Transcriptional rearrangements associated with thermal stress and preadaptation in Baikal whitefish (Coregonus baicalensis)
Ontology highlight
ABSTRACT:
ORGANISM(S): Coregonus baicalensis
PROVIDER: GSE278874 | GEO | 2024/10/15
REPOSITORIES: GEO
Similar Datasets
Project description:Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare of maraena whitefish (Coregonus maraena) exposed to inconvenient temperatures. The present study compares the physiological impact of either acute or gradual temperature rise from 18 °C to 24 °C on maraena whitefish in aquaculture. We analysed microarray-based transcriptome profiles in liver, spleen and kidney and identified a common set of diagnostic biomarkers each indicating thermal stress induced by acute or gradual temperature rise in the selected tissues. We identified common and unique tissue- and stress mode-specific pathways reflecting metabolic, cell signalling and immunologic crossroads to cope with thermal stress.
2017-06-04 | GSE95422 | GEO
Project description:In this work, we describe the transcriptional profiles of Baikal omul juveniles after acute and chronic temperature stress exposure. The juveniles were kept for 1.5 months at 9–12 °C, followed by exposure to acute stress (heating to 21 °C for 1 hour) and chronic stress (heating to 21 °C for 24 hours 3 times a week for a month) in the Experimental Freshwater Aquarium Complex for Baikal Hydrobionts at the Limnological Institute (LIN SB RAS). The information on the transcriptional profiles will contribute to further understanding of the mechanisms of adaptation of whitefish to the environment.
2024-12-03 | GSE283291 | GEO
Project description:Transcriptional rearrangements associated with thermal stress and preadaptation in Baikal whitefish (Coregonus baicalensis)
| PRJNA1169341 | ENA
Project description:Stress represents a major factor negatively affecting fish welfare in aquaculture. The head kidney is the effective centre for neuro-immune interactions in teleost as it is the main secretory organ of stress hormones and gathers major leukocyte populations. The present study investigated the influence of acute and long-term (chronic) handling stress in maraena whitefish. The aim was to define stress-related physiological changes in maraena whitefish using traditionally used and newly identified parameters. We determined the levels of the well-established biomarkers included triglycerides, lactate and cholesterol in blood plasma. In addition, the transcriptome of the head kidney of differently treated whitefish was recorded to identify new potential biomarkers and to investigate the relationship between immune functions and stress responses.
2021-09-01 | GSE183125 | GEO
Project description:We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex-specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf (limnetic) and normal (benthic) whitefish. We observed a sex-bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between sexes. Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed. We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development based on co-localization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations. 88% of eQTL-phenotypic QTL co-localization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs. Hotspots co-localized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc finger protein in one case, control gene expression directly related to adaptive phenotypic divergence. We observed little evidence of co-localization of brain eQTL with behavioral QTL, which provides insight on the genes identified by behavioral QTL studies. These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological differences appear to play a key role in this divergence. Keywords: eQTL mapping, gene expression, linkage mapping, adaptive radiation, Coregonus, microarrays
2008-09-01 | GSE12068 | GEO
Project description:We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex-specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf (limnetic) and normal (benthic) whitefish. We observed a sex-bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between sexes. Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed. We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development based on co-localization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations. 88% of eQTL-phenotypic QTL co-localization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs. Hotspots co-localized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc finger protein in one case, control gene expression directly related to adaptive phenotypic divergence. We observed little evidence of co-localization of brain eQTL with behavioral QTL, which provides insight on the genes identified by behavioral QTL studies. These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological differences appear to play a key role in this divergence. Keywords: eQTL mapping, gene expression, linkage mapping, adaptive radiation, Coregonus, microarrays The objective of this study was to elucidate the genomic distribution and sex-specificity of brain eQTL in dwarf and normal lake whitefish. Dissected brain tissue (250-350 mg) was sampled for 55 individuals from a hybrid x dwarf backcross mapping family. We used a loop design (YANG and SPEED 2002; CHURCHILL 2002) to maximize the number of sampled meioses. Each of 55 samples was technically replicated on two distinct slides, while performing dye swapping (Cy3 and Alexa) to estimate the dye intensity variation bias. After correcting for local background, raw intensity values were both log2 transformed and normalized using the regional LOWESS method implemented in the R/MANOVA software (KERR et al. 2000). We used a previously generated linkage map based on the same backcross individuals for which gene expression was measured. eQTL mapping was performed with QTL Cartographer.
