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Indel array-based genotyping of pupariation site preference among Drosophila sechellia backcross progeny

ABSTRACT: We identified 6,975 insertion/deletion events of between 10 and 100 bp in length from the Drosophila simulans and Drosophila sechellia Mercator/MAVID genomic sequence alignment. Replicate pure samples of Drosophila simulans and Drosophila sechellia gDNA were competitively hybridized to measure the expected relative hybridization intensity of alleles from each species. We used these measured intensities to assess the likelihood that the hybridization signal at each probe in an experimental animal reflected homozygosity or heterozygosity at that locus.

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

PROVIDER: GSE44443 | GEO | 2013/02/26

SECONDARY ACCESSION(S): PRJNA190706

REPOSITORIES: GEO

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Indel array-based genotyping of pupariation site preference among Drosophila sechellia backcross progeny

Project description:We identified 6,975 insertion/deletion events of between 10 and 100 bp in length from the Drosophila simulans and Drosophila sechellia Mercator/MAVID genomic sequence alignment. Replicate pure samples of Drosophila simulans and Drosophila sechellia gDNA were competitively hybridized to measure the expected relative hybridization intensity of alleles from each species. We used these measured intensities to assess the likelihood that the hybridization signal at each probe in an experimental animal reflected homozygosity or heterozygosity at that locus. Indel array Agilent-022089 sim-sech.v.1.3

2013-02-26 | E-GEOD-44443 | biostudies-arrayexpress

Indel array-based genotyping of pupariation site preference among Drosophila sechellia backcross progeny

Project description:Indel array-based genotyping of pupariation site preference among Drosophila sechellia backcross progeny

| PRJNA190706 | ENA

D. simulans vs. Sechellia bodies choice vs. no choice -Affymetrix

2008-11-25 | GSE13723 | GEO

D. simulans vs. Sechellia bodies choice vs. no choice -Affymetrix

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

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.

2010-08-03 | GSE17535 | GEO

D. simulans vs. Sechellia adult heads choice vs. no choice -DGRC Two Colour arrays with Dye Swapping

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. Our results suggest that a subset of genes reduce or lose function as a consequence of host specialization, which may explain why, in general, specialist insects tend to shift to chemically similar hosts. Moreover, if the accumulation of non- or weakly functional genes in a specialist enhances the ecological isolation between it and other species, then this process may explain why specialists are speciose. Keywords: comparative hybridization, gene expression

2008-12-03 | GSE13778 | GEO

D. simulans vs. Sechellia adult bodies choice vs. no choice -DGRC Two Colour arrays with Dye Swapping

2008-12-03 | GSE13789 | GEO

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

2021-10-04 | GSE185176 | GEO

D. simulans vs. Sechellia adult bodies choice vs. no choice -DGRC Two Colour arrays with Dye Swapping

Project description:Here we show that Drosophila sechelliaâa specialist on the fruit of Morinda citrifolia that recently diverged from its generalist sister-species, D. simulansâhas 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. sechelliaâs initial adaptation to M. citrifolia, likely contributes to D. sechelliaâs poor competitive ability off of its host, and increases ecological isolation between D. sechellia and its sister species. Our results suggest that a subset of genes reduce or lose function as a consequence of host specialization, which may explain why, in general, specialist insects tend to shift to chemically similar hosts. Moreover, if the accumulation of non- or weakly functional genes in a specialist enhances the ecological isolation between it and other species, then this process may explain why specialists are speciose. Keywords: comparative hybridization, gene expression 2 species (simulans and sechella) by choice vs no-choice treatment for octanoic & hexanoic acid blend

2010-06-24 | E-GEOD-13789 | biostudies-arrayexpress

Comparison of D. simulans/D. sechellia third instar male larvae hybrid expression values to pure-species larvae 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 F1 hybrid male third instar larvae of Drosophila simulans and its sibling species, D. sechellia. We analyzed hybrids using custom cDNA arrays we developed from RT-PCRs of spermatogenesis-related transcripts from these species and another sibling species (D. mauritiana). The results from a commercial genome-wide array and custom chip for adults of this species pair, from the custom chip and the genome-wide chip for adults of the D. simulans-D. mauritiana species pair, and from the larvae of the D. simulans-D. mauritiana species pair, are presented separately. Keywords: Comparison of pure-species Drosophila expression to hybrid expression in larvae

2006-09-13 | GSE5598 | GEO

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