Domestication reprogrammed the budding yeast life cycle

Matteo De Chiara; Benjamin Barré; Karl Persson; Amadi Onyetuga Chioma; Agurtzane Irizar; Joseph Schacherer; Jonas Warringer; Gianni Liti

Variant matrix for GWAS generated by Plink in .bed, .bim and .fam formats. The matrix contains all biallelic positions known for the sequenced isolates with MAF > 5% as well as LOF (encoded as "1" for predicted LOF and "2" for predicted functional gene), presence and absence (encoded as "1" for gene presence and "2" for gene absence gene) and CNVs (encoded as "0", "1", "2" respectively for absence, 0.5-1 copy and multiple copies). The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.08.939314 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.08.939314 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.08.939314 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.08.939314 doi: bioRxiv preprint b, Distribution of the asci production at 24 h and 72 h for the four subclades within the Wine/European clade. Feral isolates regained a high sporulation efficiency. The S. boulardii subgroup has completely lost the ability to sporulate. Box: IQR. Whiskers: 1.5 X IQR. c, Sporulation ability in water. S. cerevisiae and S. paradoxus wild strains sporulate well, but S. cerevisiae domesticated isolates do not. Boxplot of the distribution of asci production (only sporulating isolates, i.e. asci production > 0) after 8 days in water. Box: IQR. Whiskers: 1.5x IQR. d, Fraction of S. cerevisiae domesticated, wild and S. paradoxus isolates able to sporulate (i.e. asci production > 0 after 8 days) in water. . Several SNPs are linked. Lower panel: Sporulation of strains homo-or heterozygotic for the five IME1 SNPs associated to sporulation. Box: IQR. Whiskers: 1.5x IQR. All minor SNPs except H78R associate to poor spore production. c, H78R is restricted to a subset of domesticated clades and promotes spore production. Box: IQR. Whiskers: 1.5x IQR.