Ontology highlight
ABSTRACT:
PROVIDER: PRJNA655452 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12391800_1.fastq.gz | Fastqsanger.gz | |||
| SRR12391800_2.fastq.gz | Fastqsanger.gz | |||
| SRR12391801_1.fastq.gz | Fastqsanger.gz | |||
| SRR12391801_2.fastq.gz | Fastqsanger.gz | |||
| SRR12391802_1.fastq.gz | Fastqsanger.gz |
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Project description:Vegetable oils (VO) are possible substitutes for fish oil in aquafeeds but are limited by their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA). However, oilseed crops can be modified to produce n-3 LC-PUFA such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, representing a potential option to fill the gap between supply and demand of these important nutrients. Camelina sativa was metabolically engineered to produce a seed oil with around 15 % total n-3 LC-PUFA to potentially substitute for fish oil in salmon feeds. Post-smolt Atlantic salmon (Salmo salar) were fed for 11-weeks with one of three experimental diets containing either fish oil (FO), wild-type Camelina oil (WCO) or transgenic Camelina oil (DCO) as added lipid source to evaluate fish performance, nutrient digestibility, tissue n-3 LC-PUFA, and metabolic impact determined by liver transcriptome analysis. The DCO diet did not affect any of the performance or health parameters studied and enhanced apparent digestibility of EPA and DHA compared to the WCO diet. The level of total n-3 LC-PUFA was higher in all the tissues of DCO-fed fish than in WCO-fed fish with levels in liver similar to those in fish fed FO. Endogenous LC-PUFA biosynthetic activity was observed in fish fed both the Camelina oil diets as indicated by the liver transcriptome and levels of intermediate metabolites such as docosapentaenoic acid, with data suggesting that the dietary combination of EPA and DHA inhibited desaturation and elongation activities. Expression of genes involved in phospholipid and triacylglycerol metabolism followed a similar pattern in fish fed DCO and WCO despite the difference in n-3 LC-PUFA contents.
2016-12-05 | E-MTAB-4621 | biostudies-arrayexpress
Project description:Facing a bottleneck in the growth of aquaculture, and a gap in the supply and demand of the highly beneficial omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), sustainable alternatives to the traditional feeds are much needed. Therefore, in this trial, an oil extracted from newly designed plant, Camelina sativa, was tested for its n-3 replacement capabilities, using three different groups of post-smolt Atlantic salmon (Salmo salar) which were fed for 12 weeks three experimental diets; a control diet containing a blend of fish oil (5 %) and rapeseed oil (15 %) (FO), a wild-type Camelina (20 %) (WCO) and the transgenic Camelina oil (20 %) (DCO), all of them having the same basal composition. By comparing them, an overall evaluation of fish performance, fatty acid profile, feeds digestibility and gene expression was done. In the context of the new transgenic diet, there were no negative effects on the growth, survival rate or health of the fish. The whole fish n-3 levels were highest in the DCO-fed fish with EPA+DHA levels almost double compared to FO-fed fish and more than double when compared to WCO-fed ones, clearly suggesting the efficiency of the Camelina oil in providing competitive levels of n-3 LC-PUFA compared to the commercial “gold standard”.
2019-11-30 | E-MTAB-6228 | biostudies-arrayexpress
Project description:Currently, the only sustainable alternatives for dietary fish oil (FO) in aquafeeds are vegetable oils (VO) that are devoid of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA). Entirely new sources of n-3 LC-PUFA such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids through de novo production is a potential solution to fill the gap between supply and demand of these important nutrients. Camelina sativa,was metabolically engineered to produce a seed oil (ECO) with > 20 % EPA and its potential to substitute for FO in Atlantic salmon feeds was tested. Fish were fed one of three experimental diets containing FO, wild-type camelina oil (WCO) or ECO as the sole lipid sources for 7-weeks. Inclusion of ECO did not affect any of the performance parameters studied and enhanced apparent digestibility of individual n-6 and n-3 PUFA compared to dietary WCO. High levels of EPA were maintained in brain, liver and intestine (pyloric caeca), and levels of DPA and DHA were increased in liver and intestine of fish fed ECO compared to fish fed WCO likely due to increased LC-PUFA biosynthesis based on up-regulation of the genes. Fish fed WCO and ECO showed slight lipid accumulation within hepatocytes similar to that with WCO, although not significantly different to fish fed FO. The regulation of a small number of genes could be attributed to the specific effect of ECO (311 features) with metabolism being the most affected category. The EPA oil from transgenic Camelina (ECO) could be used as a substitute for FO, however it is a hybrid oil containing both FO (EPA) and VO (18:2n-6) fatty acid signatures that resulted in similarly mixed metabolic and physiological responses.
2016-03-01 | E-MTAB-3268 | biostudies-arrayexpress
Project description:This study was performed to investigate the effect of camelina oil-based diets on the immune function of Atlantic cod, as measured by gene expression in spleen. Atlantic cod were fed with one of three practical diets (three tanks per diet): a control diet using herring oil as a lipid source (FO diet), and two experimental diets using vegetable oil from Camelina sativa to replace 40% or 80% of herring oil (40CO and 80CO diets). We studied both the effect of the diet alone on basal spleen gene expression levels, as well as the effect of the diet after fish were injected with the synthetic double-stranded RNA polyriboinosinic polyribocytidylic acid (pIC), which mimics a viral immune stimulus.
