Data from: Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts

Coi A, Bigey F, Mallet S, Marsit S, Zara G, Gladieux P, Galeote V, Budroni M, Dequin S, Legras J

Date Published: February 13, 2017

DOI: http://dx.doi.org/10.5061/dryad.j315n.2

 

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Title VinVoile.VQSR.HighQualitybiall.vcf
Downloaded 10 times
Description Compressed (tgz) Vcf file containing a subset of high quality biallelic variant filtered out from the genotyping output file VQSR.vcf produced by GATK, when filtering for only variants corresponding to the best genotyping scored (Indicated with PASS). Population analysis measures (Dxy and Da) are performed on a second subset of this file after filtering genotypes according to allelic depth and genotyping quality with vcftools, with parameters: --minGQ 30 --minDP 10 --maf 0.001 . This filtered data set is used for figure 2C, and Figure S7.
Download VinVoile.VQSR.HighQualitybiall.vcf.tgz (17.40 Mb)
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Title Evaluation of variant impact on protein functions according to SIFT(4G)_ High quality biallelic variant set
Downloaded 7 times
Description Compressed file containing the impact of each variant on each annotated transcript, inferred with SIFT4G, for the file including all variant (VinVoile.VQSR.HighQualitybiall.vcf).
Download only_annotated_VinVoile.VQSR.HighQuality_...sv.tgz (1.042 Mb)
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Title Tableau-Genes retained by each tests-dyad
Downloaded 10 times
Description This table contains all genes pointed by one list : PCA differentiating flor yeast from other strains (Allyeast-set), Dxy (VinVoile.VQSR.HighQualitybiall.vcf filtered for min genotype quality of 30 and sequence depth of 10), Da (same as Dxy), XPCLR (for Jura and Spanish populations), 20% Best potentially damaging SNPs (according to SIFT) differentiating wine and flor PCA, codeml value. This table contains data for table S4 and for Figure 3.
Download Tableau-Genes retained by each tests-dyad.xlsx (89.72 Kb)
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Title DTdadi
Downloaded 9 times
Description Demographic inferences (Figure S5a and b): SNP data set for wine and Jura/Hungary flor strains, and wine and Spain/Italy flor strains at dadi format for demographic inference. Obtained with script Vcf-to-dadi.pl
Download DTdadi.zip (212.2 Kb)
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Title Vcf-to-dadi perl script
Downloaded 25 times
Description Demographic inferences (Figure S5a and b): Perl script that converts a vcf file including 2 or 3 pop with Ancestral Allele field (not necessary if folded) to a file for diffusion approximation demographic inference (dadi, Gutenkunst 2015, PLoS Genetics). Requires Bioperl, reference sequence fasta file, and variant file at VCF format (only with strains required for the analysis)
Download Vcf-to-dadi.pl (7.785 Kb)
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Title TranslocationsCompilation_outputs_delly
Downloaded 7 times
Description Compilation of delly V 0.1.1 outputs for each strain. This file contrains only events that occured more than 40 times.
Download TranslocationsCompilation_outputs_delly.txt (35.78 Kb)
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Title XPCLR selection test: Script prepares ms data and runs XPLCR
Downloaded 13 times
Download mstoXPCLR.zip (2.701 Kb)
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Title Data XPCLR of Wine and Spain Italy Flor strain
Downloaded 10 times
Description XPCLR selection test: Data for XPCLR of Wine and Spain and Italy Flor strain recombination rate 403 M. Window= 0.1 cM, window 1kb
Download DTXPCLR-Wine-Spain-italyFlor.zip (607.8 Kb)
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Title Data XPCLR of Wine and France and Hungary Flor strain
Downloaded 13 times
Description XPCLR selection test: Data for XPCLR of Wine and French (Jura) and Hungarian Flor strain recombination rate 403 M. Window= 0.1 cM, window 1kb
Download DTXPCLR-Wine_Jura-HungaryFlor.zip (887.4 Kb)
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Title Combined set of SNPS including wine and flor strains and strains from other origins(Allyeast-set)
Downloaded 12 times
Description Data for Phylogeny and population structure (Figure 1, Figure2A and B). Compressed Vcf file containing a set of biallelic variant with less than 20 % missing position among all strains, obtained from the genotyping of 20 flor and wine strains compared to 82 strains with available genome sequences (obtained from Saccharomyces genome database (http://www.yeastgenome.org/), of from the SGRP project (http://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html) (Liti et al. 2009, Population genomics of domestic and wild yeasts. Nature, 458, 337–41)
Download AssembliesGenowine20%maxmiss.tar.gz (6.493 Mb)
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Title Data for differentiation based method PCA, Dxy, Da
Downloaded 15 times
Description - plink format files AssembliesGenowine.raw and .map for PCA performed with adegenet - Vcf phased data files for each chromosome of flor and wine population - R script utilising on PopGenome performing all analysis of Theta, pi, Dxy (Da = Dxy – (Piwine+piflor)/2 ) on each chromosome datafile).
Download Differentiation-methods.zip (12.67 Mb)
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Title DT FineStructure Flor Wine Champagne
Downloaded 10 times
Description These are the data files used for the FineStructure analysis for the hybrid nature of strains of the Champagne group (Figure S1)
Download DT-FineStructure-Flor-Champagne.tgz (620.4 Kb)
Download README.txt (432 bytes)
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Title Data for Linkage desequilibrium analysis (figureS3)
Downloaded 4 times
Description ped and map files for Flor and wine populations. Files are prepared from phased vcf file . Data used with plink with options --ld-window 1000 --ld-window-kb 50 --ld-window-r2 0 --r2
Download Data_LD.tgz (1.220 Mb)
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Title Data for Estimation of recombination rates (Figure S4)
Downloaded 16 times
Description This data has been used for the genome scan of recombination rate (Figure S4) using a model with hotspot as inplemented in the "INTERVAL" module of LDHAT package. A global estimate of recombination rate has also been estimated for flor strain using PAIRWISE with the module "PAIRWISE" of the same package.
Download Wine-Flor-DT-LDhat.tgz (251.4 Kb)
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Title Data of figure4: Biofilm images used for the evaluation of the impact of each wine and flor allele on biofilm formation
Downloaded 11 times
Description The compressed archive contains the photos and the notice indicating for image its organization.
Download Biofilm_images-figure4.tgz (4.378 Mb)
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Title de-novo draft assemblies
Downloaded 7 times
Description This is a gzip/tar compressed data archive containing the draft contig de-novo assemblies generated in this study. This data is used for phylogenic trees and genes sequence alignments (Figures S2, S6, S8).
Download draft-assemblies.tgz (68.07 Mb)
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When using this data, please cite the original publication:

Coi A, Bigey F, Mallet S, Marsit S, Zara G, Gladieux P, Galeote V, Budroni M, Dequin S, Legras J (2017) Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts. Molecular Ecology 26(7): 2150–2166. http://dx.doi.org/10.1111/mec.14053

Additionally, please cite the Dryad data package:

Coi A, Bigey F, Mallet S, Marsit S, Zara G, Gladieux P, Galeote V, Budroni M, Dequin S, Legras J (2017) Data from: Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.j315n.2
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