Generation and characterization of the Arctic charr multi-organ transcriptome
Ontology highlight
ABSTRACT:
INSTRUMENT(S): 454 GS FLX+
ORGANISM(S): Salvelinus alpinus
SUBMITTER: Céline Noirot
PROVIDER: E-MTAB-3522 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general.
2011-06-01 | GSE26306 | GEO
Project description:Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general. 18 microarray slides representing 6 individuals from 3 treatment groups (Intolerant, Tolerant and Control). One test cDNA labeled with cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide Reference design: 18 slides (6 x Tolerant fish, 6x Intolerant fish, 6x Control fish) were used.
2011-06-01 | E-GEOD-26306 | biostudies-arrayexpress
Project description:Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions.
2011-07-05 | GSE29610 | GEO
Project description:Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions. 24 microarray slides representing 6 individuals from 4 treatment groups (Control, During, After and Recovery). One test cDNA labeled with Cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide. Reference design: 6x control fish, 6x group D fish, 6x group A fish, 6x group R fish.
2011-07-05 | E-GEOD-29610 | biostudies-arrayexpress
Project description:Arctic charr exposed to acute thermal stress
| PRJNA136745 | ENA
Project description:The aim of this sequencing experiment was to make available liver tissue expression for selected fish species, northern pike (Esox lucius, Eluc), coho salmon (Oncorhynchus kisutch, Okis) and Arctic charr (Salvelinus alpinus, Salp), for comparative expression studies between the species. Samples in replicate of four were sacrificed according to protocols at each of the facilities from where samples were obtained. RNA was extracted from samples and Illumina TruSeq Stranded mRNA libraries were built. Sequencing was performed in two passes on an Illumina HiSeq2500, paired-end 125bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the NCBI genomes of the respective species using STAR and gene level counting using RSEM and NCBI gene annotation.
2020-04-30 | E-MTAB-8962 | biostudies-arrayexpress
Project description:Generation and characterization of the Arctic charr multi-organ transcriptome
| PRJEB9273 | ENA
Project description:We investigated whether two sympatric Arctic charr morphs (Salvelinus alpinus) with contrasting feeding ecology, the small-benthic (SB) and the planktivorous (PL) charr of Thingvallavatn in Iceland, exhibit genetically based differences in gene expression variability, and how dominance would affect their hybrids. Through a common-garden experiment, we identified genes clusters with similar expression variability, most differing among the two morphs. In the hybrids, gene expression variability was substantially affected by maternal effects and biases towards the PL charr, while the expression of a minority of genes felt outside the range of parental values. These profiles of expression variability were consistent across mRNA and miRNA datasets. Predominant maternal effects and PL charr biases were also observed at the level of average gene expression, including candidate genes involved in the lower jaw development.
2023-01-01 | GSE193797 | GEO
Project description:Parental effects represent an important source of variation in offspring phenotypes. Depending on the specific mechanisms involved, parental effects may be caused to different degrees by either the maternal or paternal parent, and these effects may in turn act at different stages of development. In order to detect parental effects acting on gene transcription regulation and length phenotype during ontogeny, the transcriptomic profiles of two reciprocal hybrids from Laval × Rupert and Laval × domestic populations of brook charr were compared at hatching, yolk sac resorption, and 15 weeks after exogenous feeding. Using a salmonid cDNA microarray, our results show that parental effects modulated gene expression among reciprocal hybrids only at the yolk sac resorption stage. In addition, Laval × domestic and Laval × Rupert reciprocal hybrids differed in the magnitude of theses parental effects, with 199 and 630 differentially expressed transcripts, respectively. This corresponds to a maximum of 18.5% of the analyzed transcripts. These transcripts are functionally related to cell cycle, nucleic acid metabolism and intracellular protein traffic, which is consistent with observed differences associated with embryonic development and growth differences in other fish species. Our results thus illustrate how parental effects on patterns of gene transcription seem dependent on the genetic architecture of the parents. In addition, in absence of transcriptomic differences, the non-transcriptomic deposits could also act to highlight the offspring differences in length before the yolk sac resorption.
2012-12-31 | GSE42435 | GEO