Ontology highlight
ABSTRACT:
PROVIDER: PRJNA590031 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10483012.fastq.gz | Fastqsanger.gz | |||
| SRR10483013.fastq.gz | Fastqsanger.gz | |||
| SRR10483014.fastq.gz | Fastqsanger.gz | |||
| SRR10483015.fastq.gz | Fastqsanger.gz | |||
| SRR10483016.fastq.gz | Fastqsanger.gz |
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Project description:To avoid negative environmental impacts of escapees and potential inter-breeding with wild populations, the Atlantic salmon farming industry has and continues to extensively test triploid fish that are sterile. However, they often show differences in performance, physiology, behavior and morphology compared to diploid fish, with increased prevalence of vertebral deformities and ocular cataracts as two of the most severe disorders. Here, we investigated the mechanisms behind the higher prevalence of cataracts in triploid salmon, by comparing the transcriptional patterns in lenses of diploid and triploid Atlantic salmon, with and without cataracts. We assembled and characterized the Atlantic salmon lens transcriptome and used RNA-seq to search for the molecular basis for cataract development in triploid fish. Transcriptional screening showed only modest differences in lens mRNA levels in diploid and triploid fish, with few uniquely expressed genes. In total, there were 165 differentially expressed genes (DEGs) between the cataractous diploid and triploid lens. Of these, most were expressed at lower levels in triploid fish. Differential expression was observed for genes encoding proteins with known function in the retina (phototransduction) and proteins associated with repair and compensation mechanisms. The results suggest a higher susceptibility to oxidative stress in triploid lenses, and that mechanisms connected to the ability to handle damaged proteins are differentially affected in cataractous lenses from diploid and triploid salmon.
2020-07-08 | GSE153933 | GEO
Project description:This study investigated firstly, the impact of ploidy on growth performance and whole body composition of Atlantic salmon at different early freshwater stages (34 dph (days post-hatching) alevin; 109 dph; fry and 162 dph parr;) and secondly, whether phenotypic differences at these stages were reflected in protein samples collected from whole fish, white muscle or liver tissue. Female diploid and triploid Atlantic salmon (n = 3) were first fed at 35 dph and then maintained by feeding to satiation on commercial feeds. NOTE on file nomenclature - T/D refer to triploid/diploid; E* refers to sequential protein extract (1 or 2) and S3 refers to sampling time point #3 (all other files with either no suffix or long suffix are sampling time point #2)
2017-12-14 | PXD005451 | Pride
Project description:This study investigated firstly, the impact of ploidy on growth performance and whole body composition of Atlantic salmon at different early freshwater stages (34 dph (days post-hatching) alevin; 109 dph; fry and 162 dph parr;) and secondly, whether phenotypic differences at these stages were reflected in protein samples collected from whole fish, white muscle or liver tissue. Female diploid and triploid Atlantic salmon (n = 3) were first fed at 35 dph and then maintained by feeding to satiation on commercial feeds.
2017-12-14 | PXD005452 | Pride
Project description:This study investigated firstly, the impact of ploidy on growth performance and whole body composition of Atlantic salmon at different early freshwater stages (34 dph (days post-hatching) alevin; 109 dph; fry and 162 dph parr;) and secondly, whether phenotypic differences at these stages were reflected in the protein samples collectedproteome from whole fish, white muscle or liver tissue. Female diploid and triploid Atlantic salmon (n = 3) were first fed at 35 dph and then maintained by feeding to satiation on commercial feeds.
2017-12-14 | PXD005450 | Pride
Project description:Current commercially available feeds for salmon are predominantly made of plant ingredients, with consequent changes to the composition and contents of a range of nutrients and other components in the diet. There are concerns that, with these major changes in raw materials, new feeds will affect not only the composition and contents of nutrients, but also the bioavailability and, combined with the limited knowledge of micronutrient requirements for Atlantic salmon, this might impact growth performance and health of the fish. The present study investigated the effects of graded levels of a micronutrient package supplemented to feeds formulated with low levels of marine ingredients and fed to diploid and triploid Atlantic salmon throughout the freshwater phase. Specifically, fish were fed three diets containing low levels of FM and FO and identical in formulation other than being supplemented with 3 levels (L1, 100 %; L2, 200 % and L3, 400 %) of a micronutrient mix formulated as a modification of current nutrient levels reported for salmon. Duplicate groups of diploid and triploid parr were fed the experimental diets from around 30 g to seawater transfer and the effects on growth performance, feed efficiency, biochemical composition, liver histology, hepatic gene expression (transcriptome) and smoltification efficiency determined. Microarray analysis revealed that the hepatic transcriptome profile of diploid fish fed diet L2 was more similar to that observed in triploids fed diet L3 than to those fed L2, suggesting that micronutrient requirements of triploid salmon may differ from levels accepted in diploid salmon. Different levels of micronutrient supplementation affected the expression of key genes involved in lipid metabolism. In particular sterol biosynthesis pathways (steroid and terpenoid backbone synthesis) were down-regulated in both L2-fed diploids and L3-fed triploids when compared with diet L1-fed diploids and triploids, respectively. Gene sets analysis showed an up-regulation of genes involved in immune processes in triploid salmon fed diet L3. Another biological category affected by diet in triploid salmon was genetic information processing. In fish fed diet L3 down-regulation of RNA degradation, proteasome, RNA polymerase, spliceosome and ribosome was observed, suggesting a decrease in protein turnover in this group, which may indicate a decrease in energy expenditure. In addition, one-carbon metabolism was affected by diet in diploid and triploid salmon.
