Mots-Clés

Population genomics variant calling NGS comparative genomics adaptation

Description

Description and objectives:

In the context of global changes, it is urging to protect wild environments but also to promote the conservation of biodiversity in agri-food environments. It is therefore necessary to understand domestication, i.e. the process by which humans influence the evolution of species for their own use. While the evolution of domesticated plant and animal species is well studied, microbe domestication has been poorly studied apart from a few microbial model species. 

The Post-Doc will investigate the genomic diversity of two yeast species commonly found in sourdough bread, Kazachstania humilis and Kazachstania bulderi. These two species are maintained by different types of bread-making practices, and thus may have undergone different selection pressure and domestication routes. Although the Kazachstania genus is one of the closest genetically related genus of the well-known genus Saccharomyces, it is still poorly explored. The candidate will take advantage of a large strain collection of these two species built for more than 10 years of participatory research in our lab, including strains isolated world-wide as well as an unique collection of yeast collected over years in a wide diversity of French bakers. He will be able to :

• Compare and characterize the genomes of these two species (e.g., loss or/and gain of functions, copy number variations, structural variations, synteny).
• Assess the genomics diversity of each species.
• Reconstruct the evolutionary trajectories of sourdough strains with a particular interest in identifying genetic signatures of domestication.
• Investigate genomic evolution over sourdough backslopping from an adaptive laboratory evolution that will be conducted in our lab, to identify possible flour adaptation as well as yeast-yeast co-evolution genetic signature.

The candidate will  be supervised by a bioinformation (Hugo Devillers). He will be in charge of the NGS data management and he will have to build a technical and scientific monitoring to develop and adapt the analysis pipelines to the different questions of this project. In addition to managing his own scientific project, he will benefit from a collaboration with a second Post-Doc analyzing the phenotypic diversity of the same strains to investigate the link between genotype and phenotype.

Context

The Post-Doc will be part of the ADEL team (Adaptation, Diversity and EvoLution of yeasts) in the URM SPO (INRAe-Institut Agro, Univ Montpellier). This project is part of the ANR project IDOK. The candidate will benefit from the skills and the knowledge acquired for years in both sourdough breadmaking and yeast genomics and will interact with the different members of the teams involved in this project as well as another Post-Doc who will be responsible for phenotypic investigations. He will benefit from the network of national and international collaborators of the ADEL team as well as the rich scientific environment of Montpellier.

Education and qualifications

The candidate should have a PhD in bioinformatics/computer sciences or population genomics.

Essential skills/knowledges:

• Working under linux environment
• Mastering a scripting language
• Having a previous experiences in NGS analysis
• Reading writing in English
• Team working

Desirable skills/knowledges:

• Yeast genomics
• Population genomics
• Statistics

Gross, duration and funding

This position is fully funded for 2 years by the ANR project IDOK. Gross monthly salary will be between 2490 € and 2643 € according to the past experience of the candidate. The successful candidate is supposed to move to France ideally from January 2024.