Regulatory Divergence in Drosophila revealed by mRNA-seq
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA125585
ORGANISM(S): Drosophila sechellia Drosophila melanogaster x Drosophila sechellia Drosophila melanogaster
PROVIDER: GSE20421 | GEO | 2010/02/20
SECONDARY ACCESSION(S): PRJNA125585
REPOSITORIES: GEO
Similar Datasets
Project description:Deep Sequencing of mRNA from Drosophila melanogaster, Drosophila Sechellia, and their F1 hybrid. These data were generated in a study to analyze the extent and specificity of trans-splicing in Drosophila. mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D. sechellia (female 0-3d post eclosion). Separate control libraries were prepared from D. melanogaster and D. sechellia total RNA (mixed before library preparation). The results of this study identified 80 novel trans-splicing events between homologous alleles of the same gene. Keywords: RNA-Seq Keywords: Expression profiling by high throughput sequencing
2010-07-20 | GSE22588 | GEO
Project description:Deep Sequencing of mRNA from Drosophila melanogaster, Drosophila Sechellia, and their F1 hybrid. These data were generated in a study to analyze the extent and specificity of trans-splicing in Drosophila. mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D. sechellia (female 0-3d post eclosion). Separate control libraries were prepared from D. melanogaster and D. sechellia total RNA (mixed before library preparation). The results of this study identified 80 novel trans-splicing events between homologous alleles of the same gene. Keywords: RNA-Seq Keywords: Expression profiling by high throughput sequencing There were 2 total samples in this study. Paired-end mRNA-seq was used to survey trans-splicing in F1 hybrids of D. melanogaster and D. sechellia. A mixed "control" library was used to assess the frequency of false-positive trans-splicing signal resulting from errors in reference genomes, high-throughput sequencing, and RT-PCR amplification based strand-switching.
2010-07-19 | E-GEOD-22588 | biostudies-arrayexpress
Project description:Background Antennae of fruit flies are the major organs responsible for detecting environmental volatiles, e.g., egg-laying substrates. An adult antenna contains many sensilla full of olfactory sensory neurons, where olfactory receptor (Or) genes are expressed. Each sensory neuron only expresses up to three receptors, making it difficult to estimate expression levels by conventional methods. In this study, we applied Illumina RNA sequencing (RNA-seq) to study the expression levels of Or and other genes in fly antennae. Results RNA from approximately 1,200 pairs of adult antennae from each sex of Drosophila melanogaster was used to obtain the antennal transcriptome of each sex. We detected approximately 12,000 genes expressed in antennae of either sex. The most highly expressed genes included pheromone-binding genes, transmembrane transporter genes, and sensory reception genes. Among the 61 annotated Or genes, we observed 53 and 54 genes (approximately 90%) expressed (fragments per kilobase of exon per million fragments mapped (FPKM) > 0.05) in male and female antennae, respectively; approximately 25 genes were expressed with FPKM > 15. Compared to previous studies, which extracted RNA from the whole body or head and used microarrays, antenna-specific transcriptomes obtained by RNA-seq provided more reliable estimates of gene expression levels and revealed many lowly expressed genes. Ninty-one genes, including one odorant-binding protein (Obp) gene and four Or genes, were differentially expressed between male and female antennae. These sexually biased genes were enriched on the X chromosome and showed enrichment in different gene ontology categories for male and female flies. The present and previous data together suggest that a gene family with putative immune response functions is related to pheromone detection and involved in the courtship behavior of male flies. Conclusions Tissue-specific RNA-seq is powerful for detecting lowly expressed genes. Our study provides new insight into the expression of olfactory-related genes in Drosophila antennae.ophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species D. melanogaster and D. simulans. Although several odorant binding protein (Obp) genes and olfactory receptor (Or) genes were suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking. We therefore studied the antennal transcriptomes, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species. Using a very stringent definition of differential gene expression, we found 147 genes (including 11 chemosensory genes) were up-regulated while only 81 genes (including 5 chemosensory genes) were down-regulated in D. sechellia. Interestingly, Obp50a exhibited the highest up-regulation, a ~100 fold increase, and Or85c – previously reported to be a larva-specific gene– showed ~20 fold up-regulation in D. sechellia. Furthermore, Ir84a, proposed to be associated with male courtship behavior, is significantly up-regulated in D. sechellia. We also found expression divergence in most of the receptor gene families between D. sechellia and the two sibling species. Our observations suggest that the host shift of D. sechellia is associated with expression profile divergence in all chemosensory gene families and is achieved mostly by up-regulation of chemosensory genes.the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species (GSE60428) and HiC analysis in Drosophila melanogaster. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter
2017-06-01 | GSE99545 | GEO
Project description:Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species D. melanogaster and D. simulans. Although several odorant binding protein (Obp) genes and olfactory receptor (Or) genes were suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking. We therefore studied the antennal transcriptomes, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species. Using a very stringent definition of differential gene expression, we found 147 genes (including 11 chemosensory genes) were up-regulated while only 81 genes (including 5 chemosensory genes) were down-regulated in D. sechellia. Interestingly, Obp50a exhibited the highest up-regulation, a ~100 fold increase, and Or85c – previously reported to be a larva-specific gene– showed ~20 fold up-regulation in D. sechellia. Furthermore, Ir84a, proposed to be associated with male courtship behavior, is significantly up-regulated in D. sechellia. We also found expression divergence in most of the receptor gene families between D. sechellia and the two sibling species. Our observations suggest that the host shift of D. sechellia is associated with expression profile divergence in all chemosensory gene families and is achieved mostly by up-regulation of chemosensory genes.
2015-10-01 | GSE67587 | GEO
Project description:Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species D. melanogaster and D. simulans. Although several odorant binding protein (Obp) genes and olfactory receptor (Or) genes were suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking. We therefore studied the antennal transcriptomes, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species. Using a very stringent definition of differential gene expression, we found 147 genes (including 11 chemosensory genes) were up-regulated while only 81 genes (including 5 chemosensory genes) were down-regulated in D. sechellia. Interestingly, Obp50a exhibited the highest up-regulation, a ~100 fold increase, and Or85c – previously reported to be a larva-specific gene– showed ~20 fold up-regulation in D. sechellia. Furthermore, Ir84a, proposed to be associated with male courtship behavior, is significantly up-regulated in D. sechellia. We also found expression divergence in most of the receptor gene families between D. sechellia and the two sibling species. Our observations suggest that the host shift of D. sechellia is associated with expression profile divergence in all chemosensory gene families and is achieved mostly by up-regulation of chemosensory genes.
2015-10-01 | GSE67861 | GEO
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2013-11-29 | E-GEOD-50049 | biostudies-arrayexpress
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.
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