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Two postdoctoral positions in yeast comparative and population genomics are available:

 

Position 1 -

Trait heritability variation across a whole subphylum

A major challenge in current biology is to dissect the origins of the amazing phenotypic diversity observed in natural populations. Over the last decades, trait mapping in humans and other model eukaryotes have provided valuable insights but remain unsatisfying because uncovered causal loci explain only a minority of the heritability. In this respect, yeast species are attractive organisms for investigating genotype-phenotype associations because, inter alia, of their small and compact genomes. Here, the goal is to obtain an all-inclusive view of the genetic and phenotypic diversity across a whole subphylum: the Saccharomycotina yeasts. In this respect, the project will focus on (i) the genetic diversity within natural populations of various non-conventional yeast species, (ii) the mutational and recombinational landscapes within these species, and (iii) the phenotype-genotype relationships within these yeasts through QTL mapping. Altogether, it will undoubtedly contribute seminal conceptual advances to understanding the biology that lies between genotype and phenotype.

 References:

1. Brion C, Legrand S, Peter J, Caradec C, Pflieger D, Hou J, Friedrich A, Llorente B, Schacherer J. Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts. BioRxiv. 2017. [doi: https://doi.org/10.1101/117895]

2. Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C, Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J, Aury JM. de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. Gigascience. 2017. [doi: 10.1093/gigascience/giw018]

3. Brion C, Pflieger D, Souali-Crespo S, Friedrich A, Schacherer J. Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. Mol Biol Cell. 2016. [doi: 10.1091/mbc.E15-12-0816]

4. Peter J, Schacherer J. Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale. Yeast. 2016. [doi: 10.1002/yea.3142]

5. Friedrich A, Jung P, Reisser C, Fischer G, Schacherer J. Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast. Mol Biol Evol. 2015. [doi: 10.1093/molbev/msu295]

 

Position 2 -

Inheritance, expressivity and penetrance in natural populations

To date, it is clear that the understanding of traits is not only hampered by non-heritable factors such as the environment and epigenetic variation, but also confounded by the lack of complete knowledge concerning the genetic components of traits. More than a century after the rediscovery of Mendel’s law, the genetic architecture of traits still resists generalization. First, this is increasingly evident as shown by recent genome-wide association studies, where identified causal loci explained relatively little of the heritability of most complex traits, leading to the “missing heritability”. Second, we also have recently shown that monogenic mutations can display a significant, variable and continuous phenotypic expression, called expressivity, across different genetic backgrounds. Altogether, these observations clearly indicate that a better understanding of the genetic architecture of traits requires a deeper knowledge of the variability of the phenotypic effect of genetic variants across an entire population. The project is to marry classical but high-throughput genetic methods with new approaches based on population genomics to connect the phenotypic and allelic landscape by taking advantage of the powerful budding yeast model system. With our recent completion of the whole genome resequencing of over 1,011 natural isolates (http://1002genomes.u-strasbg.fr/), plus the accompanying phenotyping efforts, we have currently one of the best understanding of the natural genetic and phenotypic diversity of any eukaryote model system to date. These datasets will lay the foundation of the project, which aims to dissect the genetic expressivity hidden behind the phenotypic landscape of an entire natural population.

References:

1. Schacherer J. Beyond the simplicity of Mendelian inheritance. CR Biol. 2016. 339: 284-8. [doi: 10.1016/j.crvi.2016.04.006]

2. Hou J, Sigwalt A, Fournier T, Pflieger D, Peter J, de Montigny J, Dunham MJ, Schacherer J. The hidden complexity of Mendelian traits across natural yeast populations. Cell Rep. 2016. [doi: 10.1016/j.celrep.2016.06.048]

3. Hou J, Friedrich A, Gounot JS, Schacherer J. Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast. Nature Commun. 2015. [doi: 10.1038/ncomms8214]

4. Hou J, Friedrich A, de Montigny J, Schacherer J. Chromosomal rearrangements as a major mechanism in the onset of reproductive isolation in Saccharomyces cerevisiae. Curr Biol. 2014. [doi: 10.1016/j.cub.2014.03.063]