Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA111721 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparative Genomic Hybridization of natural Saccharomyces cerevisiae strains vs lab reference strains.
2020-12-31 | GSE136466 | GEO
Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization to explore global changes in the genomic DNA, of four S. bayanus var uvarum strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNV) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.
2016-04-15 | GSE67917 | GEO
Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.
2013-12-15 | GSE46165 | GEO
Project description:High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.
2009-05-07 | GSE14223 | GEO
Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains
2008-09-05 | GSE10267 | GEO
Project description:The environmental stresses and inhibitors encounted by Saccharomyces cerevisiae strains are main limiting factors in bioethanol fermentation. Investigation of the molecular mechanisms underlying the stresses-related phenotypes diversities within and between S. cerevisiae populations could guide the construction of yeast strains with improved stresses tolerance and fermentation performances. Here, we explored the genetic characteristics of the bioethanol S. cerevisiae strains, and elucidated the genetic variations correlated with its advantaged traits (higher ethanol yield under sever conditions and better tolerance to multiple stresses compared to an S288c derived laboratory strain BYZ1). Firstly, pulse-field gel electrophoresis combined with array-comparative genomic hybridization was used to compare the genome structure of industrial strains and the laboratory strain BYZ1.
2011-09-15 | GSE31872 | GEO
Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media. Seven S. cerevisiae strains were obtained from natural environments and different fermentation processes. The S. cerevisiae strain S288C was used as a control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.
2013-12-15 | E-GEOD-46165 | biostudies-arrayexpress
Project description:Comparative Genomic Hybridization of S. cerevisiae industrial and laboratory strains
| PRJNA145241 | ENA
Project description:To determine the genomic location of a gene that permits xylose utilization we conducted bulk segregant analysis (BSA) using Affymetrix yeast tiling arrays. BSA works by taking advantage of DNA sequence polymorphisms between different strains and the fact that it is relatively easy to pool large numbers of meiotic spore products (segregants) in yeast. Pooling segregants based on their phenotype allows the region of the genome responsible for the phenotype to be detected. This is because DNA polymorphisms in regions unlinked to the locus causing the phenotype will segregate randomly and be “evened” out, while around the genomic region of interest, sequences or polymorphisms responsible for the trait will be present in all positive segregants, and absent in all negative segregants. In our case, a Simi White wine strain (S. cerevisiae) carrying the locus responsible for xylose utilization was crossed to a laboratory strain of Saccharomyces cerevisiae; this strain was estimated to carry DNA polymorphisms relative to the laboratory strain at a level of approximately .5%. Spores from the Simi White / S288c diploid were screened for the xylose utilization phenotype and 39 positive spores were combined into one pool and 39 negative spores into another pool, and genomic DNA (gDNA) was isolated from each pool. We then hybridized the positive and negative gDNA pools to tiling microarrays that were based on the S288c reference genome with the expectation that regions of the genome derived from Simi White will hybridize less robustly to the array because of the DNA polymorphisms between Simi White and S288c. Log2 ratios of probe intensities were calculated (negative/positive), and a peak appeared in the chromosome XV right subtelomeric region that corresponds to less robust hybridization to the microarray of the positive pool gDNA coming from this region of the genome
2010-04-09 | GSE19120 | GEO
Project description:We developed an artificial genome evolution system, which we termed ‘TAQing’, by introducing multiple genomic DNA double-strand breaks using a heat-activatable endonuclease in mitotic yeast. The heat-activated endonuclease, TaqI, induced random DSBs, which resulted in diverse types of chromosomal rearrangements including translocations. Array comparative genomic hybridization (aCGH) analysis was performed with cell-fused Saccharomyces cerevisiae strains induced genome evolution by TAQing system. Some of copy number variations (CNVs) induced by massive genome rearrangements were detected in the TAQed yeast strains.
2018-05-02 | GSE90025 | GEO