Transcriptomic profiling of egg quality in seabass (Dicentrarchus labrax)
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ABSTRACT:
ORGANISM(S): Dicentrarchus labrax
PROVIDER: GSE84559 | GEO | 2016/12/31
SECONDARY ACCESSION(S): PRJNA329662
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptomic profiling of egg quality in seabass (Dicentrarchus labrax)
| PRJNA329662 | ENA
Project description:To understand the genetic basis of coping style in European seabass, fish from a full factorial mating (10 females x 50 males) were reared in common garden and individually tagged. Individuals coping style was characterized through behavior tests at four different ages, categorizing fish into proactive or reactive: a hypoxia avoidance test (at 255 days post hatching, dph) and 3 risk-taking tests (at 276, 286 and 304 dph). We observed significant heritability of the coping style, higher for the average of risk-taking scores (h2 = 0.45 ± 0.14) than for the hypoxia avoidance test (h2 = 0.19 ± 0.10). The genetic correlations between the three risk-taking scores were very high (rA = 0.96-0.99) showing that although their repeatability was moderately high (rP = 0.64-0.72), successive risk-taking tests evaluated the same genetic variation. A mild genetic correlation between the results of the hypoxia avoidance test and the average of risk-taking scores (0.45 ± 0.27) suggested that hypoxia avoidance and risk-taking tests do not address exactly the same behavioral and physiological responses. Genetic correlations between weight and risk taking traits showed negative values whatever the test used in our population i.e. reactive individual weights were larger. The results of this quantitative genetic analysis suggest a potential for the development of selection programs based on coping styles that could increase seabass welfare without altering growth performances. Overall, it also contributes to a better understanding of the origin and the significance of individual behavioral differences.
| S-EPMC5167369 | biostudies-literature
Project description:BackgroundMale European seabass, already predominant (~ 70%) in cultured stocks, show a high incidence (20-30%) of precocious sexual maturation under current aquaculture practices, leading to important economic losses for the industry. In view of the known modulation of reproductive development by swimming exercise in other teleost species, we aimed at investigating the effects of sustained swimming on reproductive development in seabass males during the first year of life in order to determine if swimming could potentially reduce precocious sexual maturation.MethodsPre-pubertal seabass (3.91 ± 0.22 g of body weight (BW)) were subjected to a 10 week swimming regime at their optimal swimming speed (Uopt) in an oval-shaped Brett-type flume or kept at rest during this period. Using Blazka-type swim tunnels, Uopt was determined three times during the course of the experiment: 0.66 m s- 1 at 19 ± 1 g BW, 10.2 ± 0.2 cm of standard length (SL) (week 1); 0.69 m s- 1 at 38 ± 3 g BW, 12.7 ± 0.3 cm SL (week 5), and also 0.69 m s- 1 at 77 ± 7 g BW, 15.7 ± 0.5 cm SL (week 9). Every 2 weeks, size and gonadal weight were monitored in the exercised (N = 15) and non-exercised fish (N = 15). After 10 weeks, exercised and non-exercised males were sampled to determine plasma 11-ketotestosterone levels, testicular mRNA expression levels of genes involved in steroidogenesis and gametogenesis by qPCR, as well as the relative abundance of germ cells representing the different spermatogenic stages by histological examination.ResultsOur results indicate that sustained swimming exercise at Uopt delays testicular development in male European seabass as evidenced by decreased gonado-somatic index, slower progression of testicular development and by reduced mRNA expression levels of follicle stimulating hormone receptor (fshR), 3-beta-hydroxysteroid dehydrogenase (3βhsd), 11-beta hydroxysteroid dehydrogenase (11βhsd), estrogen receptor-beta (erβ2), anti-mullerian hormone (amh), structural maintenance of chromosomes protein 1B (smc1β), inhibin beta A (inhba) and gonado-somal derived factor 1 (gsdf1) in exercised males as compared with the non-exercised males.ConclusionsSwimming exercise may represent a natural and non-invasive tool to reduce the incidence of sexually precocious males in seabass aquaculture.
