Ontology highlight
ABSTRACT:
PROVIDER: PRJNA971006 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We measured gene expression across the whole genome in a panel of lines selected for a wing shape trait (angular offset). The lines were created in separate experiments, originating from two widely separated populations, and including multiple replicates of one population, but all were created using the same selection regime and trait. Here we evaluate the data with two objectives: 1) to identify candidate wing shape genes for future testing and validation, and 2) to assess variation among lines in the outcome of identical selection regimes; We used microarrays to detail the global programme of gene expression underlying the phenotypic differences among strains selected for wing shape angular offset. Experiment Overall Design: Drosophila wing discs from each of 12 selected lines were dissected at 6.2 hr prior to pupariation for RNA extraction and hybridization on Affymetrix microarrays.
2008-03-13 | E-GEOD-9107 | biostudies-arrayexpress
Project description:We measured gene expression across the whole genome in a panel of lines selected for a wing shape trait (angular offset). The lines were created in separate experiments, originating from two widely separated populations, and including multiple replicates of one population, but all were created using the same selection regime and trait. Here we evaluate the data with two objectives: 1) to identify candidate wing shape genes for future testing and validation, and 2) to assess variation among lines in the outcome of identical selection regimes We used microarrays to detail the global programme of gene expression underlying the phenotypic differences among strains selected for wing shape angular offset. Keywords: strain comparison
2008-01-02 | GSE9107 | GEO
Project description:An analysis of the transcriptional profiles of weak genetic perturbations generated via P-elements measured as heterozygotes in wing imaginal discs of Drosophila melanogaster. Abstract: A major objective of genomics is to elucidate the mapping between genotypic and phenotypic space as a step toward understanding how small changes in gene function can lead to elaborate phenotypic changes. One approach that has been utilized is to examine overall patterns of co-variation between phenotypic variables of interest, such as morphology, physiology and behavior, and underlying aspects of gene activity, in particular transcript abundance on a genome wide scale. Numerous studies have demonstrated that such patterns of co-variation occur, although these are often between samples with large numbers of unknown genetic differences (different strains, or even species) or perturbations of large effect (sexual dimorphism, or strong loss of function mutations), that may represent physiological changes outside of the normal experiences of the organism. We used weak mutational perturbations in genes affecting wing development in Drosophila melanogaster, that influence wing shape relative to a co-isogenic wild-type. We profiled transcription of 1150 genes expressed during wing development in 27 heterozygous mutants, as well as their co-isogenic wild type and one additional wild-type strain. Despite finding clear evidence of expression differences between mutants and wild-type, transcriptional profiles did not co-vary strongly with shape, suggesting that information from transcriptional profiling may not generally be predictive of final phenotype. We discuss these results in the light of possible attractor states of gene expression, and how this would affect interpretation of co-variation between transcriptional profiles and other phenotypes. Total RNA was extracted from pools of wing imaginal discs for each mutant strain as well as for their co-isogenic wild-type, and one additional wild-type strain. RNA was extracted using a modified protocol using the Qiagen RNAeasy kit.
2011-01-19 | E-GEOD-26706 | biostudies-arrayexpress
Project description:We examined adaptive morphological divergence and epigenetic variation in genetically impoverished asexual populations of a freshwater snail, Potamopyrgus antipodarum from distinct environments. These populations exhibit environment-specific adaptive divergence in shell shape and significant genome wide DNA methylation differences among differentially adapted lake and fast water flow river populations. The epigenetic variation correlated with adaptive phenotypic variation in rapidly adapting asexual animal populations. This provides one of the first examples of environmentally-driven differences in epigenetics that associates with adaptive phenotypic divergence.
2017-08-18 | GSE93836 | GEO
Project description:We examined adaptive morphological divergence and epigenetic variation in genetically impoverished asexual populations of a freshwater snail, Potamopyrgus antipodarum from distinct environments. These populations exhibit environment-specific adaptive divergence in shell shape and significant genome wide DNA methylation differences among differentially adapted lake and fast water flow river populations. The epigenetic variation correlated with adaptive phenotypic variation in rapidly adapting asexual animal populations. This provides one of the first examples of environmentally-driven differences in epigenetics that associates with adaptive phenotypic divergence.