2018-11-14 | E-MTAB-6302 | biostudies-arrayexpress
Project description:To ensure sustainability of aquaculture, plant-based ingredients are being used in feeds to replace marine-derived products. However, plants contain secondary metabolites which can affect food intake and nutrient utilisation of fish. The application of nutritional stimuli during early development can induce long-term changes in animal physiology. Recently, we successfully used this approach to improve the utilisation of plant-based diets in diploid and triploid Atlantic salmon. In the present study we explored the molecular mechanisms occurring in the liver of salmon when challenged with a plant-based diet in order to determine the metabolic processes affected, and the effect of ploidy. Microarray analysis revealed that nutritional history had a major impact on the expression of genes. Key pathways of intermediary metabolism were up-regulated, including oxidative phosphorylation, pyruvate metabolism, TCA cycle, glycolysis and fatty acid metabolism. Other differentially expressed pathways affected by diet included protein processing in endoplasmic reticulum, RNA transport, endocytosis and purine metabolism. The interaction between diet and ploidy also had an effect on the hepatic transcriptome of salmon. The biological pathways with the highest number of genes affected by this interaction were related to gene transcription and translation, and cell processes such as proliferation, differentiation, communication and membrane trafficking. The present study revealed that nutritional programming induced changes in a large number of metabolic processes in Atlantic salmon, which may be associated with the improved fish performance and nutrient utilisation demonstrated previously. In addition, differences between diploid and triploid salmon were found, supporting recent data that indicate nutritional requirements of triploid salmon may differ from those of their diploid counterparts.
2017-10-24 | E-MTAB-5813 | biostudies-arrayexpress
Project description:The transcriptome response of 12 amoebic gill disease (AGD) affected Atlantic salmon were compared to 6 AGD naive Atlantic salmon at 19 days post infection. The transcriptome response was examined in the gill, liver and anterior kidney.
2008-09-01 | E-MEXP-1286 | biostudies-arrayexpress
Project description:This experiment was designed to test the effect of alpha-linolenic acid (ALA) and insulin on liver slices prepared from Atlantic salmon. Liver slices were incubated with increasing concentrations of ALA and insulin from 20µM to 100µM and 10nM to 100nM, respectively. RNA was subsequently sequenced and response was evaluated and compared to the expected response from Atlantic salmon feeding trials. The purpose of this was to evaluate liver slice culture as a cell culture system for studying lipid metabolism in Atlantic salmon.
2019-05-08 | E-MTAB-7366 | biostudies-arrayexpress
Project description:The optimal dietary requirement of omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFA), namely docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), for Atlantic salmon that promotes optimal growth and health warrants careful investigation. We used 44K microarrays to study the influence of increasing levels of dietary DHA + EPA (0, 1.0 and 1.4% of the diet, as formulated) in the presence of high linoleic acid (LA) on Atlantic salmon growth and liver transcriptome. After a 14-week feeding trial, Atlantic salmon fed diet ω3LC0 (i.e. 0% of DHA + EPA) showed significantly lower final weight and weight gain, and higher feed conversion ratio compared with ω3LC1.0 and ω3LC1.4 diet groups. The microarray experiment identified 55 and 77 differentially expressed probes (Rank Products analyses; PFP < 10%) in salmon fed diets ω3LC1.4 and ω3LC1.0 compared with those fed diet ω3LC0, respectively. The comparison between ω3LC1.4 and ω3LC1.0 revealed 134 differentially expressed probes.
2020-02-03 | GSE128472 | GEO