Data from: A population genomics insight into the Mediterranean origins of wine yeast domestication

Almeida P, Barbosa R, Zalar P, Imanishi Y, Shimizu K, Turchetti B, Legras J, Serra M, Dequin S, Couloux A, Guy J, Bensasson D, Gonçalves P, Sampaio JP

Date Published: August 3, 2015

DOI: http://dx.doi.org/10.5061/dryad.hm2jf

 

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Title S. cerevisiae whole-genome SNP alignment
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Description This is a gzip/tar compressed data archive containing the concatenated SNP alignment of S. cerevisiae. SNP alignments for each chromosome are also provided, together with the corresponding list of SNP positions.
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Title S. cerevisiae (large dataset) whole-genome SNP alignment with outgroup S. paradoxus, related to Figure S3
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Description This is a gzip/tar compressed data archive containing the concatenated SNP alignment of the large dataset with S. paradoxus as outgroup, related to Figure S3. SNP alignments for each chromosome are also provided, together with the corresponding list of SNP positions.
Download SNP-alignment-largeDataset+Spar.tgz (11.18 Mb)
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Title S. cerevisiae (restricted dataset) whole-genome SNP alignment with outgroup S. paradoxus, related to Figure 3
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Description This is a gzip/tar compressed data archive containing the concatenated SNP alignment of the restricted dataset with S. paradoxus as outgroup, related to Figure 3. SNP alignments for each chromosome are also provided, together with the corresponding list of SNP positions.
Download SNP-alignment-restrictedDataset+Spar.tgz (12.42 Mb)
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Title Structure input file used in Figure 2A
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Description This is a gzip/tar compressed data archive containing the input file used to run Structure v2.3.4 (Pritchard et al. 2000), related to figure 2A. A list file with the positions of the parsimony informative sites used is also provided.
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Title FineStructure input files used in Figure 2B
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Description This is a gzip/tar compressed data archive containing the idfile, phase and recombination input files used to run FineSTRUCTURE Version 2.0.2 (Lawson et al. 2012), related to Figure 2B.
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Title dadi input file used to infer demographic history of Wine and MO populations
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Description The joint allele frequency spectrum of Wine and Mediterranean oak (MO) populations used as input to run the demographic inference in dadi (Gutenkunst et al. 2009). Populations are defined as in the comment lines at the beginning of file.
Download allChr_scer_subset_nonCDS_wine-randMO.dadi (556.5 Kb)
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Title Raw results from VariScan, related to Table 3
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Description This is a gzip/tar compressed data archive containing the results of Variscan v2.0 (Hutter et al. 2006) for the whole-genome alignments considered, related to Table 3.
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Title Raw results from compute (libsequence analysis package), related to Table S2
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Description This is a gzip/tar compressed data archive containing the results of compute from the libsequence analysis package (http://molpopgen.org/) (Thornton 2003), related to Table S2. The archive contains results for coding sequences (CDS) and non-CDS in the Mediterranean oak population (MO) and the wine population (wine), with one file per locus. The SGD systematic name is used to identify CDS and the nucleotide positions are used to identify non-CDS.
Download libsequence-analysis-compute-results.tgz (2.646 Mb)
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Title Raw results from polydNdS (libsequence analysis package), related to Table S2
Downloaded 14 times
Description This is a gzip/tar compressed data archive containing the results of polydNdS from the libsequence analysis package (http://molpopgen.org/) (Thornton 2003), related to Table S2. The archive contains results for coding sequences (CDS) in the Mediterranean oak population (MO) and the wine population (wine), with one file per locus. The SGD systematic name is used to identify CDS.
Download libsequence-analysis-polyDnDs-results.tgz (2.223 Mb)
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Title de-novo draft assemblies
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Description This is a gzip/tar compressed data archive containing the draft contig de-novo assemblies generated in this study.
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Title Whole-genome SNP phylogeny (restricted dataset), related to Figure 3
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Description RAxML phylogenetic tree obtained from the whole-genome SNP alignment of the restricted dataset and with S. paradoxus as outgroup, related to Figure 3.
Download raxml-tree-snp-restricted-dataset.nwk (6.379 Kb)
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Title Whole-genome SNP phylogeny (restricted dataset), related to Figure S3
Downloaded 9 times
Description RAxML phylogenetic tree in newick format, obtained from the whole-genome SNP alignment of the restricted dataset and with S. paradoxus as outgroup, related to Figure 3.
Download raxml-tree-snp-large-dataset.nwk (8.31 Kb)
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Title Multilocus tree including the Chinese strains, related to Figure S4
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Description Neighbor-Joining tree in newick format, inferred from a concatenated alignment of 13 loci and including Chinese strains, related to Figure S4
Download multilocus-tree-with-Chinese-isolates.nwk (9.424 Kb)
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Title Raw data of microsatelite genotypes used in figure S1
Downloaded 30 times
Description This table contains 3 columns indicating the strain name, the locus name and the allele values (size bins). When only one allele was found the value has been doubled as the stain is assessed to be diploid. For some strains additional values can be observed (ie Bread strains). For such cases, additional lines are added to described all values found at this loci.
Download DTfinaleOctobre2010forArchive.xls (407.0 Kb)
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When using this data, please cite the original publication:

Almeida P, Barbosa R, Zalar P, Imanishi Y, Shimizu K, Turchetti B, Legras J, Serra M, Dequin S, Couloux A, Guy J, Bensasson D, Gonçalves P, Sampaio JP (2015) A population genomics insight into the Mediterranean origins of wine yeast domestication. Molecular Ecology 24(21): 5412–5427. http://dx.doi.org/10.1111/mec.13341

Additionally, please cite the Dryad data package:

Almeida P, Barbosa R, Zalar P, Imanishi Y, Shimizu K, Turchetti B, Legras J, Serra M, Dequin S, Couloux A, Guy J, Bensasson D, Gonçalves P, Sampaio JP (2015) Data from: A population genomics insight into the Mediterranean origins of wine yeast domestication. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hm2jf
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