Regulatory divergence in Drosophila melanogaster and D. simulans: a genome-wide analysis of allele-specific expression
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE17453
PROVIDER: PRJNA118723 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces which shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genome-wide in female adult heads of D. melanogaster, D. simulans and their F1 hybrids. A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level. Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy. In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility.
2009-08-05 | GSE17453 | GEO
Project description:Both cis- and trans-acting changes could accumulate and participate in complex interactions, so to isolate the cis-regulatory component of patterning evolution, we measured allele-specific spatial gene expression patterns in Drosophila melanogaster × D. simulans hybrid embryos. RNA-seq of cryosectioned slices revealed 55 genes with strong spatially-varying allele-specific expression, and several hundred more with weaker but significant spatial divergence. Combined with mathematical modeling and regulatory locus editing, we determine the SNP responsible for the allele-specific expression observed in the gene hunchback.
2017-08-04 | GSE102233 | GEO
Project description:Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces that shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genomewide in female adult heads of Drosophila melanogaster, D. simulans, and their F1 hybrids. A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level. Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy. In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility.
| S-EPMC2766316 | biostudies-literature
Project description:In order to test the hypothesis that adult hybrid misexpression results from the cascading effect of earlier-expressed developmentally important improperly regulated genes, as well as address whether Von Baer’s 3rd law (suggesting that earlier stages of development should be more similar between species than later stages) holds at the level of gene expression, we conducted whole-transcriptome Drosophila melanogaster cDNA microarray-based expression profiling of males of D. melanogaster, D. sechellia, and D. simulans, at four synchronized developmental time-points (3rd instar larval [larval], early pupal, late pupal, and newly-emerged adult [adult]). D. simulans and D. sechellia shared a most recent common ancestor (MRCA) ~0.5 to 1.0 million years ago (MYA) and form a clade that shared an MRCA with D. melanogaster approximately 5.4 MYA. In addition, we also performed the same analysis on the male interspecific F1 hybrids of the D. simulans (♀) × D. sechellia (♂) cross.
2010-08-03 | GSE17535 | GEO
Project description:Drosophila melanogaster x Drosophila simulans overview
| PRJNA158227 | ENA
Project description:D. yakuba, D. simulans, and D. sechellia gDNA competitively hybridized against D. melanogaster to evaluate aCGH as a means to identify diverged orthologs. 2 D. sechellia vs D. melanogaster hybs - with dye swap, 2 D. simulans vs D. melanogaster hybs with dye swap, and 8 D. yakuba vs D. melanogaster hybs with balanced dye swaps. D. yakuba vs. D. melanogaster were then analyzed in all 2,4,6,8 possible combinations that incorporated dye-swap to asses sources of variation.
2010-06-21 | E-GEOD-18416 | biostudies-arrayexpress
Project description:Drosophila simulans 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. simulans 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. simulans and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. simulans 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. simulans. 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. simulans. Furthermore, Ir84a, proposed to be associated with male courtship behavior, is significantly up-regulated in D. simulans. We also found expression divergence in most of the receptor gene families between D. simulans and the two sibling species. Our observations suggest that the host shift of D. simulans is associated with expression profile divergence in all chemosensory gene families and is achieved mostly by up-regulation of chemosensory genes.
2015-10-01 | GSE67862 | GEO
Project description:The differential production of pheromones is a major barrier to mating between species in Drosophila. Individuals from morphologically similar sister species can produce different sets of cuticular hydrocarbons that allow potential mates to identify them as a suitable partner. In order to elucidate cis-regulatory mechanisms behind speciation, we looked for allele-specific expression in hydrocarbon-producing oenocytes from F1 hybrids of the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. Oour RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes, and it can be used to pinpoint the genetic basis for a wide range of traits differing due to cis-regulatory divergence between any interfertile species.
2018-05-16 | GSE114478 | GEO
Project description:D. yakuba, D. simulans, and D. sechellia gDNA competitively hybridized against D. melanogaster to evaluate aCGH as a means to identify diverged orthologs.
2009-10-07 | GSE18416 | GEO
Project description:Y chromosome from different Drosophila simulans were introgressed into the same genetic background. Strains showing distinct sex-ratio distortion were clustered according to the ratio of males and females observed in the progeny. Strains showing disproportionally high number of female flies in the progeny were contrasted with strains displaying the proportion of male and females flies close to 1:1. In addition, interspecific Y chromosome from Drosophila sechellia (Ysec) was compared with D. simulans Y chromosomes. Total RNA was extracted from whole flies using TRIzol (Life Technologies). The synthesis of cDNA and its labeling with fluorescent dyes (Cy3 and Cy5) as well as hybridization reactions were carried out using 3DNA protocols and reagents (Genisphere). A minimum of 2 biological replicas was used, however this number varied according to the hybridization design (See 'Branco et. al, Natural variation of the Y chromosome suppresses sex ratio distortion and modulates testis-specific gene expression in Drosophila simulans' for details of the hybridization design). Microarrays were ~18,000-feature cDNA arrays spotted with D. melanogaster cDNA PCR products. We have recently annotated these probes using the D. simulans genome. Possible biases introduced by using a D. melanogaster platform for a D. simulans genome are minimized because the probed genomes are essentially identical except for the Y chromosomes. Slides were scanned using Axon 400B scanner (Axon Instruments) and GenePix Pro 6.0 software. Foreground fluorescence of dye intensities was normalized by the Loess method in Bioconductor / Limma.
2014-02-01 | GSE43665 | GEO