| S-EPMC5897932 | biostudies-literature
Project description:An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) I
| PRJNA336034 | ENA
Project description:An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) II
| PRJNA336035 | ENA
Project description:BackgroundThe European seabass (Dicentrarchus labrax), one of the most extensively cultured species in European aquaculture productions, is, along with the gilthead sea bream (Sparus aurata), a prospective model species for the Perciformes which includes several other commercially important species. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Revealing transcripts involved in immune response and studying their relative expression enhances the understanding of the immune response mechanism and consequently also the creation of vaccines. The analysis of expressed sequence tags (EST) is an efficient and easy approach for gene discovery, comparative genomics and for examining gene expression in specific tissues in a qualitative and quantitative way.ResultsHere we describe the construction, analysis and comparison of a total of ten cDNA libraries, six from different tissues infected with V. anguillarum (liver, spleen, head kidney, gill, peritoneal exudates and intestine) and four cDNA libraries from different tissues infected with Nodavirus (liver, spleen, head kidney and brain). In total 9605 sequences representing 3075 (32%) unique sequences (set of sequences obtained after clustering) were obtained and analysed. Among the sequences several immune-related proteins were identified for the first time in the order of Perciformes as well as in Teleostei.ConclusionThe present study provides new information to the Gene Index of seabass. It gives a unigene set that will make a significant contribution to functional genomic studies and to studies of differential gene expression in relation to the immune system. In addition some of the potentially interesting genes identified by in silico analysis and confirmed by real-time PCR are putative biomarkers for bacterial and viral infections in fish.
| S-EPMC2674461 | biostudies-literature
Project description:Fish respond to stressors by means of an array of changes that involve many biological compartments including molecular, cellular, metabolic, physiological and behavioral acclimation. Among these changes, the immune system also experiences significant alterations that are characterized by an induction of the innate non-specific responses and changes in the acquired specific response. The present investigation was undertaken to check whether the innate response of the complement system is affected after a combination of an immune challenge and a husbandry stressor. In European seabass, two different transcripts of the complement C3 protein, which correspond to two tissue-specific isoforms, have been detected in liver. They may come from post-transcriptional modifications at the pre-mRNA level or from alternative splicing in order to generate a diversified repertoire of protein isoforms in some fish species according to the tissue were they are located. After cloning the hepatic C3, the quantification of seabass isoforms showed specific responses, thus confirming the possible specialized roles of the C3 different isoforms in terms of defence immunity. On one hand, a stronger esbC3_2 expression was observed in front to the viral challenge, suggesting a specific participation of this molecule in front to viruses. This observation is in agreement with previous studies in trout macrophages in our lab, demonstrating that the immune response to viral infections was stronger than to bacterial ones. On the other hand, the esbC3_1 expression appeared stronger after bacterial challenge, especially under high density conditions. Our results confirm the hypothesis of an immune-activation of specific isoforms of the C3 protein of the complement system as a non-specific response in front to either immune or other type of stressors. In order to confirm our hypothesis, we created an oligonucleotide microarray (Agilent Technologies) containing 6275 annotated transcripts, each with x3 specific probes, and 4516 ESTs with 1 probe/target sequence. Gene expression profiles obtained from the livers of fish held under high density culture conditions highlighted a significant contrast in the liver response. In total, 54 transcripts were differentially expressed (GDE; fold change FC >2) in treatment over the control (p<0.01)/201 (p<0.05). Oligonucleotide probes were used to construct a high-density seabass microarray based on the Agilent 4 × 44 K design format (http://www.agilent.com/), which covers 13,199 unique transcripts of Dicentrarchus labrax. Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slides using the Agilent’s SurePrint Tecnology; oligo design was carried out by Agilent and three or more non-overlapping probes were designed for each EST cluster. The number of transcripts represented by three is 6,275, while 6,924 targets EST have only one probe.
