GEO DataSets

(Submitter supplied) Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, deleterious mutations may also have an important role by promoting adaptive genetic changes that are otherwise inaccessible. Here we study the capacity of the baker’s yeast genome to compensate the complete loss of genes during evolution, and explore the long-term consequences of this process. more...

Organism:

Saccharomyces cerevisiae BY4741; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

34 Samples

Download data: TXT

(Submitter supplied) Background: The impact of genetic interaction networks on evolution is a fundamental issue. Previous studies have demonstrated that the topology of the network is determined by the properties of the cellular machinery. Functionally related genes frequently interact with one another, and they establish modules, e.g., modules of protein complexes and biochemical pathways. In this study, we experimentally tested the hypothesis that compensatory evolutionary modifications, such as mutations and transcriptional changes, occur frequently in genes from perturbed modules of genetically interacting genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16244

17 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

4 related Platforms

65 Samples

Download data: TXT

(Submitter supplied) One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL7293 GPL9294 GPL11382

22 Samples

Download data: TXT

(Submitter supplied) One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10930

43 Samples

Download data: TXT

(Submitter supplied) Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces bayanus

Type:

Genome variation profiling by array; Genome variation profiling by genome tiling array

6 related Platforms

52 Samples

Download data: GPR, TXT

(Submitter supplied) To investigate how organisms mitigate the deleterious effects of mistranslation during evolution, a mutant tRNA was expressed in S. cerevisiae. The expression of Candida Ser-tRNACAG from a low copy plasmid in S. cerevisiae promoted mistranslation events by random incorporation of both serine and leucine at CUG codons. As mistranslation causes an overload of the protein quality pathways, it disrupts cellular protein homeostasis leading to a major fall in fitness. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

22 Samples

Download data: TXT

(Submitter supplied) It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive.  Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes.  Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces paradoxus; Saccharomyces mikatae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21862 GPL9377 GPL21861

10 Samples

Download data: TXT

(Submitter supplied) The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time.Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms.We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes, including point mutations, structural changes, and insertion variation, that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in glucose-, sulfate, or phosphate-limited chemostats for ~ 200 generations.We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation.Global mutation detection in 10 clonal isolates identified 32 point mutations. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome variation profiling by array

4 related Platforms

190 Samples

Download data: TXT, ZIP

(Submitter supplied) Alteration of normal ploidy (aneuploidy) is an important mechanism of evolution of species. It has been linked to a rapid response to stress and is regarded as a hallmark of cancer. While increased genomic instability of aneuploid cells can accelerate genetic diversification and facilitate adaptation, these cells also face the adverse effects of gene imbalance, resulting in fitness cost. Here, to understand the mechanisms through which cells respond to aneuploidy and develop tolerance leading to fitness restoration, we subjected disomic (i.e. more...

Organism:

Saccharomyces cerevisiae W303

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25517

45 Samples

Download data: TSV

(Submitter supplied) Variation in gene expression arises from cis- and trans-regulatory mutations, which contribute differentially to expression divergence. Here, we compare the impacts on gene expression and fitness for cis- and trans-regulatory mutations affecting expression of the TDH3 gene in Saccharomyces cerevisiae. We use the effects of cis-regulatory mutations to isolate effects of trans-regulatory mutations caused by impacts on TDH3 from pleiotropic impacts on other genes, providing a rare distribution of pleiotropic effects. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

188 Samples

Download data: SF, TXT

(Submitter supplied) In some of the earliest uses of genome-wide gene-expression microarrays and array-based Comparative Genomic Hybridization (aCGH), a set of diploid yeasts that had undergone experimental evolution under aerobic glucose limitation was used to explore how gene expression and genome structure had responded to this selection pressure. To more deeply understand how adaptation to one environment might constrain or enhance performance in another we have now identified the adaptive mutations in this set of clones using whole-genome sequencing, and have assessed whether the evolved clones had become generalists or specialists by assaying their fitness under three contrasting growth environments: aerobic and anaerobic glucose limitation and aerobic acetate limitation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

36 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

135 Samples

Download data: TXT

(Submitter supplied) Genetic variation that underlies phenotypic differences provides the material on which evolutionary selection acts. Gene duplication/amplification is one type of genetic variation that can allow an organism to rapidly respond to environmental changes by increasing gene dosage. While the potential benefits afforded by gene amplification during evolution are well known, there is also a significant fitness cost to increasing gene dosage including resource shortages and burdening cellular systems. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

90 Samples

Download data: TXT

(Submitter supplied) We used RNA-Seq to measure transcript abundance in 15 Saccharomyces cerevisiae strains from a diverse range of genetic lineages when growing in rich media (YPD) to characterize differential expression across strains.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

45 Samples

Download data: TXT

(Submitter supplied) Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4131

7 Samples

Download data: PDF, TXT

(Submitter supplied) Escherichia coli was evolved under growth conditions in which the carbon substrate alternated between glucose and either glycerol, xylose, or acetate with every tube of growth. Controls were also evolved to each substrate individually, without switching.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15010

23 Samples

Download data: TXT

(Submitter supplied) Here, we used RNA-seq to quantify expression conservation across many Ascomycete yeasts.

Organism:

Lachancea waltii; Saccharomyces cerevisiae; Schizosaccharomyces japonicus; Schizosaccharomyces octosporus; Saccharomyces bayanus; Yarrowia lipolytica; Naumovozyma castellii; Schizosaccharomyces pombe; Nakaseomyces glabratus; Kluyveromyces lactis; Candida albicans

Type:

Expression profiling by high throughput sequencing

11 related Platforms

11 Samples

Download data: TXT

(Submitter supplied) In order to generate data produce a generalizable sequence-to-expression model, we randomly sampled ~21 million 80 bp sequences and tested their activity as promoters (in yeast) by measuring expression level by FACS (sorting into 18 bins).

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

36 Samples

Download data: TXT

(Submitter supplied) A central question in genetics and evolution is the extent to which mutations have outcomes that change depending on the genetic context in which they occur. Pairwise interactions between mutations have been systematically mapped within and between genes, and contribute substantially to phenotypic variation amongst individuals. However, the extent to which genetic interactions themselves are stable or dynamic across genotypes is unclear. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL17342

8 Samples

Download data: TXT