Temporary position OT-28112
Bioinformatics engineer for large-scale genomic data analysis in bees
31326 Castanet Tolosan
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
You will be welcomed into the GenPhySE unit at INRAE in Toulouse, as part of the BeeGees team working on the genetic diversity and genomics of honey bees (http://genphyse.inrae.fr/poles). Your work will focus on analysing sequencing data as part of the FecDist project, which studies bee fertilisation in the natural environment with a view to controlling the male pathway in selection schemes.
Project description
Reproduction in the honeybee Apis mellifera has characteristics that are unique among farmed species. The queen, the only fertile female in a colony, makes one or more nuptial flights a few days after her birth and mates in flight with several males — the drones — whose sperm she stores in her spermatheca. In order to select the genetic strains they are interested in, breeders saturate the environment by placing drone hives, producing large numbers of drones with the desired genetics. However, as many beekeepers use the same strategy at the same time, with different genetic backgrounds and breeding interests, the effectiveness of this practice is questionable. In order to test the effectiveness of queen fertilisation control, we have placed drone hives at various distances around a fertilisation apiary. The detection of alleles specific to different males will be carried out by sequencing complete genomes with ‘short reads’, both by sequencing worker bees from fertilised queens and males from male hives. Two approaches will be considered: (i) the search for diagnostic alleles at SNP markers and (ii) the analysis of alleles of the sex-determining gene in honey bees, complementary sex determiner (csd), for which more than 100 different coding alleles are known.
You will be specifically responsible for analysing massive sequencing data. Data available in the laboratory for more than 1,000 haploid drone genomes will be used to refine our knowledge of the hypervariable csd locus. Analysis of the FecDist project's mixed sequencing data will enable the identification of SNP alleles specific to each male origin and their detection in the sequences of worker daughters of fertilised queens.
Remote working is possible, with a maximum of two days per week.
Training and skills
Knowledge required: bioinformatics
Appreciated experience: Experience with high-throughput sequencing data processing and the use of Linux computing clusters. Experience with reproducible workflow systems (Nextflow, Snakemake or equivalent) and an interest in bees/beekeeping would be an advantage.
Skills sought: team work and collaboration
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
All persons employed by or hosted at INRAE, a public research establishment, are subject to the Civil Service Code, particularly with regard to the obligation of neutrality and respect for the principle of secularism. In carrying out their functions, whether or not they are in contact with the public, they must not express their religious, philosophical or political convictions through their behaviour or by what they wear. > Find out more: fonction publique.gouv.fr website (in French)