2011-04-23 | E-GEOD-28812 | biostudies-arrayexpress
Project description:A healthy gastrointestinal microbiota is essential for host fitness, and strongly modulated by host diet. In aquaculture, a current challenge is to feed carnivorous fish with plant-feedstuffs in substitution of fish meal, an unsustainable commodity. Plants have a limited nutritive value due to the presence of non-starch polysaccharides (NSP) which are not metabolized by fish. In this work we assessed the effects of NSP-enriched diets on European seabass gut microbiota and evaluate the selective pressure of plant feedstuffs towards gut microbes with NSP-hydrolytic potential, i.e. capable to convert indigestible dietary constituents in fish metabolites. Triplicate groups of European seabass juveniles were fed a fish meal-based diet (control) or three plant-based diets (SBM, soybean meal; RSM, rapeseed meal; SFM, sunflower meal) for 6 weeks, before recovering intestinal samples for microbiota analysis, using the Illumina's MiSeq platform. Plant-based diets impacted differently digesta and mucosal microbiota. A decrease (p = 0.020) on species richness, accompanied by a decline on the relative abundance of specific phyla such as Acidobacteria (p = 0.030), was observed in digesta samples of SBM and RSM experimental fish, but no effects were seen in mucosa-associated microbiota. Plant-based diets favored the Firmicutes (p = 0.01), in particular the Bacillaceae (p = 0.017) and Clostridiaceae (p = 0.007), two bacterial families known to harbor carbohydrate active enzymes and thus putatively more prone to grow in high NSP environments. Overall, bacterial gut communities of European seabass respond to plant-feedstuffs with adjustments in the presence of transient microorganisms (allochthonous) with carbohydrolytic potential, while maintaining a balanced core (autochthonous) microbiota.
| S-EPMC7801451 | biostudies-literature
Project description:Fish respond to stressors by means of an array of changes that involve many biological compartments including molecular, cellular, metabolic, physiological and behavioral acclimation. Among these changes, the immune system also experiences significant alterations that are characterized by an induction of the innate non-specific responses and changes in the acquired specific response. The present investigation was undertaken to check whether the innate response of the complement system is affected after a combination of an immune challenge and a husbandry stressor. In European seabass, two different transcripts of the complement C3 protein, which correspond to two tissue-specific isoforms, have been detected in liver. They may come from post-transcriptional modifications at the pre-mRNA level or from alternative splicing in order to generate a diversified repertoire of protein isoforms in some fish species according to the tissue were they are located. After cloning the hepatic C3, the quantification of seabass isoforms showed specific responses, thus confirming the possible specialized roles of the C3 different isoforms in terms of defence immunity. On one hand, a stronger esbC3_2 expression was observed in front to the viral challenge, suggesting a specific participation of this molecule in front to viruses. This observation is in agreement with previous studies in trout macrophages in our lab, demonstrating that the immune response to viral infections was stronger than to bacterial ones. On the other hand, the esbC3_1 expression appeared stronger after bacterial challenge, especially under high density conditions. Our results confirm the hypothesis of an immune-activation of specific isoforms of the C3 protein of the complement system as a non-specific response in front to either immune or other type of stressors. In order to confirm our hypothesis, we created an oligonucleotide microarray (Agilent Technologies) containing 6275 annotated transcripts, each with x3 specific probes, and 4516 ESTs with 1 probe/target sequence. Gene expression profiles obtained from the livers of fish held under high density culture conditions highlighted a significant contrast in the liver response. In total, 54 transcripts were differentially expressed (GDE; fold change FC >2) in treatment over the control (p<0.01)/201 (p<0.05).
2011-04-23 | GSE28812 | GEO
Project description:Traceability of seafood has become crucial with market globalization and consumer's awareness. The present study used PCR-DGGE and 454 pyrosequencing to assess if bacterial communities fingerprint associated to seabass (Dicentrarchus labrax) skin mucus can be used to discriminate the geographic origin of fishes cultured in three semi-intensive fish farms. PCR-DGGE and pyrosequencing results were congruent and suggested that this molecular approach has the potential to trace fish farms with a spatial resolution <500 m. Pyrosequencing results provided a detailed insight into the bacterial community composition of seabass skin mucus and revealed the existence of a core of bacterial communities within family Pseudomonadaceae and Rhodobacteraceae. This approach also allowed to recognized key OTUs that are potentially relevant to discriminate the geographic origin of the fish being surveyed. Overall, the present study increased our knowledge on farmed seabass microbiome and demonstrated that specific and unique bacterial taxa can act as natural signatures that allow us to trace fish to its respective geographic origin. Our study provides valuable clues that should be more investigated in future studies as a way to fulfill current traceability needs in the global trade of seafood.
| S-EPMC5605529 | biostudies-literature