Research-oriented Master 2 internship: Metagenomic analysis of honeys as a tool for traceability and monitoring of the infestation level of the varroa parasite

Background: The host lab has extensive experience in the genomic characterization of honey bees (Apis mellifera) used by French beekeepers. As part of the MALLAURIE project – Honey and bees: the contribution of sequencing based solely on hive products to more international and ethical sampling – we aim at obtaining honey bee genetic data via a non-lethal strategy, through sequencing DNA extracted from honey.

Objective of the internship: The aim of the internship will be to develop a metagenomic approach for the characterisation of DNA present in honey, other than belonging to honey bees. The focus will be on two other major types of organisms: plants and the varroa parasite.

Thanks to a collaboration with the UMR Abeilles & Environnement (INRAE Avignon), we have set up a pilot study following hives that were migrated on different floral resources over the course of the season, including different species of varying pollen and nectar content, and with a general expectation of an increase in varroa infestation during the season. In addition, we have extracted DNA from a large number of honey samples of various origins.

All the samples are anonymized before sequencing. The student will lead the investigation in order to propose a potential geographical origin of the honeys using the sequencing reads from the plants. Some additional questions may be investigated depending on the progress made during the internship.

Available data :

At the start of the internship, we will have around 80-100 honey samples sequenced at relatively low coverage on 2 to 3 MiSeq runs (~50 of which will come from the pilot study carried out with INRAE in Avignon), as well as a full NovaSeq run for high-coverage sequencing of 10-20 samples.

Ideal candidate :

The master student will have a certain taste for exploring large datasets and bioinformatics, with the use of a command-line computing softwares, ideally with a good knowledge of at least a scripting language (R, python, bash). Scientific knowledge in genomics and/or population genomics would be appreciated.

Hosting structure and location :

You will be hosted in the Cytogene team of the UMR GenPhySE at the INRAE Occitanie-Toulouse center (Castanet-Tolosan, France). The laboratory is easily accessible from downtown Toulouse (metro line B + “L6” express bus).

Internship period and compensation:

  • The internship will ideally be between January and June 2024, with the possibility of adjustment depending on the student’s availability (e.g. March to September period).
  • A stipend is associated with this internship (contractual amount at INRAE: 4,05€/hour, i.e. ~550€/month on a 35-hour per week basis).

To apply contact Supervisors: Thibault Leroy, (main supervisor) Kamila Tabet,

References (more available upon request):

Bovo, S., Utzeri, V.J., Ribani, A. et al. Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity. Sci Rep 10, 9279 (2020).

Wragg, D., Eynard, S. E., Basso, B., Canale-Tabet, K., Labarthe, E., Bouchez, O., Bienefeld, K., Bieńkowska, M., Costa, C., Gregorc, A., Kryger, P., Parejo, M., Pinto, M. A., Bidanel, J-P,

Servin, B., Le Conte, Y., & Vignal, A. (2022). Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones. Molecular Ecology Resources, 22, 3068– 3086.

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