Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole-genome sequencing and phenotyping of 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species-wide phenotypic landscape of this yeast. Genomic analyses support a single 'out-of-China' origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms. A common feature is the extensive loss of heterozygosity, which represents an essential source of inter-individual variation in this mainly asexual species. Most of the single nucleotide polymorphisms, including experimentally identified functional polymorphisms, are present at very low frequencies. The largest numbers of variants identified by genome-wide association are copy-number changes, which have a greater phenotypic effect than do single nucleotide polymorphisms. This resource will guide future population genomics and genotype-phenotype studies in this classic model system.
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Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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Site | Modification | Modifier | Source | Reference |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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File | Description | |
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1011Matrix.gvcf.bz2 | All SNPs and indels called at the population level of the 1011 yeast genomes in gzip2 format. From Peter J, et al. Nature (2018) PMID:29643504. | |
genesMatrix_CopyNumber.tab.gz | Estimated copy number (CN) for each pangenomic ORF, per isolate. Values are given for haploid genome, so that non-integer values can be found (different CN on homologous chromosomes). From Peter J, et al. Nature (2018) PMID:29643504. | |
1011Assemblies-filesize-wc.txt | File size and wordcount of the 1011 yeast genome assemblies (original name GENOMES_ASSEMBLED-filesize-wc.txt). From Peter J, et al. Nature (2018) PMID:29643504. | |
1011DistanceMatrixBasedOnORFs.tab.gz | For each couple of strains, the value is the number of ORFs which are present only in one out of the two isolates. From Peter J, et al. Nature (2018) PMID:29643504. | |
genesMatrix_Frameshift.tab.gz | For each isolate, the presence/absence (1/0) of homozygous frameshift is reported in each gene, based on the number of bases affected by indels. From Peter J, et al. Nature (2018) PMID:29643504. | |
1011DistanceMatrixBasedOnSNPs.tab.gz | For each pair of strains, the value is the SNPs-based percentage of non-identical bases. Heterozygous differences were half-weighted compared to the homozygous differences. From Peter J, et al. Nature (2018) PMID:29643504. | |
phenoMatrix_35ConditionsNormalizedByYPD.tab.gz | Growth ratio between 35 stress conditions and standard YPD medium 30C for 971 isolates. From Peter J, et al. Nature (2018) PMID:29643504. | |
1011-yeast-genomes.README | Information about the 1011 yeast genomes from Peter J, et al. Nature (2018) PMID:29643504. | |
md5.txt | MD5SUM file checksums. From Peter J, et al. Nature (2018) PMID:29643504. | |
1011Assemblies-checksum-md5.txt | MD5SUM sequence checksums of the 1011 yeast genome assemblies (original name GENOMES_ASSEMBLED-checksum-md5.txt). From Peter J, et al. Nature (2018) PMID:29643504. |