Genomic evolution of experimental Chlorovirus evolution
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PROVIDER: PRJEB45939 | ENA |
REPOSITORIES: ENA
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Project description:Strong selection and high mutation supply characterize experimental Chlorovirus evolution
| PRJEB46915 | ENA
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:Tribolium castaneum experimental evolution
| PRJNA552902 | ENA
Project description:microarray experiment to test the gene expression in long term lines of mutator and non-mutator yeast. Here we use an experimental evolution approach to investigate the conditions required for evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ~6700 generations four out of eight experimental mutator lines had evolved a decreased mutation rate.
2012-02-02 | GSE35440 | GEO
Project description:microarray experiment to test the gene expression in long term lines of mutator and non-mutator yeast. Here we use an experimental evolution approach to investigate the conditions required for evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ~6700 generations four out of eight experimental mutator lines had evolved a decreased mutation rate. 2 condition experiment, derived experimental evolution strains compared to their ancestor strain. We compared the expression profile of one of the mutator lines (m8) after 6700 generations with its mutator ancestor, and as a control, an evolved non mutator after 6700 generations was compared to to its non-mutator ancestor. In order to prepare cells for expression microarray, glass tubes containing 3 ml of YPD were inoculated from overnight cultures, and grown until the OD600 was approximately 0.3.
2012-02-02 | E-GEOD-35440 | biostudies-arrayexpress
Project description:The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under three different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e., selection for fitness via eggs, via sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, GO-term and KEGG pathway analysis suggests that metabolic changes (e.g., biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.
2023-09-29 | GSE242254 | 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.
2015-04-15 | GSE67871 | GEO
Project description:Pseudogene repair driven by selection pressure applied in experimental evolution
| PRJNA506264 | ENA
Project description:Experimental evolution is a powerful approach to study how ecological forces shape microbial genotypes and phenotypes, but to date strains were predominantly adapted to conditions specific to laboratory environments. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in the dairy environment and it is generally believed, that dairy strains originate from the plant niche. Here we investigated the adaptive process from the plant to the dairy niche and show that during the experimental evolution of a L. lactis plant isolate in milk, several mutations are selected that affect amino acid metabolism and transport. Three independently evolved strains were characterized by whole genome re-sequencing, revealing 4 to 28 mutational changes in the individual strains. Two of the adapted strains showed clearly increased acidification rates and yields in milk, and contained three identical point mutations. Transcriptome profiling and extensive phenotyping of the wild-type plant isolate compared to the evolved mutants, and a "natural" dairy isolate confirmed that major physiological changes associated with improved performance in the dairy environment relate to nitrogen metabolism. The deletion of a putative transposable element led to a significant decrease of the mutation rate in two of the adapted strains. These results specify the adaptation of a L. lactis strain isolated from mung bean sprouts to growth in milk and they demonstrate that niche-specific adaptations found in environmental microbes can be reproduced by experimental evolution.
2010-03-03 | GSE20373 | GEO
Project description:Experimental evolution is a powerful approach to study how ecological forces shape microbial genotypes and phenotypes, but to date strains were predominantly adapted to conditions specific to laboratory environments. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in the dairy environment and it is generally believed, that dairy strains originate from the plant niche. Here we investigated the adaptive process from the plant to the dairy niche and show that during the experimental evolution of a L. lactis plant isolate in milk, several mutations are selected that affect amino acid metabolism and transport. Three independently evolved strains were characterized by whole genome re-sequencing, revealing 4 to 28 mutational changes in the individual strains. Two of the adapted strains showed clearly increased acidification rates and yields in milk, and contained three identical point mutations. Transcriptome profiling and extensive phenotyping of the wild-type plant isolate compared to the evolved mutants, and a "natural" dairy isolate confirmed that major physiological changes associated with improved performance in the dairy environment relate to nitrogen metabolism. The deletion of a putative transposable element led to a significant decrease of the mutation rate in two of the adapted strains. These results specify the adaptation of a L. lactis strain isolated from mung bean sprouts to growth in milk and they demonstrate that niche-specific adaptations found in environmental microbes can be reproduced by experimental evolution. Multiple loop design with 12 samples and 16 dual label arrays. Each sample is hybrdized at least on two different arrays and with both dyes.
2010-06-24 | E-GEOD-20373 | biostudies-arrayexpress