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

ABSTRACT: 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

ORGANISM(S): Drosophila melanogaster x Drosophila sechellia Drosophila sechellia Drosophila melanogaster

PROVIDER: GSE22588 | GEO | 2010/07/20

SECONDARY ACCESSION(S): PRJNA128387

REPOSITORIES: GEO

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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: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

Cis regulatory effects on A-to-I RNA editing in Drosophila melanogaster, Drosophila sechellia and their F1 hybrids

Project description:We applied microfluidic multiplex PCR and deep sequencing (mmPCR-seq) to quantify RNA editing levels at targeted sites in Drosophila melanogaster, Drosophila sechellia and the species-specific alleles of their F1 hybrids to understand the contribution of cis and trans regulatory factors to regulating RNA editing levels.

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Drosophila Divergence 20091001

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

Drosophila Divergence 20091001

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.

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Transcriptional profiling of two drosophila species: Drosophila melanogaster versus Drophila sechellia

Project description:Transcriptional profiling of 3 day old virgin male and female adults comparing control male Drosophila melanogaster (MDM) versus male D sechellia (MDS) and comparing control female Drosophila melanogaster (FDM) versus female D sechellia (FDS). Goal was to determine why D sechellia is tolerant to octanoïc acid, the major toxic compound of Morinda citrifolia fruit

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Developmental time-course study of Drosophila melanogaster, D. sechellia, D. simulans, and D. sim x D.s sec hybrids

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.

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Genomics analysis of hexanoic acid exposure in Drosophila species

Project description:We analyze the gene expression response to hexanoic acid in Drosophila simulans, Drosophila melanogaster, and Drosophila sechellia

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Comparison of D. simulans/D. mauritiana F1 male hybrid genome-wide expression values to pure-species parents

Project description:Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression. In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed compared to non-sex-biased genes in sterile F1 male hybrids of Drosophila species. In this study, we examined and compared patterns of misexpression in 4 day old sterile male F1 hybrids of Drosophila simulans and its sibling species, D. mauritiana. We analyzed hybrids using genome-wide D. melanogaster arrays from the Drosophila Genome Resource Center (DGRC). The results from a custom array (GPL4022) for this species pair, from the custom array and the genome-wide array for the D. simulans-D. sechellia species pair, and from the larvae of these two species pairs using the custom array, are presented separately. Keywords: Comparison of pure-species Drosophila expression to hybrid expression

2006-09-13 | GSE5601 | GEO

Comparison of D. simulans/D. sechellia F1 male hybrid genome-wide expression values to pure-species parents

Project description:Species often produce sterile hybrids early in their evolutionary divergence, and some evidence suggests that hybrid sterility may be associated with deviations or disruptions in gene expression. In support of this idea, many studies have shown that a high proportion of male-biased genes are underexpressed compared to non-sex-biased genes in sterile F1 male hybrids of Drosophila species. In this study, we examined and compared patterns of misexpression in 4 day old sterile male F1 hybrids of Drosophila simulans and its sibling species, D. sechellia. We analyzed hybrids using genome-wide D. melanogaster arrays from the Drosophila Genome Resource Center (DGRC). The results from a custom array (GPL4022) for this species pair, from the custom array and the genome-wide array for the D. simulans-D. mauritiana species pair, and from the larvae of these two species pairs using the custom array, are presented separately. Keywords: Comparison of pure-species Drosophila expression to hybrid expression

2006-09-13 | GSE5607 | GEO

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