Multiple species
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA646232 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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: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. Non-replicated small RNA samples from four melanogaster-subgroup species.
2014-07-22 | E-GEOD-56244 | biostudies-arrayexpress
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
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:To explore how brains change upon species evolution, we generated the first whole central brain comparative single-cell transcriptomic atlases of three closely-related but ecologically-distinct drosophilids: D. melanogaster, D. simulans and D. sechellia. D. melanogaster and D. simulans are cosmopolitan generalists, while the island endemic D. sechellia exhibits extreme niche specialism on the ripe noni fruit of the Morinda citrifolia shrub. The global cellular composition of central brains is well-conserved in the three Drosophila species, but we predicted a few cell types (perineurial glia, sNPF and Dh44 neurons) with divergent frequencies. Gene expression analysis revealed that distinct cell types within the central brain evolve at different rates and patterns; notably, several glial cell types exhibit the greatest divergence between species. Compared to D. melanogaster, the cellular composition and gene expression patterns of the central brain in D. sechellia displays greater deviation than those of D. simulans, indicating that the distinctive ecological specialization of D. sechellia is reflected in the structure and function of its brain. Gene expression changes in D. sechellia encompass metabolic and ecdysone signaling genes, indicative of adaptations to its novel ecological demands. Additional single-cell transcriptomic analysis on D. sechellia revealed genes and cell types responsive to noni juice supplementation, showing glial cells as key sites for both physiological and genetic adaptation to novel conditions. Our comparative transcriptomic atlases of drosophilid brains will provide an entry point to more broadly study the evolvability of nervous systems across and beyond the Drosophila genus.
2023-11-21 | GSE247965 | 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.
2014-11-18 | GSE63333 | GEO
Project description:Extensive sex-biased expression has been seen in multiple surveys D. melanogaster. We were interested in broadly sampling sex-biased expression of orthologs and species- or lineage-specific genes in the Drosophila genus. To appropriately assay gene expression in multiple species, we used custom microarrays designed against each of six species that broadly sample the phylogenetic space represented by the newly completed genomes (D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis and D. mojavensis) and an array designed against D. melanogaster to determine the overall patterns of sex-biased expression in those species and their chromosome linkage. Keywords: other
2007-11-08 | GSE6640 | GEO
Project description:Here we show that Drosophila sechellia—a specialist on the fruit of Morinda citrifolia that recently diverged from its generalist sister-species, D. simulans—has rapidly accumulated loss-of-function alleles and reduced gene expression at genes affecting olfaction, detoxification, and metabolism. While D. sechellia increases expression of genes involved with oogenesis and fatty acid metabolism when on its host, many more genes show reduced expression in D. sechellia. For several functionally related genes, this decrease in expression is associated with loss-of-function alleles. The rapid accumulation of these alleles potentially affected D. sechellia’s initial adaptation to M. citrifolia, likely contributes to D. sechellia’s poor competitive ability off of its host, and increases ecological isolation between D. sechellia and its sister species. Keywords: comparative hybridization, gene expression
2008-11-25 | GSE13723 | GEO
Project description:Here we show that Drosophila sechelliaM-bM-^@M-^Ta specialist on the fruit of Morinda citrifolia that recently diverged from its generalist sister-species, D. simulansM-bM-^@M-^Thas rapidly accumulated loss-of-function alleles and reduced gene expression at genes affecting olfaction, detoxification, and metabolism. While D. sechellia increases expression of genes involved with oogenesis and fatty acid metabolism when on its host, many more genes show reduced expression in D. sechellia. For several functionally related genes, this decrease in expression is associated with loss-of-function alleles. The rapid accumulation of these alleles potentially affected D. sechelliaM-bM-^@M-^Ys initial adaptation to M. citrifolia, likely contributes to D. sechelliaM-bM-^@M-^Ys poor competitive ability off of its host, and increases ecological isolation between D. sechellia and its sister species. Keywords: comparative hybridization, gene expression 2 species (simulans and sechella) by choice vs no-choice treatment for octanoic & hexanoic acid blend
2008-11-25 | E-GEOD-13723 | biostudies-arrayexpress