Ontology highlight
ABSTRACT:
PROVIDER: PRJEB55541 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10108628_1.fastq.gz | Fastqsanger.gz | |||
| ERR10108628_2.fastq.gz | Fastqsanger.gz | |||
| ERR10108629_1.fastq.gz | Fastqsanger.gz | |||
| ERR10108629_2.fastq.gz | Fastqsanger.gz | |||
| ERR10108630_1.fastq.gz | Fastqsanger.gz |
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Project description:A study evaluating the effect of stress resistance selection of Drosophila melanogaster. Abstract; Here, we report a detailed analysis of changes in gene expression in Drosophila melanogaster selected for multiple ecologically relevant environmental stress resistance traits. We analyzed females from three biological replicates from seven selection regimes and one control regime using whole genome gene expression arrays. Replicated selection lines were selected for resistance to acute heat survival, high temperature knock down, constant 30 degress C during development, cold shock survival, desiccation and starvation, respectively. Additionally, a set of replicated lines was selected for increased longevity. When compared to gene expression profiles of control lines, we were able to detect consistent selection responses at the transcript level in each specific selection regime and also found a group of differentially expressed genes that were generally changed among all selected lines. Replicated selection lines clustered together, i.e. showed similar changes in gene expression (compared to controls) and thus showed that 10 generations of artificial selection gives a clear signal among gene expression profiles. The changes in gene expression in lines selected for increased longevity, desiccation and starvation resistance, respectively, showed high similarities. Cold resistance selected lines showed little differentiation from controls. Different methods of heat selection (heat survival, heat knock down and constant 30 degrees C) showed little similarity verifying that different mechanism are involved in high temperature adaptation. The direction of change in gene expression in the selected lines showed a consistent pattern for each selection regime. For most selection regimes and in the comparison of all selected lines and controls exclusively up- or down regulation of gene expression among significant differentially expressed genes was found. The different responses to selection expressed in individual selection regimes and among all selected lines indicate that we have identified genes involved in stress specific and general stress response mechanisms. Experiment Overall Design: gene expression was measured in biological triplicates of control flies and flies selected for resistance to various stressors.
2009-02-07 | E-GEOD-6558 | biostudies-arrayexpress
Project description:Thomas Hunt Morgan and colleagues identified variation in gene copy number in Drosophila in the 1920s and 1930s and linked such variation to phenotypic differences [Bridges, C. B. (1936) Science 83, 210]. Yet the extent of variation in the number of chromosomes, chromosomal regions, or gene copies, and the importance of this variation within species, remain poorly understood. Here, we focus on copy-number variation in Drosophila melanogaster. We characterize copy-number polymorphism (CNP) across genomic regions, and we contrast patterns to infer the evolutionary processes acting on this variation. Copy-number variation in D. melanogaster is non-randomly distributed, presumably due to a mutational bias produced by tandem repeats or other mechanisms. Comparisons of coding and noncoding CNPs, however, reveal a strong effect of purifying selection in the removal of structural variation from functionally constrained regions. Most patterns of CNP in D. melanogaster suggest that negative selection and mutational biases are the primary agents responsible for shaping structural variation. Keywords: comparative genomic hybridization
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Project description:Drosophila melanogaster desiccation selection raw sequence reads
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Project description:Phenotypic differences between closely related species are thought to arise primarily from changes in gene expression due to mutations in cis-regulatory sequences (enhancers). However, it has remained unclear, how frequently mutations alter enhancer activity or create functional enhancers de novo. Here, we use STARR-seq, a recently developed quantitative enhancer assay, to determine genome-wide enhancer activity profiles for five Drosophila species in the constant trans-regulatory environment of D. melanogaster S2 cells. We find that the function of a large fraction of D. melanogaster enhancers is conserved in their orthologous sequences due to selection and stabilizing turnover of transcription factor motifs. Moreover, hundreds of enhancers have been gained since the D. melanogaster M-bM-^@M-^S D. yakuba split about 11 million years ago without apparent adaptive selection and can contribute to gene expression changes in vivo. Our finding that enhancer activity is often deeply conserved and frequently gained provides important functional insights into regulatory evolution. STARR-seq was performed in S2 cells with paired-end sequencing in two replicates and respective inputs using genomic DNA from different Drosophila species. RNA-seq was performed in a non-stranded manner without replicates for two Drosophila species.
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Project description:Drosophila melanogaster selection lines confronted with Aspergillus nidulans
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Project description:A study evaluating the effect of stress resistance selection of Drosophila melanogaster. Abstract Here, we report a detailed analysis of changes in gene expression in Drosophila melanogaster selected for multiple eological relevant environmental stress resistance traits. We analyzed females from three biological replicates from seven selection regimes and one control regime using whole genome gene expression arrays. Replicated selection lines were selected for resistance to acute heat survival, high temperature knock down, constant 30°C during development, cold shock survival, desiccation and starvation, respectively. Additionally, a set of replicated lines was selected for increased longevity. When compared to gene expression profiles of control lines, we were able to detect consistent selection responses at the transcript level in each specific selection regime and also found a group of differentially expressed genes that were generally changed among all selected lines. Replicated selection lines clustered together, i.e. showed similar changes in gene expression (compared to controls) and thus showed that 10 generations of artificial selection gives a clear signal among gene expression profiles. The changes in gene expression in lines selected for increased longevity, desiccation and starvation resistance, respectively, showed high similarities. Cold resistance selected lines showed little differentiation from controls. Different methods of heat selection (heat survival, heat knock down and constant 30°C) showed little similarity verifying that different mechanism are involved in high temperature adaptation. The direction of change in gene expression in the selected lines showed a consistent pattern for each selection regime. For most selection regimes and in the comparison of all selected lines and controls exclusively up- or down regulation of gene expression among significant differentially expressed genes was found. The different responses to selection expressed in individual selection regimes and among all selected lines indicate that we have identified genes involved in stress specific and general stress response mechanisms. Keywords: control versus selected
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