Undefined
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB55833 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR10167739_1.fastq.gz | Fastqsanger.gz | |||
| ERR10167739_2.fastq.gz | Fastqsanger.gz | |||
| ERR10167740_1.fastq.gz | Fastqsanger.gz | |||
| ERR10167740_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 39 |
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Project description:Adaptive laboratory evolution is highly effective for improving desired traits through natural selection. However, its applicability is inherently constrained to growth-correlated traits precluding traits of interest that incur a fitness cost, such as metabolite secretion. Here, we introduce the concept of tacking trait enabling natural selection of fitness-costly metabolic traits. The concept is inspired from the tacking maneuver used in sailing for traversing upwind. We use first-principle metabolic models to design an evolution niche wherein the tacking trait and fitness become correlated. Adaptive evolution in this niche, when followed by the reversal to the original niche, manifests in the improvement of the desired trait due to biochemical coupling between the tacking and the desired trait. We experimentally demonstrated this strategy, termed EvolveX, by evolving wine yeasts for increased aroma production. RNA-sequencing was performed for parental and evolved strains in the respective evolution niche and in natural grape must.
2021-12-30 | E-MTAB-10019 | biostudies-arrayexpress
Project description: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. Although the evolutionary importance of gene duplication has long been appreciated, little is known about natural variation in the tolerance of duplication of specific genes. To investigate this question, we expressed the same high-copy gene overexpression (OE) library in a laboratory strain and 14 different wild S. cerevisiae isolates, together representing 4 lineages and several admixed strains, to explore the natural variation in tolerance to gene OE. Our results distinguish universal effects common to many studied strains versus strain-specific effects including broad-scale and gene-specific differences in the consequences of OE. These results raise important implications for the accessibility of evolutionary trajectories afforded by gene OE, depending on genetic background.
2021-04-07 | GSE171586 | GEO
Project description:Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally reproduced one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol into soil isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferred by HGT but is selectively neutral under environmentally-relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small and negative frequency-dependent.
2024-01-03 | MSV000093756 | MassIVE
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:Adaptive laboratory evolution is highly effective for improving desired traits through natural selection. However, its applicability is inherently constrained to growth-correlated traits precluding traits of interest that incur a fitness cost, such as metabolite secretion. Here, we introduce the concept of tacking trait enabling natural selection of fitness-costly metabolic traits. The concept is inspired from the tacking maneuver used in sailing for traversing upwind. We use first-principle metabolic models to design an evolution niche wherein the tacking trait and fitness become correlated. Adaptive evolution in this niche, when followed by the reversal to the original niche, manifests in the improvement of the desired trait due to biochemical coupling between the tacking and the desired trait. We experimentally demonstrate this strategy, termed EvolveX, by evolving wine yeasts for increased aroma production. Our results pave the way for precision laboratory evolution for biotechnological and ecological applications.
2022-07-12 | PXD023171 | Pride
Project description:Histological transformation of follicular lymphoma to aggressive form occurs 2-3% per year with poor outcome. Divergent evolution and an altered tumour-microenvironment (TME) have been implicated during transformation. However, phenotypic consequences of this evolution and its implication in TME remain unknown. To address this, we performed single cell whole genome and whole transcriptome sequencing of paired pre/post transformation patient samples. We further performed scWTS of additional samples from patients without transformation. Our analysis revealed evolutionary dynamics of transformation at unprecedented resolution. Integration of scWGS and scWTS identified pathways upregulated during evolution. scWTS analysis revealed a shifting TME landscape, with an exhausted signature emerging during transformation. Using multi-color immunofluorescence we transferred these findings to a TME-based transformation biomarker, subsequently validated in independent pretreatment cohorts. Taken together, our results provide a comprehensive view of the combined genomic and phenotypic evolution of malignant cells during transformation, and shifting cross-talk between malignant cells and TME.
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Project description:Stable microbial community in compacted bentonite after 5 years of exposure to natural groundwater
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Project description:Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing
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Project description:Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution
| PRJEB63577 | ENA
Project description:<p>Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutualistic communities for improving secretion of fitness-costly metabolites through natural selection. In this strategy, metabolic cross-feeding connects secretion of the target metabolite, despite its cost to the secretor, to the survival and proliferation of the entire community. We thus co-evolved wild-type lactic acid bacteria and engineered auxotrophic <em>Saccharomyces cerevisiae</em> in a synthetic growth medium leading to bacterial isolates with enhanced secretion of two B-group vitamins, viz., riboflavin and folate. The increased production was specific to the targeted vitamin, and evident also in milk, a more complex nutrient environment that naturally contains vitamins. Genomic, proteomic and metabolomic analyses of the evolved lactic acid bacteria, in combination with flux balance analysis, showed altered metabolic regulation towards increased supply of the vitamin precursors. Together, our findings demonstrate how microbial metabolism adapts to mutualistic lifestyle through enhanced metabolite exchange.</p>
2021-07-02 | MTBLS2217 | MetaboLights