Missions

Certain eukaryotic species undergo systematic programmed DNA elimination (PDE), consisting of the partial destruction of chromosomes in their soma during development. Although described as early as 1887, PDE has remained mysterious due to the limitations of model systems and sequencing technologies. In particular, fundamental questions about the function and evolution of PDE remain unclear. Recently, Marie Delattre's team discovered that nematodes of the genus Mesorhabditis undergo PDE, where nearly 30% of the genome is eliminated in the soma, mainly targeting transposons. Several recent data suggest that PDE may serve to control transposons rather than the few hundred protein-coding genes that are also eliminated.
We have launched a project to decipher the origin of PDE in Mesorhabditis by testing whether the sequence specifying chromosome breakage originates from a transposon and by identifying the associated nuclease(s). This project is based on the sequencing and analysis of the somatic and germline genomes of several species of nematodes of the genus Mesorhabditis.

Activités

The postdoc will be responsible for studying the evolution of PDE in Mesorhabditis, analyzing both intraspecific polymorphism and interspecific divergence. He or she will be responsible for the entire project, from developing the analysis protocol to writing articles. He or she will be able to draw on the expertise of the project's partner teams and will also be able to recruit and supervise master's students.

Compétences

Analysis skills
This project requires strong bioinformatics skills for comparative genome analysis: mastery of variant calling protocols, programming/scripting languages (Python, R, bash), the use of computing clusters, and FAIR practices. This project also requires a good command of evolutionary genomics and population genetics methods and concepts (selection tests).
Skills in genome assembly and annotation would be appreciated.
Furthermore, as with all research work, this project requires good scientific communication skills (oral presentation + article writing).

Contexte de travail

The postdoc will be recruited to the Bioinformatics, Phylogeny and Evolutionary Genomics (BPGE- https://lbbe.univ-lyon1.fr/en/bioinformatics-phylogeny-and-evolutionary-genomics-group) team at the Laboratory of Biometry and Evolutionary Biology (LBBE) and will be supervised by Laurent Duret (CNRS Senior Researcher). The BPGE team is internationally recognized for its work on genome evolution. This project will also be carried out in close collaboration with the team of Marie Delattre (ENS-Lyon), who discovered PDE in Mesorhabditis nematodes.
The LBBE offers an extremely stimulating work environment (scientific events/skills exchanges at various levels, both internal and external) and has first-rate research facilities (computing cluster; team of IT specialists supporting researchers).
The laboratory is located on the LyonTech La Doua university campus in Villeurbanne.
In addition to all this:
• Professional support with internal training at the laboratory
• The possibility of teleworking
• A company restaurant offering lunch at an attractive price.
• Partial reimbursement of transportation costs (75%)
+ sustainable mobility allowance of up to €300/year
• A site accessible by public transportation (Tram T1 + T4 + bus)
• 44 days of vacation/RTT per year
• Financial contribution to mutual insurance costs