2017-08-18 | GSE99911 | GEO
Project description:An analysis of the transcriptional profiles of weak genetic perturbations generated via P-elements measured as heterozygotes in wing imaginal discs of Drosophila melanogaster. Abstract: A major objective of genomics is to elucidate the mapping between genotypic and phenotypic space as a step toward understanding how small changes in gene function can lead to elaborate phenotypic changes. One approach that has been utilized is to examine overall patterns of co-variation between phenotypic variables of interest, such as morphology, physiology and behavior, and underlying aspects of gene activity, in particular transcript abundance on a genome wide scale. Numerous studies have demonstrated that such patterns of co-variation occur, although these are often between samples with large numbers of unknown genetic differences (different strains, or even species) or perturbations of large effect (sexual dimorphism, or strong loss of function mutations), that may represent physiological changes outside of the normal experiences of the organism. We used weak mutational perturbations in genes affecting wing development in Drosophila melanogaster, that influence wing shape relative to a co-isogenic wild-type. We profiled transcription of 1150 genes expressed during wing development in 27 heterozygous mutants, as well as their co-isogenic wild type and one additional wild-type strain. Despite finding clear evidence of expression differences between mutants and wild-type, transcriptional profiles did not co-vary strongly with shape, suggesting that information from transcriptional profiling may not generally be predictive of final phenotype. We discuss these results in the light of possible attractor states of gene expression, and how this would affect interpretation of co-variation between transcriptional profiles and other phenotypes.
2011-01-19 | GSE26706 | GEO
Project description:We have compared allelic and gene expression variation using individual-based RNA-seq data from four regional populations of the Glanville fritillary butterfly (Melitaea cinxia) in northern Europe. Two of the populations represent fragmented habitat and two continuous habitat. Based on sequence information, we constructed genealogy for four populations. Based on gene expression, we found 1841 genes to be differentially expressed between two different landscape types. Our results demonstrate genomic adaptations to living in fragmented landscapes, which are likely to be related to phenotypic life-history adaptations that have been documented for many species. RNA-seq from thorax, 174 individuals from four populations.
2014-07-04 | E-GEOD-47692 | biostudies-arrayexpress
Project description:We have compared allelic and gene expression variation using individual-based RNA-seq data from four regional populations of the Glanville fritillary butterfly (Melitaea cinxia) in northern Europe. Two of the populations represent fragmented habitat and two continuous habitat. Based on sequence information, we constructed genealogy for four populations. Based on gene expression, we found 1841 genes to be differentially expressed between two different landscape types. Our results demonstrate genomic adaptations to living in fragmented landscapes, which are likely to be related to phenotypic life-history adaptations that have been documented for many species.
2014-07-04 | GSE47692 | GEO
Project description:The interplay between phenotypic plasticity and adaptive evolution has long been an important topic of evolutionary biology. This process is critical to our understanding of a species evolutionary potential in light of rapid climate changes. Despite recent theoretical work, empirical studies of natural populations, especially in marine invertebrates, are scarce. In this study, we investigated the relationship between adaptive divergence and plasticity by integrating genetic and phenotypic variation in Pacific oysters from its natural range in China. Genome resequencing of 371 oysters revealed unexpected fine-scale genetic structure that is largely consistent with phenotypic divergence in growth, physiology, thermal tolerance and gene expression across environmental gradient. These findings suggest that selection and local adaptation are pervasive and together with limited gene flow shape adaptive divergence. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and likely favored by selection in organisms facing dynamic environments such as oysters. Divergence in heat response and tolerance implies that the evolutionary potential to a warming climate differs among oyster populations. We suggest that trade-offs in energy allocation are important to adaptive divergence with acetylation playing a role in energy depression under thermal stress.
2018-07-27 | PXD008057 | Pride
Project description:Here we present genome-wide high-coverage genotyping data on a panel of 75 human samples from Western Balkan region, Europe, that are used in addition to public data in studing the genetic variation of Southern Europe that was sequenced to the avwerage depth of 1X.
2014-08-22 | GSE59032 | GEO