2008-09-01 | E-GEOD-12068 | biostudies-arrayexpress
Project description:In this work, we describe the transcriptional profiles of peled juveniles after acute and chronic temperature stress exposure. The juveniles were kept for 1.5 months at 9–12 °C and then exposed to acute stress (heating to 21 °C for 1 hour) and chronic stress (heating to 21 °C for 24 hours 3 times a week for a month) in the Experimental Freshwater Aquarium Complex for Baikal Hydrobionts at the Limnological Institute (LIN SB RAS). The information on the transcriptional profiles will contribute to further understanding of the mechanisms of adaptation of whitefish to the environment.
2024-12-03 | GSE283290 | GEO
Project description:Coregonid fishes are among the most successful groups in the subarctic, boreal, and subalpine fresh waters of the northern hemisphere. Limnetic-benthic sympatric species-pairs from two different evolutionary lineages, the North American lake whitefish (Coregonus clupeaformis species complex), and the European whitefish (Coregonus lavaretus species complex), are becoming the subject of close attention to explore the role of natural selection during the ecological speciation. Baikal endemic coregonids, limnetic omul (Coregonus migratorius), and benthic lacustrine whitefish (Coregonus baicalensis) are the only representatives of another unique lineage that has not left the lake since the divergence from the two above. Due to Pleistocene oscillations sympatric limnetic-benthic divergence has been replicated here many times within the same water body over a long geological period in contrast to both Europe and America where sympatric species-pairs are the results of post-glacial secondary-contacts between glacial isolates during the Late Pleistocene on the territory of each continent. Mitochondrial genomes encode genes that are essential for respiration and metabolism. Data on complete mitogenomes of Baikal endemic coregonids provided here will complement ongoing investigations on energy metabolism as the main biological function involved in the divergence between limnetic and benthic whitefish.
| S-EPMC7748752 | biostudies-literature
Project description:Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare and particular health status of maraena whitefish (Coregonus maraena) farmed at four different stocking densities. Transcriptome profiling revealed that numerous stress-related signaling pathways were activated in liver and kidney under ED and HD conditions, such as ERK/MAPK, mTOR, glucocorticoid receptor, SAPK/JNK and JAK/Stat signalling, as well as p38 and p53 signalling. Moreover, several stress-relevant effector pathways were found to be overexpressed including glycolysis and glycogen degradation. Strikingly, a high number of upregulated genes in kidney and in liver of fish kept at HD (compared to MD fish) were related to immunological processes, such as Acute-phase response signalling, B cell receptor signaling, CD28 signaling in T helper cells, and Interleukin-6 signaling.
2016-01-06 | GSE76543 | GEO
Project description:Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare and particular health status of maraena whitefish (Coregonus maraena) farmed at four different stocking densities. Transcriptome profiling revealed that numerous stress-related signaling pathways were activated in liver and kidney under ED and HD conditions, such as ERK/MAPK, mTOR, glucocorticoid receptor, SAPK/JNK and JAK/Stat signalling, as well as p38 and p53 signalling. Moreover, several stress-relevant effector pathways were found to be overexpressed including glycolysis and glycogen degradation. Strikingly, a high number of upregulated genes in kidney and in liver of fish kept at HD (compared to MD fish) were related to immunological processes, such as Acute-phase response signalling, B cell receptor signaling, CD28 signaling in T helper cells, and Interleukin-6 signaling. Four stocking density conditions were investigated: an uncrowded âmoderateâ density (MD: 33 kg trout/m³) , an elevated density (ED: 60 kg/m³ ), a low density (LD: 10 kg/m³ ), and high density (HD: 100 kg/m³). The experiment was performed twice, randomly assigned to identical glass tanks with MD (100 individuals), ED (180 individuals), LD (30 individuals), and HD (300 individuals). Trout were sampled 8 d after experimental onset.
2016-01-06 | E-GEOD-76543 | biostudies-arrayexpress