Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA839395 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This experiment set contains the arrays referenced in Ferea, TL, et al. titled "Systematic changes in gene expression patterns following adaptive evolution in yeast"(Proc Natl Acad Sci USA 1999 96(17):9721-6). A Saccharomyces cerevisiae population was cultured for many generations under conditions to which it is not optimally adapted. These experiments were designed to investigate adaptive evolution under natural selection.
2005-06-16 | E-SMDB-98 | biostudies-arrayexpress
Project description:Yeast transcription factor Yap1 mediates adaptive response against H2O2 and the cystein thiol reactive Michael acceptor, N-ethylmaleimid (NEM) and acrolein. The response against H2O2 was found to be distinct from that against NEM and acrolein. We used microarray experiment to identify two subsets of Yap1-dependent genes that correspond to these two adaptive responses.
2010-12-30 | GSE19213 | GEO
Project description:Gene copy-number variation, which provides the raw material for the evolution of novel genes, is surprisingly widespread in natural populations. Experimental evolution studies have demonstrated an extremely high spontaneous rate of origin of gene duplications. When organisms are suboptimally adapted to their environment, gene duplication may compensate for reduced fitness by amplifying promiscuous activity of a gene, or increasing dosage of a suboptimal gene. The overarching goal of this study is to inverstigate whether CNVs constitute a common mechanism of adaptive genetic change during compensatory evolution and to further characterize the role of natural selection in dictating their evolutionary spread at a population-genomic level. Outcrossing populations of C. elegans with low fitness were evolved for >200 generations and the frequencies of CNVs in these populations were analyzed by oligonucleotide array comparative genome hybridization, quantitative PCR, and single-worm PCR. Multiple duplications and deletions were detected in intermediate to high frequencies and several lines of evidence suggest that the changes in frequency were adaptive. 1) Many copy-number changes reached high frequency, were near fixation, or were fixed in a short time. 2) Many independent duplications and deletions in high frequency harbor overlapping regions which likely include genes that are under selection for either higher or lower rates of expression. 3) The size spectrum of deuplications and deletions in the adaptive recovery populations is significantly larger than that of spontaneous copy-number variants in mutation accumulation experiments. This is expected if larger CNVs are more likely to encompass genes that are being selected for altered gene dosage. Out results validate the great potential borne by gene copy-number changes for compensatory evolution and adaptation. Experimental genome evolution of copy-number variants in 25 experimental lines compared to 5 ancestral control lines.
2015-04-15 | E-GEOD-67871 | biostudies-arrayexpress
Project description:RNA-seq reads from the outcrossing species Arabidopsis lyrata were produced from flowers to study the consequences of the transition from the ancestral state (outcrossing) to the derived state (selfing) that is observed in the sister species Arabidopsis thaliana. This was done in the context of examining another species pair (Capsella rubella versus Capsella grandiflora, which are selfing and outcrossing, respectively). These samples were generated to complement part of this larger study. Briefly, the shift from outcrossing to selfing is common in flowering plants, but neither the genomic consequences nor the speed with which they appear are well understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self-compatible <200,000 years ago. We present a reference genome for the species, and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor C. grandiflora. There is a clear shift in the expression of genes associated with flowering phenotypes; a similar shift is seen in the related genus Arabidopsis, where self-fertilization evolved about 1 million years ago. DNA sequence polymorphisms distinguishing the two Capsella species reveal rapid genome-wide relaxation of purifying selection in C. rubella but without a concomitant change in transposable element abundance. Overall, we document that the transition to selfing may be typified by shifts in expression for genes that function in pollen and flower development, along with a measurable reduction of purifying selection.
2013-04-02 | GSE45676 | GEO
Project description:Yeast transcription factor Yap1 mediates adaptive response against H2O2 and the cystein thiol reactive Michael acceptor, N-ethylmaleimid (NEM) and acrolein. The response against H2O2 was found to be distinct from that against NEM and acrolein. We used microarray experiment to identify two subsets of Yap1-dependent genes that correspond to these two adaptive responses. Wild-type yeast BY4741 cells were grown in early exponential phase and treated with H2O2, NEM, or acrolein. RNAs were then extracted and hybridized on Affymetrix microarrays.
2010-12-30 | E-GEOD-19213 | biostudies-arrayexpress
Project description:Type 1 NKT cells play a critical role in controlling the strength and character of adaptive and innate immune responses. Their functional characteristics are distinct from conventional T cells, and are induced by a transcriptional program initiated by positive selection on CD4+CD8+ (double positive, DP) thymocytes. Here we examined transcriptional events in four immature thymic NKT cell subsets in a novel Vα14 TCR transgenic strain bearing greatly expanded numbers of CD24+CD44- NKT cells. We used a transcriptional regulatory network approach to map TCR validation to the transition from DP T to DP NKT cells, and positive selection and lineage commitment to the transition from DP NKT to CD4 NKT
2021-12-15 | GSE106720 | GEO
Project description:We used flower bud transcriptomes from Collinsia rattanii and its predominantly outcrossing sister species, C. linearis, to explore the genomic basis of mating system and phenotypic evolution in Collinsia, a self-compatible genus. Transcriptional regulation of enzymes involved in pollen formation may influence floral traits that distinguish selfing and outcrossing Collinsia species through pleiotropic functions. These patterns provide clues about parallel evolution in selfing plants.
2021-05-12 | GSE174273 | GEO