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Regulatory Divergence in Drosophila revealed by mRNA-seq

ABSTRACT: Regulatory Divergence in Drosophila revealed by mRNA-seq

OTHER RELATED OMICS DATASETS IN: GSE20421

PROVIDER: PRJNA125585 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR035892_1.fastq.gz	Fastqsanger.gz
	SRR035892_2.fastq.gz	Fastqsanger.gz
	SRR035893_1.fastq.gz	Fastqsanger.gz
	SRR035893_2.fastq.gz	Fastqsanger.gz
	SRR035894_1.fastq.gz	Fastqsanger.gz

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Regulatory Divergence in Drosophila revealed by mRNA-seq (trans-splicing)

Project description:Regulatory Divergence in Drosophila revealed by mRNA-seq (trans-splicing)

| PRJNA128387 | ENA

Regulatory Divergence in Drosophila revealed by mRNA-seq

Project description:These data were generated in a study to analyze the genetic causes of gene regulatory divergence. 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, "D_mel_x_D_sec"). A mixed mRNA- seq library was prepared from D. melanogaster and D. sechellia poly(A) + RNA (mixed before library preparation, "D_mel_+_D_sec). Finally, separate mRNA-seq libraries were prepared from poly(A)+ RNA from each species ("D_mel" and "D_sec"). The results of this study showed that 78% of genes expressed in the two species are differentially expressed, and that cis- and trans-regulatory divergence affect 51% and 66% of expressed genes, respectively. Keywords: RNA-Seq

2010-02-20 | GSE20421 | GEO

Regulatory Divergence in Drosophila revealed by mRNA-seq (trans-splicing)

2010-07-20 | GSE22588 | GEO

Regulatory Divergence in Drosophila revealed by mRNA-seq (trans-splicing)

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

Regulatory divergence in Drosophila revealed by mRNA-seq.

Project description:The regulation of gene expression is critical for organismal function and is an important source of phenotypic diversity between species. Understanding the genetic and molecular mechanisms responsible for regulatory divergence is therefore expected to provide insight into evolutionary change. Using deep sequencing, we quantified total and allele-specific mRNA expression levels genome-wide in two closely related Drosophila species (D. melanogaster and D. sechellia) and their F(1) hybrids. We show that 78% of expressed genes have divergent expression between species, and that cis- and trans-regulatory divergence affects 51% and 66% of expressed genes, respectively, with 35% of genes showing evidence of both. This is a relatively larger contribution of trans-regulatory divergence than was expected based on prior studies, and may result from the unique demographic history of D. sechellia. Genes with antagonistic cis- and trans-regulatory changes were more likely to be misexpressed in hybrids, consistent with the idea that such regulatory changes contribute to hybrid incompatibilities. In addition, cis-regulatory differences contributed more to divergent expression of genes that showed additive rather than nonadditive inheritance. A correlation between sequence similarity and the conservation of cis-regulatory activity was also observed that appears to be a general feature of regulatory evolution. Finally, we examined regulatory divergence that may have contributed to the evolution of a specific trait--divergent feeding behavior in D. sechellia. Overall, this study illustrates the power of mRNA sequencing for investigating regulatory evolution, provides novel insight into the evolution of gene expression in Drosophila, and reveals general trends that are likely to extend to other species.

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Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic

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.

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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

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