Scopel, E.F.C, Hose J., Bensasson D., Gasch, A.P. Genetic variation in aneuploidy prevalence and tolerance across the Saccharomyces cerevisiae phylogeny

Data tables, alignments, trees and scripts used for phylogenetic and logistic regression (glm) analysis of aneuploidy, genetic clade, ecology, ploidy and heterozygosity in S. cerevisiae

Bensasson, D., Dicks, J., Ludwig, J.M., Bond, C.J., Elliston, A., Roberts, I.N., James, S.A., 2019. Diverse lineages of Candida albicans live on old oaks. Genetics Genetics 10.1534/genetics.118.301482

Data for ploidy and admixture analysis in Candida albicans

Bensasson, D., Dicks, J., Ludwig, J.M., Bond, C.J., Elliston, A., Roberts, I.N., James, S.A., 2018. Diverse lineages of Candida albicans live on old oaks. Genetics (in press). Previously in: bioRxiv 341032. https://doi.org/10.1101/341032

Bensasson etalTableS1.xlsx

Table S1 referred to in the Bensasson et al 2018 paper.

Bensasson_etalTableS3.tsv

Table S3 referred to in the manuscript. This is a table in text format with tab separated values summarizing heterozygosity analyses for every strain. This includes exact counts of high quality heterozygous base calls (highQualityHetCount); the total length of high quality sequence (highQualityLength; bases with a phred-scaled quality score over 40); the proportion of high quality heterozygous sites; the length of regions that have undergone Loss of Heterozygosity (LOHlength) assessed in 100 kb windows; heterozygosity analysis after excluding LOH regions, centromeres and annotated repeats (annotationLohFilteredHetCount, annotationLohFilteredLength, annotationLohFilteredHeterozygosity); heterozygosity analysis after excluding LOH regions, centromeres and annotated repeats, and regions with more than double the expected read depth (depthFilteredHetCount, depthFilteredLength, depthFilteredHeterozygosity); heterozygosity analysis at 948,860 nucleotide sites that are common to all strains (sitesIn950kbHetCount, sitesIn950kbLength, sitesIn950kbHeterozygosity).

bchr1.mfa.zip to bchrR.mfa.zip

The whole chromosome alignments of 62 strains that were concatenated (using alcat.pl) and used to generate the genome-wide phylogeny in Figure 2a. Note that all insertions relative to the reference strain SC5314 haplotype A version 22 (GCF_000182965.3 from the NCBI reference database) were excluded. As a result, these alignments are on the same coordinate system as the reference and therefore it's corresponding annotations. These sequences were generated by mapping Illumina reads to a reference, therefore as well as insertions, large insertions, duplications, and all other rearrangements will be missed. Low quality sequence (phred-scaled quality below 1 in 10,000, ie q40) is represented with "n". Heterozygous sites are represented using IUPAC ambiguity codes.

Alignments of Hirakawa et al (2015) genomes

Our whole chromosome alignments of the short-read genome data published in Hirakawa et al (2015; doi: 10.1101/gr.174623.114) are the example dataset (chr1.mfa to chrR.mfa) in faChrompaintData/. They were generated in the same way as the bchr*.mfa.zip alignments.

Tilakaratna, V., Bensasson, D., 2017. Habitat Predicts Levels of Genetic Admixture in Saccharomyces cerevisiae. G3: Genes, Genomes, Genetics g3.117.041806. https://doi.org/10.1534/g3.117.041806

CEN1.tree to CEN16.tree

These are 16 neighbour joining F84 distance trees in Newick format: one for each of 16 centromere loci in Saccharomyces cerevisiae. The bootstrap values shown are from a total of 10,000 bootstraps, and trees are unrooted. The 80 S. cerevisiae strains shown in each tree were completely homozygous and are fully described in Table S1 of Tilakaratna and Bensasson.

CEN1forcbyc.gfa to CEN1forcbyc.gfa

These are 16 alignments in gapped fasta format for centromeres and flanking DNA used to generate the trees.

EBI-ENA Data Archive Scerevisiae DB.tsv

Chapter 2 Footprints of Human Migration in the Population Structure of Wild Baker's Yeast

Supplemental tables 1-8: PenaCh2_SupplementalTables.xlsx

Chapter 3 Climate can predict the species ranges of sympatric yeasts from forests

Supplemental tables 3.1-3.5: PenaCh3_SupplementalTables.xlsx

Ward, A.K. (2025). Developing the wine yeast Lachancea thermotolerans as a model for evolutionary genomics (Publication No. 31846584)[Doctoral dissertation, University of Georgia]. ProQuest Dissertations and Theses Global.

Data and supplementary tables for Audrey Ward's 2025 dissertation "Developing the wine yeast Lachancea thermotolerans as a model for evolutionary genomics" at the University of Georgia under the direction of Douda Bensasson.