Transcriptome analysis of threespine sticklebacks acclimated in different salinities
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ABSTRACT:
ORGANISM(S): Gasterosteus aculeatus
PROVIDER: GSE58447 | GEO | 2015/01/01
SECONDARY ACCESSION(S): PRJNA252659
REPOSITORIES: GEO
Similar Datasets
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: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: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:Transcriptome analysis of threespine sticklebacks acclimated in different salinities
| PRJNA252659 | ENA
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:The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom that naturally tolerates a broad range of salinities, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypoosmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling at 8 time points across 10 hours. We found substantial remodeling of the transcriptome, with over half of the genome differentially expressed in at least one time point. The peak response occurred within 1 hour, with strong repression of genes involved in functions related to cell growth and osmolyte production, and strong induction of genes implicated in stress defense such as scavenging reactive oxygen species and maintaining osmotic balance. Notably, transcripts largely returned to baseline levels within 4–10 hours, with growth resuming shortly thereafter, suggesting that gene expression dynamics may be useful for predicting acclimation. Moreover, comparison to a study of expression profiling following months-long acclimation of C. cryptica to freshwater revealed little overlap between the genes and processes differentially expressed in cells exposed to acute stress versus fully acclimated conditions. Altogether, this study highlights the power of time-resolved transcriptomics to reveal fundamental insights into how cells dynamically respond to an acute environmental shift and provides new insights into how diatoms mitigate natural salinity fluctuations and have successfully diversified across freshwater habitats worldwide.
2022-06-23 | GSE206725 | GEO
Project description:We examine whether there are differences in gene expression between aggressive versus nonaggressive behavioral types of individuals within a natural population of male threespined sticklebacks (Gasterosteus aculeatus). We compared gene expression profiles of aggressive male sticklebacks to nonaggressive males in four regions of the brain (brainstem, cerebellum, diencephalon and telencephalon). We identified new candidate genes related to aggressiveness, including SLC38a, a solute carrier which has been linked to GABAergic neuron reuptake of glutamine.
2017-02-28 | GSE78861 | GEO
Project description:In many habitats, microorganisms are exposed to high or fluctuating salinities and evolved specific acclimation strategies to thrive in those environments. Euryhaline microorganisms can grow in a broad range of salinities, from low ionic strength like freshwater up to twofold seawater salinities. Here, we analyzed the salt acclimation process of the euryhaline model cyanobacterium Synechocystis sp. PCC 6803 in a multi-omics approach by combining transcriptomic, proteomic and metabolomic analyses. The Overall, the comparison of salt-induced proteome and transcriptome changes revealed a good correleation between the proteome and transcriptome that as most the majority of stably up-regulated proteins also showed elevated mRNA transcript levels. However, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably also involves the action of small regulatory RNAs acting at the post-transcriptional level. In addition to the rapid and stable steady upregulation of compatible solute biochemistry, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably involves the action of small regulatory RNAs. Moreover, the coordinated induction of several stress proteins known to be involved in iron and oxidative stress responses as well as of mechano-sensitive channels was observed. Based on these data, an extended salt stimulon can be defined comprising many proteins directly or indirectly related to compatible solute metabolism, ion and water movements as well as a defined set of small regulatory RNAs. Moreover, the massive accumulation of the compatible solute glucosylglycerol had large impact on the overall carbon and nitrogen metabolism. Our comprehensive data set provides the basis for future attempts to engineer cyanobacterial salt tolerance and to search for processes regulating this important environmental acclimation process.
2022-01-07 | GSE174316 | GEO
Project description:Algae of the genus Dunaliella are known to be able to grow in a wide range of salinities. To investigate which genes may be important for growth under extremely low or high salinities, a survey of the Dunaliella sp. transcriptome was performed by microarray analysis. For the cDNA microarray 778 expressed sequence tags (ESTs) were generated from a cDNA library of Dunaliella sp. The cDNA microarray was used to compare the transcription profile of cells that were acclimated to extreme saline conditions (0.08 M and 4.5 M NaCl) with the transcription profile of cells acclimated to an intermediate salinity at 1.5 M NaCl. The comparative microarray analysis indicated that 211 out of the 778 ESTs differed in their expression levels more than two-fold in cells grown at extreme different salinity when compared to cells grown at intermediate salinity (1.5M NaCl). The sequences of these 211 cDNAs were classified into 169 non-redundant gene clusters. Of these genes, the expression of 36 genes was increased and 69 genes were suppressed in cells grown at low salinity. The expression of 49 genes was increased and 85 genes were suppressed in cells grown at high salinity. One-hundred thirty four genes have been revealed to show up- and down-regulation by high salinity (4.5M NaCl). Of the high salinity-regulated genes 52% were also influenced by low salinity (0.08M NaCl), revealing a dense overlap between low and high salt responses. Only 35 genes are regulated independently by low salt condition. Strong relationships, however, were observed in the expression of these extreme salinity-responsive genes based on Venn diagram analysis, which found 70 genes that responded to these two salinity conditions. Refined expression analysis using gene-specific primers and real-time PCR for selected transcripts was in agreement with microarray results for most genes tested. This study provides the first large-scale survey of the transcriptome in the microalga Dunaliella sp. and it provides a platform for further functional investigation of differentially expressed genes in Dunaliella. Keywords: Low salt(0.08M NaCl) or high salt(4.5M NaCl)-acclimated cells
2010-01-01 | GSE10271 | GEO