Ontology highlight
ABSTRACT:
PROVIDER: PRJNA622478 | ENA |
REPOSITORIES: ENA
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Project description:European sculpins (Cottus) harbor an example of a recent hybrid speciation event, which entails the invasion of a new habitat by the hybrid species. We compare the transcriptomes of both parental species and the hybrid species to understand how they differ. F2 crosses between the parent species are compared to the hybrid species and its parent species to identify unique patterns of the hybrid species due to the initial hybridization process or respectively to other processes. See the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology no doi yet) for more information.
2012-03-27 | GSE36755 | GEO
Project description:European sculpins (Cottus) harbor an example of a recent hybrid speciation event, which entails the invasion of a new habitat by the hybrid species. We compare the transcriptomes of both parental species and the hybrid species to understand how they differ. F2 crosses between the parent species are compared to the hybrid species and its parent species to identify unique patterns of the hybrid species due to the initial hybridization process or respectively to other processes. See the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology no doi yet) for more information. The transcriptome was compared between an invasive hybrid species of Cottus (Sieg population n = 8) and its parent species C.rhenanus and C.perifretum. Expression profiles of both parental populations were assessed by two independent replicate population (C.rhenanus: Broel and Naaf; C.perifretum Laarse Beek and Witte Nete; each population n = 8). The transcriptomes of F2 crosses between the populations of C.rhenanus and C.perifretum were assessed with for independent crosses with 4 biological replicates for each cross (n = 4 x 4 = 16). We used a custom design microarray with probes designed based on transcriptome sequencing. We used a newly developed calibration method to account for differences in individual probe binding behavior and to detect and remove probes unfit for analysis. Data stored as “normalized data” are normalized and quality filtered based on this new calibration method and normalized for interarray comparability by division by the 75%tile signal intensity for each array. Please refer to the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology; no doi yet) for more information.
2012-03-26 | E-GEOD-36755 | biostudies-arrayexpress
Project description:Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, “species” also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbor stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.
2016-10-28 | GSE89262 | GEO
Project description:[original Title] Transcriptomic responses to heat-stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success. Invasive species are increasingly prevalent in marine ecosystems worldwide. Although many studies have examined the ecological effects of invasives, little is known about physiological mechanisms that might contribute to invasive success. The mussel Mytilus galloprovincialis, a native of the Mediterranean Sea, is a successful invader on the central and southern coasts of California, where it has largely displaced the native congener, Mytilus trossulus. It has been previously shown that thermal responses of several physiological traits may underlie the capacity of M. galloprovincialis to out-compete M. trossulus in warm habitats. To elucidate possible differences in stress-induced gene expression between these congeners, we developed an oligonucleotide microarray with 8,874 probes representing 4,488 different genes that recognized mRNAs of both species. In acute heat-stress experiments, 1,531 of these genes showed temperature-dependent changes in gene expression that were highly similar in the two congeners. In contrast, 96 genes showed species-specific responses to heat-stress, functionally characterized by their involvement in oxidative stress, proteolysis, energy metabolism, ion transport, cell signaling, and cytoskeletal reorganization. The gene that showed the biggest difference between the species was the gene for the molecular chaperone small heat shock protein 24, which was highly induced in M. galloprovincialis and showed only a small change in M. trossulus. These different responses to acute heat-stress may help to explain—and predict—the invasive success of M. galloprovincialis in a warming world.
2010-10-11 | GSE19031 | GEO
Project description:New Plectosphaerellaceous species from Dutch garden soil
| PRJEB32847 | ENA
Project description:New Plectosphaerellaceous species from Dutch garden soil
| PRJEB32474 | ENA
Project description:The invasive marine mussel Mytilus galloprovincialis has displaced the native congener Mytilus trossulus from central and southern California, but the native species remains dominant at more northerly sites that have high levels of freshwater input. To determine the extent to which interspecific differences in physiological tolerance to low salinity might explain limits to the invasive species’ biogeography, we used an oligonucleotide microarray to compare the transcriptional responses of these two species to an acute decrease in salinity. Among 6,777 genes on the microarray, 117 genes showed significant changes that were similar between species, and 12 genes showed significant species-specific responses to salinity stress. Osmoregulation and cell cycle control were important aspects of the shared transcriptomic response to salinity stress, whereas the genes with species-specific expression patterns were involved in mRNA splicing, polyamine synthesis, exocytosis, translation, cell adhesion, and cell signaling. Forty-five genes that changed expression significantly during salinity stress also changed expression during heat stress, but the direction of change in expression was typically opposite for the two forms of stress. These results (i) provide insights into the role of changes in gene expression in establishing physiological tolerance to acute decreases in salinity, and (ii) indicate that transcriptomic differences between M. galloprovincialis and M. trossulus in response to salinity stress are subtle and involve only a minor fraction of the overall suite of gene regulatory responses.
2011-01-10 | GSE25111 | GEO