Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA152665 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Saccharomyces pastorianus is the yeast used to make lager beer; it is known to be an interspecific hybrid formed by the fusion between S. cerevisiae and S. bayanus genomes. This data set queries 17 S. pastorianus strains, collected at various times over the last 125 years from various breweries located in different geographical locations, which were obtained from CBS and DBVPG culture collections. The data in this set represent array-CGH experiments performed with these strains, using "2-species" custom Agilent arrays (the "2-species" arrays contain probes spaced every ~2 kb across the whole genomes of both S. cerevisiae and S. bayanus; the probes are unique and specific for each genome). The data set also contains 3 self-self hybridizations (S. cerevisiae + S. bayanus DNA mixed together in equimolar amounts, then labeled green or red in separate reactions, then hybridized to the "2-species" arrays) used for normalization in CGH-Miner analysis. A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
2008-07-23 | GSE12177 | GEO
Project description:Four hybrid yeast strains isolated from a variety of industrial substrates were hybridized to an array-CGH platform containing probes to query the whole genomes of seven different Saccharomyces species. For most of the strains we found evidence of multiple interspecific hybridization events and multiple introgressed regions. The strains queried were GSY205 (isolated from a cider fermentation), GSY505 (a contaminant from a lager beer fermentation), GSY2232 (a commercial wine yeast strain), and GSY312 (a commercial lager beer strain). Additionally, 3 different rare viable spores derived from laboratory-created interspecific S. cerevisiae-S. bayanus (aka S. uvarum) hybrids were queried, before and after evolution in chemostats, via S. cerevisiae-S. bayanus microarrays.
2016-12-01 | GSE35549 | GEO
Project description:Hybrid progeny can enjoy increased fitness and stress tolerance relative to their ancestral species, a phenomenon known as hybrid vigor. Though this phenomenon has been documented throughout the Eukarya, evolution of hybrid populations has yet to be explored experimentally in the lab. To fill this knowledge gap we created a pool of Saccharomyces cerevisiae and S. bayanus homoploid and aneuploid hybrids, and then investigated how selection in the form of incrementally increased temperature or ethanol impacted hybrid genome structure and adaptation. During 500 generations of continuous ammonia-limited, glucose-sufficient culture, temperature was raised from 25C to 46??C. This selection invariably resulted in nearly-complete loss of the S. bayanus genome, although the dynamics of genome loss differed among independent replicates. Temperature-evolved isolates were significantly more thermal tolerant and exhibited greater phenotypic plasticity than parental species and founding hybrids. By contrast, when the same hybrid pool was subjected to increases in exogenous ethanol from 0% to 14%, selection favored euploid S. cerevisiae x S. bayanus hybrids. Ethanol-evolved isolates exhibited significantly greater ethanol tolerance relative only to S. bayanus and one of the founding hybrids tested. Adaptation to thermal and ethanol stress manifested as heritable changes in cell wall structure demonstrated by resistance to zymolyase or micafungin treatment. This is the first study to show experimentally that the fate of interspecific hybrids critically depends on the type of selection they encounter during the course of evolution. Array-CGH was performed on the S. cerevisiae parent strain CEN.PK (GSY2160), the S. bayanus parent strain CBS7001 (GSY2161) and on the F1 interspecific hybrid resulting from mating the 2 parents (GSY2168). Additionally, three rare viable spores obtained after sporulation of the F1 were assayed by array-CGH (F2a, F2b, F2c). A large pool of F2 spores (and probably some number of F1 hybrid cells) were subjected to gradually increasing temperatures, in three independent vessels, with populations sampled at various generation times. Likewise, the same pool was used to found populations in an additional three independent vessels, which were then subjected to gradually increasing ethanol concentrations (at constant temperature). Array-CGH was performed on three different clones from each of the three temperature vessels at the final 500 generation time point (T500 clones). Biological replicates of the T500 clones were performed (T500-new). Two self-self array-CGH hybridization controls were also performed (self-control). Array-CGH was performed on one clone from each of the three ethanol vessels taken at the 400 generation timepoint (EtOH400gen clones).
