Société Française de Bioinformatique

Mots-Clés

Génomique évolutive S. cerevisiae Domestication Variation génétique délétère

Description

Context: Domestication leads to radical phenotypic changes and may have dratic consequences on species’ genetic variation. For instance, domesticated species carry increased levels of deleterious mutations than their wild relatives – a phenomena known as the cost of domestication. By causing the loss or altering normal gene function, deleterious mutations may reduce organismal fitness and therefore impact crop and stock productivity.
Saccharomyces cerevisiae is the most promient yeast species used in industrial fermentation processes such as wine-making, brewering and baking. This species is one of the earliest domesticated species. Research has shown that for instance the rate of sporulation in domesticated strains is dimished relative to that of wild strains. Nonetheless, comprehensive studies on the effect of domestication and the complexities of S. cerevisiae life-cycle on the distribution of deleterious variation are still lacking.

Objectives: We propose a M1 intership (6-8 weeks) to a student interested in understanding the consequences of domestication on the deleterious mutation landscape of S. cerevisiae. The student will specifically contribute to (1) implement a pipeline to quantify the levels of deleterious variation within genomes and across different S. cerevisiae clades using tools like SIFT, GERP++ and Direct Coupling Analysis and genotype matrices in the form of VCF files, (2) associate strain-specific measures of deleterious mutational burden with genomic windows targeted by artificial (positive) selection and (3) growth phenotypes to assess the impact of deleterious mutation accumulation on fitness. There is also the possibility of developing new mutational burden statistcis by integrating genomes with transcriptomes.

This project represents a unique opportunity to unravel how domestication has shaped the genetic burden of deleterious mutations in Saccharomyces cerevisiae—one of the earliest and most industrially vital domesticated species—by integrating computational methods, statistics and whole-genome data.

Environment:

1. A stimulating research environment within a team recognized for its expertise in functional genomics, yeast genetics and genotype-to-phenotype relatioships;
2. Supportive and attentive supervision;
3. Local high performance computing facilities;
4. The lab has a long-standing history of research in S. cerevisiae, resulting in a large collection of natural isolates and large-scale multi-omic datasets.

Requirements: M1 students of Masters in Computational Biology, Genomics, Bioinformatics