2014-12-31 | GSE54358 | GEO
Project description:Soybean is a rich source of protein and oil and a primary feedstock for biodiesel production. Previous research on soybean indicated that protein, oil and yield are controlled quantitatively in soybean seeds. However, genetic mechanisms controlling seed composition and yield in soybean remain unknown. We used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean varieties, which differ in seed weight, yield, protein content and oil content. Some of the differentially expressed genes identified in this study may play important roles in controlling these traits.
2015-04-29 | GSE21598 | GEO
Project description:MicroRNAs and siRNAs are important regulators of plant development and seed formation, yet their population and abundance in the oil crop Brassica napus are still less understood, especially at different developmental stages and among cultivars with varied seed oil contents. Here, we systematically analyzed the small RNA expression profiles of Brassica napus seeds at early embryonic developmental stages in a high oil content and a low oil content Brassica napus cultivars, both cultured in two environments. A total of 50 conserved miRNAs and 11 new miRNAs were identified, together with some new miRNA targets. Expression analysis revealed some miRNAs with varied expression levels in different seed oil content cultivars or at different embryonic developmental stages. A large amount of 23-nt small RNAs with specific nucleotide composition preference were also identified, which may present new classes of functional small RNAs.
2011-12-28 | GSE34727 | GEO
Project description:Camelina is an annual oilseed plant that is gaining momentum as a biofuel winter cover crop. Understanding gene regulatory networks (GRNs) is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. Also, we performed RNA-seq assays of Camelina's seed at 5, 8, and 11 days post-anthesis (DPA) to improve the transcriptomic resolution of the early stages of the Camelina seed development. We identified ~350 TFs highly co-expressed with lipid-related genes (LRGs). After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16/22 TF using DNA affinity purification sequencing (DAP-seq). Enrichment analyses supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes and aspects unique to Camelina. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confident and shortlist of Camelina TFs involved in controlling lipid metabolism during seed development.
2022-01-13 | GSE184283 | GEO
Project description:New de novo sources of omega 3 (n-3) long chain polyunsaturated fatty acids (LC-PUFA) are required as alternatives to fish oil in aquafeeds in order to maintain adequate levels of the beneficial fatty acids, eicosapentaenoic and docosahexaenoic (EPA and DHA, respectively). The present study investigated the use of an EPA+DHA oil derived from a transgenic Camelina sativa in feeds for Atlantic salmon (Salmo salar) containing low levels of fishmeal (35 %) and fish oil (10 %), reflecting current commercial formulations, to determine the impacts on intestinal transcriptome, tissue fatty acid profile and health of farmed salmon. Post-smolt Atlantic salmon were fed for 12-weeks with one of three experimental diets containing either a blend of fish oil/rapeseed oil (FO), wild-type camelina oil (WCO) or transgenic camelina oil (DCO) as added lipid source. The DCO diet did not affect any of the fish performance or health parameters studied. Analyses of the mid and hindgut transcriptomes showed only mild effects on metabolism. Flesh of fish fed the DCO diet accumulated almost double the amount of n-3 LC-PUFA than fish fed the FO or WCO diets, indicating that these oils from transgenic oilseeds offer the opportunity to increase the n-3 LC-PUFA in farmed fish to levels comparable to those found twelve years ago.
2017-05-31 | E-MTAB-5529 | biostudies-arrayexpress
Project description:MicroRNAs and siRNAs are important regulators of plant development and seed formation, yet their population and abundance in the oil crop Brassica napus are still less understood, especially at different developmental stages and among cultivars with varied seed oil contents. Here, we systematically analyzed the small RNA expression profiles of Brassica napus seeds at early embryonic developmental stages in a high oil content and a low oil content Brassica napus cultivars, both cultured in two environments. A total of 50 conserved miRNAs and 11 new miRNAs were identified, together with some new miRNA targets. Expression analysis revealed some miRNAs with varied expression levels in different seed oil content cultivars or at different embryonic developmental stages. A large amount of 23-nt small RNAs with specific nucleotide composition preference were also identified, which may present new classes of functional small RNAs. Examination of small RNA profiles in 2 different seed oil content rapeseed culvitars at 2 locations.
2011-12-28 | E-GEOD-34727 | biostudies-arrayexpress
Project description:This study was performed to investigate assess the impacts of CO and/or CM containing diets on Atlantic salmon hepatic gene expression in order to identify candidate molecular biomarkers of responses to camelina-containing diets. Atlantic salmon were fed diets with complete or partial replacement of FO and/or FM with camelina oil (CO) and/or camelina meal (CM) in a 16-week trial (Control diet: FO; Test diet: 100% FO replacement with CO, with solvent-extracted FM and inclusion of 10% CM (100COSEFM10CM). A 44K microarray experiment identified liver transcripts that responded to 100COSEFM10CM (associated with reduced growth) compared to FO controls at week 16.
2015-05-12 | GSE56784 | GEO