2012-07-31 | E-GEOD-24479 | biostudies-arrayexpress
Project description:Saccharomyces pastorianus is the yeast used to make lager beer; it is known to be an interspecific hybrid formed by the fusion between S. cerevisiae and S. bayanus genomes. This data set queries 17 S. pastorianus strains, collected at various times over the last 125 years from various breweries located in different geographical locations, which were obtained from CBS and DBVPG culture collections. The data in this set represent array-CGH experiments performed with these strains, using "2-species" custom Agilent arrays (the "2-species" arrays contain probes spaced every ~2 kb across the whole genomes of both S. cerevisiae and S. bayanus; the probes are unique and specific for each genome). The data set also contains 3 self-self hybridizations (S. cerevisiae + S. bayanus DNA mixed together in equimolar amounts, then labeled green or red in separate reactions, then hybridized to the "2-species" arrays) used for normalization in CGH-Miner analysis. A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Keywords: strain_or_line_design
2008-07-22 | E-GEOD-12177 | biostudies-arrayexpress
Project description:We created a multi-species microarray platform, containing probes to the whole genomes of seven different Saccharomyces species, with very dense coverage (one probe every ~500 bp) of the S. cerevisiae genome, including non-S288c regions, mitochondrial and 2 micron circle genomes, plus probes at fairly dense coverage (one probe every ~2,100 bp) for each of the genomes of six other Saccharomyces species: S. paradoxus, S. mikatae, S. kudriavzevii, S. bayanus, S. kluyveri and S. castellii. We performed array-Comparative Genomic Hybridization (aCGH) using this platform, examining 83 different Saccharomyces strains collected across a wide range of habitats; of these, 69 were widely used commercial S. cerevisiae wine strains, while the remaining 14 were from a wide range of other industrial and natural habitats. Thus, we were able to sample much of the pan-genome space of the Saccharomyces genus. We observed interspecific hybridization events, introgression events, and pervasive copy number variation (CNV) in all but a few of the strains. These CNVs were distributed throughout the strains such that they did not produce any clear phylogeny, suggesting extensive mating in both industrial and wild strains. To validate our results and to determine whether apparently similar introgressions and CNVs were identical by descent or recurrent, we also performed whole genome sequencing on nine of these strains. These data may help pinpoint genomic regions involved in adaptation to different industrial milieus, as well as shed light on the course of domestication of S. cerevisiae.
2012-02-01 | GSE26689 | GEO
Project description:To study the evolution of nucleosome positioning we mapped nucleosome positioning in two species of yeasts. Identified differences in nucleosome positioning were classified into cis-based changes or trans-bseed changes based on the pattern of nucleosomes in the hybrid. This analysis was performed for wild-type strains as well as for strains deleted of 5 chromatin regulatoirs allolwing us to examine their roles in determining nucleosome positioning. Illumina sequencing of mono-nucleosome fragments isolated by MNase digestion. Samples include pooled DNA fragments of S. cerevisiae and S. paradoxus or DNA fragments of the interspecific hybrid. Experiments were performed for WT strains as well as strains deleted of 5 chromatin regulators.
2010-03-01 | E-GEOD-18939 | biostudies-arrayexpress
Project description:The S. cerevisiae hybrid karyotypes were analyzed by array-CGH to identify small regions of duplication or homeologous chromosomal exchange occurring during the strain construction.
2008-09-16 | GSE12776 | GEO
Project description:The S. cerevisiae hybrid karyotypes were analyzed by array-CGH to identify small regions of duplication or homeologous chromosomal exchange occurring during the strain construction.
2008-09-16 | GSE12775 | GEO
Project description:We assess the prevalence of polygenic evolution in pathways between the yeasts S. cerevisiae and S. bayanus. We first established short-read sequencing methods to detect cis-regulatory variation in a diploid hybrid between the species. We then formulated an analytic strategy to test for the scenario in which selective pressure in one species, to increase or decrease the activity of a pathway, has driven the accumulation of cis-regulatory variants that act in the same direction on gene expression. Application of this test revealed a variety of yeast pathways with evidence for directional regulatory evolution. Measurement of allele-specific expression of each ortholog in a diploid hybrid between Saccharomyces species
2010-02-22 | E-GEOD-19837 | biostudies-arrayexpress