Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39189 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Loss of heterozygosity drives adaptation in hybrid yeast
| PRJNA376031 | ENA
Project description: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. We initiated laboratory evolutionary experiments with over 180 haploid yeast genotypes, all of which initially displayed slow growth due to the deletion of a single gene. Compensatory adaptation was rapid and pervasive, and it promoted the genomic divergence of parallel evolving populations. The accumulated mutations did not restore wild type genomic expression states and generated diverse growth phenotypes across environments. Taken together, gene loss initiates genomic changes that can influence evolutionary potential upon environmental change.
2014-08-27 | GSE55373 | GEO
Project description:Investigation of rapid evolutionary adaptation events of Magnaporthe oryzae of HOG1 deficient mutants. Osmosensitive mutants adapt and re-gain osmoregulatory capabilities. Proteomics and phosphoproteomics were analyzed to shed light on the underlying processes.
2023-04-13 | PXD034481 | JPOST Repository
Project description: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 bakerM-bM-^@M-^Ys yeast genome to compensate the complete loss of genes during evolution, and explore the long-term consequences of this process. We initiated laboratory evolutionary experiments with over 180 haploid yeast genotypes, all of which initially displayed slow growth due to the deletion of a single gene. Compensatory adaptation was rapid and pervasive, and it promoted the genomic divergence of parallel evolving populations. The accumulated mutations did not restore wild type genomic expression states and generated diverse growth phenotypes across environments. Taken together, gene loss initiates genomic changes that can influence evolutionary potential upon environmental change. Evolved yeast-lines were generated by growing strains for 400 doublings during 104 days on YPD medium in 96 wells plates, 8 evolved lines were selected for microarray analysis. Two independent colonies of the wild type control, evolved and corresponding ancestor knock-out strains were grown to early midlog and used for transcription profiling by dual channel array against a common reference.
2014-08-27 | E-GEOD-55373 | biostudies-arrayexpress
Project description:The hypothesis that increased fitness within a selective environment must be accompanied by a loss of fitness in other non-selective environments leads to the notion of evolutionary tradeoffs. Experimental evolution provides an approach to test the existence of evolutionary tradeoffs, characterize their general quality, and reveal their genetic origins. To examine the underlying mechanism for a fitness trade-off, we constructed the evolutionary trajectories of Escherichia coli K-12 at increasing temperatures up to 45.3°C, and found diverging mutational histories that led to adaptive phenotypes with and without fitness trade-offs at low temperatures. We identified genetic changes in cellular respiration, iron metabolism and methionine biosynthesis that regulated gene expression to achieve thermal adaptation and determined the presence and absence of a fitness trade-off. Our results suggested that evolutionary trade-off could be generated by a regulatory protein mutation that was beneficial in the selective conditions but forced suboptimal proteome allocation under non-selective environments.
2020-11-17 | GSE140478 | GEO
Project description:Leishmania survival inside insect and mammalian hosts depends on the parasite’s capacity to develop into promastigote and amastigote stages, respectively. Promastigotes can be maintained in vitro in culture medium mimicking the insect milieu in which the parasites are surviving, differentiating and proliferating. We previously showed that the maintenance of the parasites in this in vitro environment lead to a progressive loss of infectivity together with genomic changes, notably chromosome amplifications. In contrast to classical eukaryotes Leishmania do not regulate expression of protein coding genes by transcriptional control, thus ruling out regulated gene expression changes in adaptation. In the absence of classical transcriptional regulation, Leishmania has evolved and emphasized other forms of control that are relevant for evolutionary adaptation, notably regulation of RNA abundance by gene dosage variation. In order to identify the biological signals that correlate with the observed fitness trade off we observed during L. donovani culture adaptation we combined DNAseq and RNAseq with label-free quantitative proteomics. Promastigotes freshly derived from splenic amastigotes purified from the spleen of infected hamsters were maintained in culture for 2 (EP) and 20 (LP) passages. Total protein extracts from four EP and four LP promastigotes were prepared for label free MS analysis.
2022-03-03 | PXD020236 | Pride
Project description:The mechanism of evolution in different conditions can be examined from various molecular aspects that constitute a cell, namely, transcript, protein or metabolite abundance. We have analyzed transcript and metabolite abundance changes in evolved and ancestor strains in three different evolutionary conditions, namely, excess-nutrient adaptation, prolonged stationary phase adaptation and adaptation due to environmental shift, in two different strains of Escherichia coli K-12 (MG1655 and DH10B).
2007-10-02 | E-MEXP-1166 | biostudies-arrayexpress
Project description: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. By combining qPCR, array CGH, restriction digestion and CHEF gels, and whole genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. Over a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that are driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolve under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared to single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.
2013-09-25 | GSE47854 | GEO