Natural variation in the transcriptional response of Drosophila melanogaster to oxidative stress
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ABSTRACT:
PROVIDER: PRJNA731676 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14612037_1.fastq.gz | Fastqsanger.gz | |||
| SRR14612037_2.fastq.gz | Fastqsanger.gz | |||
| SRR14612038_1.fastq.gz | Fastqsanger.gz | |||
| SRR14612038_2.fastq.gz | Fastqsanger.gz | |||
| SRR14612039_1.fastq.gz | Fastqsanger.gz |
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Project description:Broadly distributed species must cope with diverse and changing environmental conditions, including various forms of stress. Cosmopolitan populations of Drosophila melanogaster are more tolerant to oxidative stress than those from the species’ ancestral range in sub-Saharan Africa, and the degree of tolerance is associated with an insertion/deletion polymorphism in the 3’ untranslated region of the Metallothionein A (MtnA) gene that varies clinally in frequency. We examined oxidative stress tolerance and the transcriptional response to oxidative stress in cosmopolitan and sub-Saharan African populations of D. melanogaster, including paired samples with allelic differences at the MtnA locus. We found that the effect of the MtnA polymorphism on oxidative stress tolerance was dependent on the genomic background, with the deletion allele increasing tolerance only in a northern, temperate population. Genes that were differentially expressed under oxidative stress included MtnA and other metallothioneins, as well as those involved in glutathione metabolism and other genes known to be part of the oxidative stress response or the general stress response.
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Project description:Maternal gene products supplied to the egg during oogenesis drive the earliest events of development in all metazoans. After the initial stages of embryogenesis, maternal transcripts are degraded as zygotic transcription is activated; this is known as the maternal to zygotic transition (MZT). Altering the abundances of maternally deposited factors in the laboratory can have a dramatic effect on development, adult phenotypes and ultimately fitness. Zygotic transcription activation is a tightly regulated process, where the zygotic genome takes over control of development from the maternal genome, and is required for the viability of the organism. Recently, it has been shown that the expression of maternal and zygotic transcripts have evolved in the Drosophila genus over the course of 50 million years of evolution. However, the extent of natural variation of maternal and zygotic transcripts within a species has yet to be determined. We asked how the maternal and zygotic pools of mRNA vary within and between populations of D. melanogaster. In order to maximize sampling of genetic diversity, African lines of D. melanogaster originating from Zambia as well as DGRP lines originating from North America were chosen for transcriptomic analysis. Single embryo RNA-seq was performed before and after zygotic genome activation to determine which transcripts are maternally deposited and which are zygotically expressed within and between these populations. Differential gene expression analysis has been used to quantify quantitative changes in RNA levels within populations as well as fixed expression differences between populations at both stages. Generally, we find that maternal transcripts are more highly conserved, and zygotic transcripts evolve at a higher rate. We find that there is more within-population variation in transcript abundance than between populations and that expression variation is highest post- MZT between African lines. Determining the natural variation of gene expression surrounding the MZT in natural populations of D. melanogaster gives insight into the extent of how a tightly regulated process may vary within a species, the extent of developmental constraint at both stages and on both the maternal and zygotic genomes, and reveals expression changes allowing this species to adapt as it spread across the world.
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Project description:To measure natural variation in ER stress transcriptional response in a subset of lines from the Drosophila Genetic Reference Panel Transcriptional response to Tunicamycin and control conditions was measured at 8 hours of exposure (20 lines) and 20 hours of exposure (8 lines).
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Project description:Transcriptional profiling of Drosophila melanogaster 2nd chromosome substitution lines; Background chromosomes are identical across lines; 2nd chromosomes are different across line and can be homozygous or heterozygous within each line Keywords: Natural variation
2010-05-06 | GSE12191 | GEO
Project description:Climate change is one of the main factors shaping the distributions and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are specially threatened by these challenging dry environments, thanks to their small size and thus large surface area to volume ratio. Drosophila melanogaster is a great model to study the response of populations to rapidly changing conditions, because of its southern African origin and recent and fast worldwide spreading. Desiccation stress response is a complex and extensively studied trait, however the natural variation and underlying molecular and physiological mechanisms responsible for the tolerance in natural European D. melanogaster populations has never been studied. Here we subjected to desiccation stress 74 natural D. melanogaster European strains, belonging to five different climate zones. We found that the strains belonging to the cold semi-arid climates are more tolerant compared to the others, and that this tolerance can be explained by the combination of altitude and evaporation. The tolerant strains had a lower level of initial water content and lost less water during desiccation stress. We found that the reduction in the water loss happens through a decrease in the respiration rate in desiccation stress conditions, and by having a less permeable cuticle prior the stress exposure. The decreased rate of respiration in the tolerant strains is a consequence of the down-regulation of genes related to diverse metabolic processes. Moreover, we found that the genes related to response to stimulus and environmental sensing are up-regulated only in the tolerant strains. We also identified four transposable element insertions, which might be responsible for changes in gene expression. Overall, our study for the first time described the physiological and transcriptomic changes underlying the desiccation tolerance of natural European D. melanogaster strains, and generated a list of putative mutations shaping desiccation stress response.
2020-12-31 | GSE153850 | GEO
Project description:Background: Differences in levels of gene expression among individuals are an important source of phenotypic variation within populations. Recent microarray studies have revealed that expression variation is abundant in many species, including Drosophila melanogaster. However, previous expression surveys in this species generally focused on a small number of laboratory strains established from derived populations. Thus, these studies were not ideal for population genetic analyses. Results: We surveyed gene expression variation in adult males of 16 D. melanogaster strains from two natural populations, including an ancestral African population and a derived European population. Levels of expression polymorphism were nearly equal in the two populations, but a higher number of differences was detected when comparing strains between populations. Expression variation was greatest for genes associated with few molecular functions or biological processes, as well as those expressed predominantly in males. Our analysis also identified genes that differed in expression level between the European and African populations, which may be candidates for adaptive regulatory evolution. Genes involved in flight musculature and fatty acid metabolism were over-represented in the list of candidates. Conclusions: Overall, stabilizing selection appears to be the major force governing gene expression variation within populations. However, positive selection may be responsible for much of the between-population expression divergence. The nature of the genes identified to differ in expression between populations may reveal which traits were important for local adaptation to the European and African environments. Keywords: Natural variation
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Project description:Anopheles natural genome variation
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