OakvVintopTags

EdgeR output for differentially expressed genes in oak versus vineyard strains

Data from: A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae.

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.vcf

SNPs 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

Ch10 alignment

Alignment file of Chromosome 10 sanger sequencin

DCtopTags

EdgeR output for DC-specific differentially expressed genes

Ch9 tree file

MrBayes tree file for Chromosome

PCAraw

raw file for PCA analysi

DCvVintopTags

EdgeR output for differentially expressed genes in DC versus vineyard strains

DC16.vcf

SNPs 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

Chr4 tree file

Mr. Bayes tree file for Chromosome