Ontology highlight
ABSTRACT:
PROVIDER: PRJNA644748 | ENA |
REPOSITORIES: ENA
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Project description:The comparison of transcriptome profiles among populations is a powerful tool for investigating the role of gene expression change in adaptation to new environments. In this study, we use massively parallel sequencing of 39 cDNAs obtained from large samples of adult males, to compare a population of Drosophila simulans from a natural reserve within its ancestral range (eastern Africa) with a derived population collected in the strongly anthropized Rhone valley (France). The goal was to scan for adaptation linked to the invasion of new environments by the species. Among 15,090 genes retained for the analysis, 794 were found to be differentially expressed between the two populations. We observed an increase in expression of reproduction-related genes in eastern Africa, and an even stronger increase in expression of Cytochrome P450, Glutathione transferase and Glucuronosyl transferase genes in the derived population. These three gene families are involved in detoxification processes, which suggests that pesticides are a major environmental pressure for the species in this area. The survey of the Cyp6g1 upstream region revealed the insertion of a transposable element, Juan, in the regulatory sequence that is almost fixed in the Rhoˆne Valley, but barely present in Mayotte. This shows that Cyp6g1 has undergone parallel evolution in derived populations of D. simulans as previously shown for D. melanogaster. The increasing amount of data produced by comparative population genomics and transcriptomics should permit the identification of additional genes associated with functional divergence among those differentially expressed. Two samples for two populations, with diverse medium. Each sample composed of 100 males from a 100 different wild-caught females
2013-11-22 | E-GEOD-49127 | biostudies-arrayexpress
Project description:The comparison of transcriptome profiles among populations is a powerful tool for investigating the role of gene expression change in adaptation to new environments. In this study, we use massively parallel sequencing of 39 cDNAs obtained from large samples of adult males, to compare a population of Drosophila simulans from a natural reserve within its ancestral range (eastern Africa) with a derived population collected in the strongly anthropized Rhone valley (France). The goal was to scan for adaptation linked to the invasion of new environments by the species. Among 15,090 genes retained for the analysis, 794 were found to be differentially expressed between the two populations. We observed an increase in expression of reproduction-related genes in eastern Africa, and an even stronger increase in expression of Cytochrome P450, Glutathione transferase and Glucuronosyl transferase genes in the derived population. These three gene families are involved in detoxification processes, which suggests that pesticides are a major environmental pressure for the species in this area. The survey of the Cyp6g1 upstream region revealed the insertion of a transposable element, Juan, in the regulatory sequence that is almost fixed in the Rhoˆne Valley, but barely present in Mayotte. This shows that Cyp6g1 has undergone parallel evolution in derived populations of D. simulans as previously shown for D. melanogaster. The increasing amount of data produced by comparative population genomics and transcriptomics should permit the identification of additional genes associated with functional divergence among those differentially expressed.
2013-11-22 | GSE49127 | GEO
Project description:The abundance of transposable elements and DNA repeat sequences in mammalian genomes raises the question whether such insertions represent passive evolutionary baggage or may influence the expression of complex traits. We addressed this question in Drosophila melanogaster where the effects of single transposable elements on complex traits can be assessed in genetically identical individuals reared in controlled environments. Here we demonstrate that single P-element insertions in the intergenic region between the Gustatory receptor 5a (Gr5a) and Trapped in endoderm 1 (Tre1), which encodes an orphan receptor, exert complex pleiotropic effects on fitness traits, including selective nutrient intake, resistance to starvation and heat stress, and life span. Mutations in this region interact epistatically with downstream components of the insulin signaling pathway. Transposon-induced sex-specific and sex-antagonistic effects further accentuate the complex influences intergenic transposable elements can contribute to complex phenotypes. Keywords: Transcriptional profiles of P-element insertion lines in the Tre1/GR5a region of Drosophila
2006-05-31 | GSE4789 | GEO
Project description:Hybrid incompatibility between Drosophila melanogaster and D. simulans is caused by a lethal interaction of the proteins encoded by the Hmr and Lhr genes. In D. melanogaster the loss of HMR results in mitotic defects, an increase in transcription of transposable elements and a deregulation of heterochromatic genes. To investigate the molecular mechanisms that mediate HMRs function, we measured genome-wide localization of HMR in D. melanogaster by chromatin immunoprecipitation. Interestingly, we find HMR localizing to genomic insulator sites that can be classified into two groups. One group that belongs to the gypsy class of insulators and another one that separates HP1a binding regions from active promoters. The activity of these promoters is strongly affected in Hmr mutant flies. Our data provide a novel link between HMR and insulator proteins and suggest a key role for genome organization in the formation of species.
2017-01-31 | GSE86106 | GEO
Project description:Curration of small RNAs from four melanogaster-subgroup species (Drosophila simulans, Drosophila sechellia, Drosophila erecta, and Drosophila yakuba) for the purpose of non-coding RNA annotation and comparative genomics assessment.
2014-07-22 | GSE56244 | GEO
Project description:We identified 6,975 insertion/deletion events of between 10 and 100 bp in length from the Drosophila simulans and Drosophila sechellia Mercator/MAVID genomic sequence alignment. Replicate pure samples of Drosophila simulans and Drosophila sechellia gDNA were competitively hybridized to measure the expected relative hybridization intensity of alleles from each species. We used these measured intensities to assess the likelihood that the hybridization signal at each probe in an experimental animal reflected homozygosity or heterozygosity at that locus.
2013-02-26 | GSE44443 | GEO
Project description:We analyze the gene expression response to hexanoic acid in Drosophila simulans, Drosophila melanogaster, and Drosophila sechellia
2021-10-04 | GSE185176 | GEO
Project description:In order to characterize duplication polymorphisms in Drosophila simulans, we applied comparative genome hybridization (CGH) using tiling arrays originally designed to cover the full euchromatic genome of its sister species D. melanogaster. We only used the ~900,000 probes in the tiling arrays that had a perfect and unique match to the D. simulans genome (droSim1). We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates. The probabilities of mutation were parsed to make duplication calls. The supplementary file linked to each Sample record contains for each probe, its location in the D. simulans genome and its posterior probability of being duplicated (output from the Hiddem Markov Model)
2011-09-01 | GSE29260 | GEO
Project description:We used DamID-seq to analyze the genome-wide binding patterns of the group B Sox proteins Dichaete and SoxNeuro in four species of Drosophila: D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura. Both binding site turnover between species and a comparison of the binding properties of the two partially-redundant transcription factors were analyzed. We found that, despite widespread turnover, genomic intervals that are commonly bound by both Dichaete and SoxNeuro are highly conserved in Drosophila. DamID for Dichaete (Dichaete-Dam) was performed in D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura, while DamID for SoxNeuro (SoxN-Dam) was performed in D. melanogaster and D. simulans. The control experiment, Dam-only, was performed in all species. Three biological replicates were sequenced for each condition in each species.
2014-11-18 | E-GEOD-63333 | biostudies-arrayexpress