PhD Fellowship in Bioinformatics

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

The coevolution between plants and microbes is an exciting and promising discipline to understand and employ positive interactions in light of reducing pesticides in farming. This PhD program is part of the ERC Starting Grant project HoloE2Plant aiming at validating the holobiont concept by looking at the simultaneous evolution of the host and its microbiome. During the PhD program the candidate will (i) analyze bacterial, fungal and plant genomes to create high quality reference genomes, (ii) individuate genomic variants among parental and evolved microbial populations, (iii) analyze plant allele frequency variations among parental and evolved populations and (iv) analyze metabarcoding data during an experimental evolution assay. The PhD candidate will be under the responsibility of the ECOGEN team (https://www.lipme.fr/en/ecogen-1). The main objective of the ECOGEN team is to understand and predict biotic interactions with plants in the context of global changes. The PhD student will be under the co-supervision of Fabrice Legeai (IGEPP (équipe EGI) / IRISA (équipe Genscale) at Rennes. 

 

The PhD position is part of the HoloE2Plant project – Exploring the Holobiont Concept through Plant Experimental Evolution – coordinated by Claudia Bartoli at INRAE in Toulouse, France. 

This position is fully funded by the European Research Council (ERC) and does not require applying through a Doctoral School competition. The successful candidate will contribute to the study of coevolution between fast-cycling Brassica rapa plants and synthetic microbial communities that are artificially assembled under laboratory conditions. 

As a first step, the candidate will generate high-quality reference genomes for both microbial communities (bacteria and fungi) and the parental plant populations. Through an innovative coevolutionary experiment, evolved microbial and plant populations will be generated. The PhD candidate will analyze these evolved populations in comparison to their respective parental lines. For microbial genomes, the candidate will investigate structural and point genomic variations. For the evolved plants, sequencing reads will be mapped to the B. rapa reference genome, and allele frequency changes between evolved and parental populations will be assessed. The goal is to determine whether the microbial communities influence plant evolution at the genomic level. Microbial genomic variation will be correlated with plant allele frequencies using Genome-Wide Association Studies (GWAS) to identify potential signs of microbial–plant coevolution or coadaptation. The PhD candidate will also contribute to the analysis of metabarcoding data (fungal and bacterial markers) generated throughout the coevolutionary experiment. These datasets will be produced by another PhD student already working on the project. Therefore, close collaboration and strong interaction between the two students will be essential.

 Due to the close collaboration with Fabrice Legeai (IGEPP (EGI team) / IRISA (Genscale team)) in Rennes, this position requires mobility between Toulouse and Rennes. The PhD candidate will be jointly supervised by the ECOGEN team at INRAE Toulouse (https://www.lipme.fr/en/ecogen-1) and Fabrice Legeai in Rennes. We are looking for candidates with a strong academic background, having completed a five-year Master's degree (3+2) or equivalent (as recognized by NARIC), in Bioinformatics. The ideal candidate will have: i) Solid experience using bioinformatics tools for analyzing bacterial, fungal, and plant genomes ii) Strong skills in statistics and programming, particularly in R and Python (obligatory) iii) Good command of English, with demonstrated ability in scientific writing and communication iv) Proven ability to work effectively as part of a team.

To apply, please send your CV, a motivation letter and your Master’s degree transcripts. Only complete applications will be considered.

Solid skills in bioinformatics and programming in Python and R are obligatory. Skills in population genomics and evolution are also required for this position.

Training and skills

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

How to apply

I send my CV and my motivation letter