Adaptation dynamics in stressful environments
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB46680 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6391430_1.fastq.gz | Fastqsanger.gz | |||
| ERR6391430_2.fastq.gz | Fastqsanger.gz | |||
| ERR6391440_1.fastq.gz | Fastqsanger.gz | |||
| ERR6391440_2.fastq.gz | Fastqsanger.gz | |||
| ERR6391460_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 282 |
Similar Datasets
Project description:Bacterial rapid adaptation to alkaline environments
| PRJNA1125898 | ENA
Project description:CGH arrays for Smukowski Heil, et al MBE 2017. Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we address these questions using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae x Saccharomyces uvarum and their parentals. We evolved these strains in nutrient limited conditions for hundreds of generations and sequenced the resulting cultures to identify genomic changes. Analysis of 16 hybrid clones and 16 parental clones identified numerous point mutations, copy number changes, and loss of heterozygosity events, including species biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated loss of heterozygosity at the high affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the loss of heterozygosity is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity, and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation.
2017-02-21 | GSE95086 | GEO
Project description:Purpose: Monitor modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments, and its impact on gene expression Importance: Aneuploidy is usually detrimental in multicellular organisms, but in several micro-organisms (fungi being the best-studied) it can be tolerated and even beneficial. Leishmania – a protozoan parasite killing more than 30,000 persons each year – is emerging as a new model for aneuploidy studies: unexpectedly high levels of aneuploidy are found in clinical isolates. Leishmania lacks classical regulation of transcription through inducible promoters, so aneuploidy could represent a major adaptive strategy of this parasite to modulate gene dosage in response to stressful environments. For the first time, we document the dynamics of aneuploidy throughout the life cycle of the parasite, in vitro and in vivo. We show its adaptive impact on transcription and its intertwinement with regulation. Besides offering a new model for aneuploidy studies, we show that further genomic studies should be done directly in clinical samples (without parasite isolation) and that adequate methods should be developed for this.
2017-04-10 | GSE97453 | GEO
Project description: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. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of continuous phase in the chemostat.We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose or phosphate-limited environments combined with the batch phase population dynamics early in our experiments to allow several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes.Thus, the reproducibility of evolution varies with specific selective pressures reflecting the constraints inherent in the system-level organization of metabolic processes in the cell.We were able to relate some of the observed adaptive mutations (e.g. transporter gene amplifications) to known features of the relevant metabolic pathways, but many of the mutations pointed to genes not previously associated with the relevant physiology. Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways. Keywords: gene expression, CGH, and TSE analysis
2008-11-08 | GSE13435 | GEO
Project description: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. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of continuous phase in the chemostat.We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose or phosphate-limited environments combined with the batch phase population dynamics early in our experiments to allow several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes.Thus, the reproducibility of evolution varies with specific selective pressures reflecting the constraints inherent in the system-level organization of metabolic processes in the cell.We were able to relate some of the observed adaptive mutations (e.g. transporter gene amplifications) to known features of the relevant metabolic pathways, but many of the mutations pointed to genes not previously associated with the relevant physiology. Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways. Keywords: gene expression, CGH, and TSE analysis consult individual records for details of analysis This Dataset consists of several experiments: Gene expression experiments found in Figure 1a of paper: Design: RNA from each evolved clone or population grown in chemostat culture is compared to RNA from matching ancestor strains grown in the same conditions. Samples: GSM339025-GSM339088 CGH experiments found in Figure 2A, Figure 3, and Table S2: Experiment design: DNA from each evolved clone or population is hybridized vs DNA from the matched ancestor strain Samples: GSM339089-GSM339146 CGH experiments found in Table S3: Experiment design: DNA from each segregant derived from an evolved strain is hybridized vs DNA from the matched ancestor strain Samples: GSM339147-GSM339158 Gel band CGH experiments found in Figure S1: Experiment design: Chromosomes from evolved strains were run on a gel and excised. DNA from the bands is hybridized vs matched ancestor genomic DNA Samples: GSM339159-GSM339184 TSE CGH experiments found in Table S4: Experiment design: DNA linked to Ty1/Ty2 sequences was extracted from evolved strains and ancestor strains, and compared to ancestral extracted or genomic DNA as indicated. Samples: GSM339185-GSM339212 CGH experiments for experiments in Figure S7: Experiment design: DNA from 2 strains transformed with a SUL1 plasmid hybridized vs DNA from the matched ancestor strain Samples: GSM339213 and GSM339214
2010-05-18 | E-GEOD-13435 | biostudies-arrayexpress
Project description:Evolutionary processes involved in the adaptation of Saccharomyces cerevisiae to anthropic environments.
| PRJEB7675 | ENA
Project description:To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.
2024-06-24 | GSE270261 | GEO
Project description:The bacterial lifestyle that disguises stressful adaptations
| PRJNA613082 | ENA
Project description:Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce their long-term evolutionary potential. However, appropriate short-term plastic responses to new environmental conditions might not require high levels of standing genetic variation. In this study, we tested whether mating system variation among populations, and associated changes in genetic variability, affected short-term responses to environmental challenges. We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a perennial plant, <i>Arabidopsis lyrata</i>, under constant growth chamber conditions and an outdoor common garden environment outside its native range. We found no effect of inbreeding on survival, flowering phenology or short-term physiological responses. Specifically, naturally occurring inbreeding had no significant effects on the plasticity of metabolome profiles, using either multivariate approaches or analysis of variation in individual metabolites, with inbreeding populations showing similar physiological responses to outbreeding populations over time in both growing environments. We conclude that low genetic diversity in naturally inbred populations may not always compromise fitness or short-term physiological capacity to respond to environmental change, which could help to explain the global success of selfing mating strategies.
2019-10-25 | MTBLS883 | MetaboLights
Project description:Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments
| PRJNA428984 | ENA