenses (75%)
+ sustainable mobility package of up to €300/year
- A site accessible by public transport (Tram T1 + T4 + bus)
- 44 days vacation / RTT per year
- Financial contribution to health insurance costs