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PROVIDER: PRJNA1152725 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Complete submergence represses photosynthesis and aerobic respiration causing rapid mortality in most terrestrial plants, but some species have evolved traits allowing them to survive prolonged flooding. Here, we studied the response to submergence of two species and their F1 hybrid in the genus Rorippa, which is related to the model Arabidopsis. We showed that these species have high tolerance to complete, deep submergence, but R. sylvestris survived longer than R. amphibia and the F1 hybrid. While the former restricted growth upon submergence, the latter two genotypes showed induced stem and petiole elongation and had higher aerenchyma contents, indicative of a low oxygen escape strategy. Arabidopsis GeneChip microarrays were used for whole-genome transcript profiling of roots of young plants exposed to air or a 24-h submergence treatment, using a probe mask based on hybridisation of genomic DNA of both species to the arrays. The induction by the submergence treatment of genes involved in glycolysis and fermentation and repression of many energy consuming pathways was similar to the response to low oxygen of Arabidopsis and rice. Notably, sucrose synthases, glycolysis and fermentation genes were more strongly induced in the less tolerant R. amphibia than in R. sylvestris, which might indicate faster carbohydrate consumption of the former, while some genes involved in hydrogen peroxide scavenging were strongly and specifically induced in the latter. F1 hybrids showed a generally weaker response to submergence and an additive mode of gene action, which did not change by the submergence treatment. Keywords: stress response and a comparison of genotypes
2009-12-01 | GSE13641 | GEO
Project description:Pregnane X receptor (PXR) is generally considered the most important sensor of natural and anthropogenic xenobiotics in vertebrates. In Xenopus, however, PXR plays a role in neural development and it is irresponsive to xenobiotics. We report a first broad-spectrum amphibian xenobiotic receptor, which is an ortholog of the mammalian constitutive androstane receptor (CAR). The low basal activity and pronounced responsiveness to activators such as drugs and steroids displayed by the Xenopus CAR resemble PXR, which both trace back to a common ancestor early in the divergence of land vertebrates. The constitutive activity of CAR emerged first in Sauropsida (reptiles and birds) and it is common to all fully terrestrial land vertebrates (Amniota). This activity can be mimicked by humanizing just two amino acids of the Xenopus CAR. These results demonstrate a remarkable plasticity of CAR which enabled its employment as Xenopus xenosensors. They open way to toxicogenomic and bioaugmentation studies in amphibians, a critically endangered taxon of land vertebrates. Taken together, we provide evidence for a much earlier origin of CAR, for its conservation in tetrapods which exceeds that of PXR, and for its remarkable functional plasticity which enabled its role as a PXR-like xenosensor in Amphibia. We used microarrays to detect global transcriptional changes in Xenopus laevis livers following pregnenolone and artemisinin treatment in order to identify target genes of xlCAR. Arteminisin or pregnenolone were injected intraperitoneally into three frogs on two consecutive days. The control group received in parallel two DMSO injections. All frogs were sacrificed 24 h after the second injection by decapitation, and livers were immediately frozen in liquid nitrogen. After RNA isolation, specimens within the same experimental group were pooled.
2011-10-10 | E-GEOD-28510 | biostudies-arrayexpress
Project description:Complete submergence represses photosynthesis and aerobic respiration causing rapid mortality in most terrestrial plants, but some species have evolved traits allowing them to survive prolonged flooding. Here, we studied the response to submergence of two species and their F1 hybrid in the genus Rorippa, which is related to the model Arabidopsis. We showed that these species have high tolerance to complete, deep submergence, but R. sylvestris survived longer than R. amphibia and the F1 hybrid. While the former restricted growth upon submergence, the latter two genotypes showed induced stem and petiole elongation and had higher aerenchyma contents, indicative of a low oxygen escape strategy. Arabidopsis GeneChip microarrays were used for whole-genome transcript profiling of roots of young plants exposed to air or a 24-h submergence treatment, using a probe mask based on hybridisation of genomic DNA of both species to the arrays. The induction by the submergence treatment of genes involved in glycolysis and fermentation and repression of many energy consuming pathways was similar to the response to low oxygen of Arabidopsis and rice. Notably, sucrose synthases, glycolysis and fermentation genes were more strongly induced in the less tolerant R. amphibia than in R. sylvestris, which might indicate faster carbohydrate consumption of the former, while some genes involved in hydrogen peroxide scavenging were strongly and specifically induced in the latter. F1 hybrids showed a generally weaker response to submergence and an additive mode of gene action, which did not change by the submergence treatment. Experiment Overall Design: We used replicated clones of Rorippa amphibia, Rorippa sylvestris and their F1 hybrid. Plants were grown on sand in pots for three weeks, completely submerged in rain water for 24 h, or kept in air as a control. Three biological controls were collected per genotype, each consisting of a pool of three individuals. Roots were separated from the shoots, quickly rinsed and immediately frozen and used for RNA extraction and hybridization to Arabidopsis Ath1 GeneChips. Genomic DNA of Rorippa amphibia and Rorippa sylvestris was also hybridized to the GeneChips in order to filter out badly performing probes due to sequence divergences from Arabidopsis.
2009-12-04 | E-GEOD-13641 | biostudies-arrayexpress
Project description:Functional modifications shape the ability of populations to cope with anthropogenic environmental changes. These modifications are mediated by complex interactions between transmitted and non-transmitted changes which limit their prediction. To study how these changes are intertwined with evolutionary processes in a case of persistent anthropogenic environmental change, we characterized population structure, genetic diversity and individual response on gene expression of the tree frog Hyla orientalis along a gradient of radioactive contamination around the Chernobyl nuclear power plant. We detected lower effective population size in populations most exposed to ionizing radiation that is not compensated by migrations from surrounding areas. We also highlight a decreased body condition of frogs living in the most contaminated area, a peculiar transcriptomics signature and stop-gained mutations in genes involved in energy metabolism. Population most exposed to ionizing radiation in the Chernobyl exclusion zone experience both genetic drift and functional changes that collectively point towards deleterious effects of ionizing radiation on tree frogs and potential difficulty to adapt to this novel environment.
2023-06-15 | GSE211060 | GEO
Project description:Two species of frogs Transcriptome
| PRJNA374468 | ENA
Project description:Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. This work is funded by Agency Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT; "Genome Science" Grant ID 221S0002). Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors)
2016-10-24 | E-GEOD-73419 | biostudies-arrayexpress