ArticleMolecular biology and evolution2014
A high-definition view of functional genetic variation from natural yeast genomes.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 papers.
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174 citing papers in PubMed, 301 citations in OpenAlex.
- Paralogs of thebioRxiv : the preprint server for biology · 2026Article
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- Genotypic and Phenotypic Diversity of Maudiozyma humilis: The Multiple Evolutionary Trajectories of a Domesticated Yeast.Genome biology and evolution · 2026Article
- Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution.Nature ecology & evolution · 2026Article
- From one genome to thousands, and beyond.FEMS yeast research · 2026Review
- Predicting natural variation in the yeast phenotypic landscape with machine learning.Molecular systems biology · 2025Article
- Footprints of Human Migration in the Population Structure of Wild Baker's Yeast.Molecular ecology · 2025Article
- Refining the resolution of the yeast genotype-phenotype map using single-cell RNA-sequencing.eLife · 2025Article
- Core gene set of the speciesbioRxiv : the preprint server for biology · 2025Article
- Horizontal Transfer and Recombination Fuel Ty4 Retrotransposon Evolution in Saccharomyces.Genome biology and evolution · 2025Article
- ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel.Nucleic acids research · 2025Article
- Sterol-Targeted Laboratory Evolution Allows the Isolation of Thermotolerant and Respiratory-Competent Clones of the Industrial Yeast Saccharomyces cerevisiae.Microbial biotechnology · 2025Article
- Impact of inter-species hybridisation on antifungal drug response in the Saccharomyces genus.BMC genomics · 2024Article
- Phenotyping of a new yeast mapping population reveals differences in the activation of the TORC1 signalling pathway between wild and domesticated yeast strains.Biological research · 2024Article
- Article
- Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade.G3 (Bethesda, Md.) · 2023Article
- Single nucleotide polymorphisms associated with wine fermentation and adaptation to nitrogen limitation in wild and domesticated yeast strains.Biological research · 2023Article
- Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation.Journal of molecular evolution · 2023Review
- Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.iScience · 2023Article
114 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 7 institutions in 5 countries.
Funding
Abstract
The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies.
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