Freshwater systems
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1016429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27187793_1.fastq.gz | Fastqsanger.gz | |||
| SRR27187793_2.fastq.gz | Fastqsanger.gz | |||
| SRR27187794_1.fastq.gz | Fastqsanger.gz | |||
| SRR27187794_2.fastq.gz | Fastqsanger.gz | |||
| SRR27187795_1.fastq.gz | Fastqsanger.gz |
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Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment. This is the RNA-seq experiment, DNA methylation data (bisulfite-seq) is provided under accession number GSE82310.
2021-11-03 | GSE186925 | GEO
Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment.
2017-05-30 | GSE82310 | GEO
Project description:Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic planktonic bacteria, dwelling in freshwater systems (lakes, ponds, and streams) across all climatic zones and across all continents. This includes habitats characterised by strongly fluctuating environmental conditions. So the experiments were designed to mimick winter and summer scenarios with additional impact of UV irradiation. Comparative transcriptomic studies were conducted to analyse gene-expression levels in contrasting experimental conditions. Overall, molecular candidates were revealed that may contribute in rapid acclimatisation of this strain in their immediate environment.
2017-10-31 | GSE98129 | GEO
Project description:In order to identify gene expression difference between marine and freshwater stickleback populations, we compared the transcriptomes of seven adult tissues (eye, gill, heart, hypothalumus, liver, pectoral muscle, telencephalon) between a marine population sampled from the mouth of the Little Campbell river in British Columbia (LITC) and a freshwater population (Fishtrap Creek, FTC) from northern Washington. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents.
2011-12-30 | GSE34783 | GEO
Project description:In order to identify gene expression difference between marine and freshwater stickleback populations, we compared the transcriptomes of seven adult tissues (eye, gill, heart, hypothalumus, liver, pectoral muscle, telencephalon) between a marine population sampled from the mouth of the Little Campbell river in British Columbia (LITC) and a freshwater population (Fishtrap Creek, FTC) from northern Washington. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents. Four to five fish from each population were used as biological replicates for each of the seven tissues. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents. All fish were of similar age and were raised in the same aquarium (salinity: 3.5 ppt), with a plastic divider separating the marine and freshwater groups. One male and four females were sampled from each population. Microarray experiments were performed in a 2-color format on custom Agilent arrays: experimental RNA samples were labeled with Cy5, and the common reference RNA sample was labeled with Cy3. The reference RNA was total RNA isolated from a large number of 7-day-post-hatch embryos from the freshwater population of Bear Paw Lake, Alaska (BEPA). One technical replicate was used for each array, and one of the hypothalamus samples (Hyp_FTC#3) was excluded from further analysis due to poor quality indicators. FTC#1 liver and LITC#2 pectoral muscle samples did not yield RNA of sufficient quality for the microarray experiment, and were also excluded from hybridization.
2011-12-30 | E-GEOD-34783 | biostudies-arrayexpress
Project description:Fish gills represent a complex organ that perform multiple physiological functions and is composed of several cell types. Among these cells, ionocytes are implicated in the maintenance of ion homeostasis. However, because the ionocyte represents only a small percent of whole gill tissue, its specific transcriptome can be overlooked among the numerous cell types included in the gill. The objective of this study is to better understand ionocyte functions by comparing the RNA expression of this cell type in freshwater and seawater adapted rainbow trout. To realize this objective, ionocytes were captured from gill cryosections using laser capture microdissection after immunohistochemistry. Then, transcriptome analyses were performed on an Agilent trout oligonucleotide microarray. Gene expression analysis identified 108 unique annotated genes differentially expressed between freshwater and seawater ionocytes, with a gene fold higher than 3. Most of these genes were up regulated in freshwater cells. Interestingly, several genes implicated in ion transport, extracellular matrix and structural cellular proteins appeared up regulated in freshwater ionocytes. Among them, several ion transporters, such as CIC2, SLC26A6, and NBC, were validated by qPCR and/or in situ hybridization. The latter technique allowed us to localize the transcripts of these ion transporters in only ionocytes and more particularly in the freshwater cells. Genes involved in metabolism and also several genes implicated in transcriptional regulation, cell signaling and the cell cycle were also over-expressed in freshwater ionocytes. In conclusion, laser capture microdissection combined with microarray analysis allowed for the determination of the cell signature of scarce cells in fish gills, such as ionocytes, and aided characterization of the transcriptome of these cells in freshwater and seawater adapted trout.
2015-10-08 | GSE69409 | GEO
Project description:Comparison of freshwater tolerant (accession CCAP 1310/196, origin Hopkins River Falls, Victoria, Australia) and strictly marine strain (accession CCAP 1310/4, origin San Juan de Marcona, Peru) of E. siliculosus under different salinites
2009-12-19 | E-TABM-731 | biostudies-arrayexpress
Project description:Chlorella sp. HS2 is a halotolerant microalga exhibiting relatively high biomass productivity and substantially high lipid accumulation in marine growth media, which suggests this alga as an important crop for industrial algal cultivation systems. To determine pathways leading to HS2's acclimation responses to salt stress, we performed RNA-seq analysis with triplicated cultures grown in freshwater and marine media at both exponential and stationary growth phases. We then run de novo assembly to obtain HS2 transcriptome, which in turn was annotated and processed to extract dysregulated pathways. Results showed a large proportion of down-regulated genes, for instance photosynthesis and TCA pathways. Photosynthesis appeared, however, to recover at the stationary phase, while the general down-regulation pattern was maintained.
2020-03-12 | GSE146789 | GEO
Project description:Planktonic and sediment microbiomes from two recreational freshwater systems in Salta, Argentina
| PRJNA772538 | ENA
Project description:Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome‐wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.
2020-05-15 | GSE123659 | GEO