Genomes assembly and phasing: towards a better view of the evolutionary history of yeast

Comprehensive genomic variant maps are essential for exploring genome evolution as well as its phenotypic consequences in natural populations. In this context, yeasts, with their small and compact genomes as well as their various natural and anthropized niches, represent valuable models. To date, short-read sequencing has provided genome- and species-wide views of primarily single nucleotide and copy number variants within many yeast species, and in particular in Saccharomyces cerevisiae for which more than 1,000 natural isolates were already sequenced using Illumina technology. More recently, the emergence of long-read sequencing, such as Oxford Nanopore technologies, provides an unprecedented opportunity to investigate underexplored aspects of genome variability. Indeed, through the construction of highly contiguous genome assemblies, the efficient detection of structural variants (e.g. long indels, inversions, translocations) becomes possible, and can lead to a better understanding of phenotypic variation. In addition, the ability of long reads to link many variable elements together opens the way for the phasing of non-homozygous individuals. Exploring the haplotypes of polyploid isolates of Saccharomyces cerevisiae from different beer-brewing clades allowed for example to gain better insight into the differential evolutionary trajectories of this polyphyletic population. Moreover, by comparing fully phased genes, we could highlight independent domestication, evolution, and adaptation events across subpopulations.