10.5061/DRYAD.BT5V6
Clowers, Katie J.
University of Wisconsin-Madison
Will, Jessica L.
University of Wisconsin-Madison
Gasch, Audrey P.
University of Wisconsin-Madison
Data from: A unique ecological niche fosters hybridization of oak-tree and
vineyard isolates of Saccharomyces cerevisiae.
Dryad
dataset
2015
Environmental stress
ecological divergence
allele-specific expression
2015-10-29T14:51:34Z
2015-10-29T14:51:34Z
en
https://doi.org/10.1111/mec.13439
191437160 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Differential adaptation to distinct niches can restrict gene flow and
promote population differentiation within a species. However, in some
cases the distinction between niches can collapse, forming a hybrid niche
with features of both environments. We previously reported that
distinctions between vineyards and oak soil present an ecological barrier
that restricts gene flow between lineages of Saccharomyces cerevisiae.
Vineyard isolates are tolerant to stresses associated with grapes while
North American oak strains are particularly tolerant to freeze-thaw
cycles. Here, we report the isolation of Saccharomyces cerevisiae strains
from Wisconsin cherry trees, which display features common to vineyards
(e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome
sequencing revealed that the isolated strains are highly heterozygous and
represent recent hybrids of the oak x vineyard lineages. We found that the
hybrid strains are phenotypically similar to vineyard strains for some
traits, but are more similar to oak strains for other traits. The cherry
strains were exceptionally good at growing in cherry juice, raising the
possibility that they have adapted to this niche. We performed
transcriptome profiling in cherry, oak, and vineyard strains and show that
the cherry-tree hybrids display vineyard-like or oak-like expression,
depending on the gene sets, and in some cases the expression patterns
linked back to shared stress tolerances. Allele-specific expression in
these natural hybrids suggested concerted cis-regulatory evolution at sets
of functionally regulated genes. Our results raise the possibility that
hybridization of the two lineages provides a genetic solution to the
thriving in this unique niche.
DC6.vcfSNPs identified in cherry strain DC 6 using GATK. SNPs were called
on both DC 6 and DC 16, then sites for each strain were separated, and all
non-SNP positions removed using
VCFtools.DCM6.PASS_SNPs.NonREF.recode.vcfDC16.vcfSNPs identified in cherry
strain DC 16 using GATK. SNPs were called on both DC 6 and DC 16, then
sites for each strain were separated, and all non-SNP positions removed
using VCFtools.DCM16.PASS_SNPs.NonREF.recode.vcfRNAseqCountsRead counts
for each gene across all strains analyzed in
EdgeR.Counts.txtOakvVintopTagsEdgeR output for differentially expressed
genes in oak versus vineyard strains.DCtopTagsEdgeR output for DC-specific
differentially expressed genes.DCvOaktopTagsEdgeR output for
differentially expressed genes in DC versus oak strains.DCvVintopTagsEdgeR
output for differentially expressed genes in DC versus vineyard
strains.PCAsnpsVCF file containing all of the genotype data used for
PCA.25Strains_latest_snp_R64-1-1_NonREF.recode.vcfPCAmap Filemap file
created for PCA.25Strains.mapPCA ped fileped file used for
PCA25Strains.pedPCArawraw file for PCA analysis25Strains.rawCh4
alignmentAlignment file of Chromosome 4 sanger sequencingCh4.nexChr4 tree
fileMr. Bayes tree file for Chromosome 4Ch4.nex.con.treCh9
alignmentAlignment file of Chromosome 9 sanger sequencingCh9.nexCh10
alignmentAlignment file of Chromosome 10 sanger sequencingCh10.nexCh9 tree
fileMrBayes tree file for Chromosome 9Ch9.nex.con.treCh10 tree fileMrBayes
tree file for Chromosome 10Ch10.nex.con.tre