A metagenomic survey of virological hazards in consumer-ready oysters
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB79522 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Entomo-virological surveillance. Genome sequencing and assembly
| PRJNA1158770 | ENA
Project description:Background Triploidy can occur in all species but is often lethal in birds and mammals. In amphibian, invertebrates and numerous species of fishes, triploid animals are viable and undistinguishable from diploid individuals. Gametogenesis is often affected and most animals are sterile for at least one sex, and gametes for the other sex are often unfertile. Although the majority of triploid oysters are sterile (beta individuals, 3nb), a low but persistent proportion of male and female animals produce gametes (alpha individuals, 3na). Thus, oysters constitute a unique model to study the effect of triploidy on germ cells development of both male and females. In this study, we used microarray to study the consequences of polyploidy on triploid oyster germ cells mitosis and meiosis. Results We compared the transcriptome of gonads of 3na and 3nb oyster gonads over the course of gametogenesis to the transcriptome of diploid (2n) oyster gonads. This study allowed us to reveal an increase in DNA repair and apoptosis through the NF-kappaB pathway, and a decrease in actin remodeling and chromatin remodeling in all 3n oysters. The comparison of 3na and 3nb individuals with 2n revealed that a pachytene checkpoints may be responsible for the success in gametogenesis of 3na individuals and for the observed delay in gametogenesis. However, the sterility of 3nb individuals can be explained by a disruption of sex determinism mechanisms. Indeed 3nb females express male-specific genes including enkurin and an Elav-like gene, and 3nb males express female-specific genes including Forkhead box L2 and beta-catenin. Conclusions Our results bring back to the front of the research field the questions of genetic sex determinism, mitosis/meiosis control, pachytene checkpoint, and cell type specific DNA damage pathways. Furthermore, this study identifies numerous new candidate genes which function should now be studied in details in oysters and in other triploid animals in order to elucidate the complex mechanisms involved in the regulation of triploid cells division.
2015-03-26 | GSE40855 | GEO
Project description:Bacteria and archaea associated with wild oysters in the North Sea
| PRJNA965952 | ENA
Project description:The shellfish aquaculture industry provides a sustainable food source and jobs for a growing population. Oysters are the primary aquaculture species produced in the United States and account for a significant portion of seafood exports. Shellfish hatcheries have been experiencing frequent mass mortality events over the last couple of decades that occur approximately 10-14 days after oyster settlement. Settlement is a process that shellfish such as oysters undergo in which they transform from a free-swimming pelagic larvae to a sessile juvenile oyster. In order for this energy-intensive process to be successful, the oyster has to undergo behavioral and morphological changes. This is a vulnerable period in the oyster life cycle and conditions need to be such that they aren’t creating added stress. However, due to the oysters’ vulnerability, this is often a time when bacterial infections can occur, which when occurring with environmental conditions that are unfavorable, can prove to be fatal. In order to help oysters survive this process, scientists at the Taylor Shellfish Hatchery in Quilcene, WA has experimented with altering abiotic and biotic factors such as algal diet densities, pH, water flow rate, among others. At this hatchery, Pacific oysters are typically reared at 23˚C, however preliminary research results have suggested that oysters may have a higher survival rate when held at 29˚C during the settlement period. This pilot experiment attempts to identify differences in protein expression between oyster seed held at 23˚C and 29˚C during the settlement period using novel proteomic technology. Our proteomic results, paired with survival data, suggest that holding oyster seed at 29˚C during the settlement period results in higher survival rates.
2022-03-03 | PXD015434 | Pride
Project description:Summer mortality of Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. A large genetic basis and a high heritability were demonstrated for the observed variation in resistance to summer mortality, which offered the possibility to develop lines of oysters that were resistant (R) or susceptible (S) to summer mortality. Previously, genome-wide expression profiling of R and S oyster gonads highlighted reproduction and antioxidant defense as constitutive pathways that operate differentially between these two lines. Here, we show that signaling in innate immunity also operates differentially between these lines and we postulated that it is at the main origin of their difference of survival in the field. From the already published microarray data, we employed an ANOVA analysis that reveals a specific “immune” profile at the date preceding the mortality. In addition, we conducted a microarray profiling of two other tissues, gills and muscle, that also showed an over-representation of the immune genes (46%) among the selected genes. Eleven genes were pinpointed to be simultaneously differentially expressed between R and S lines in the three tissues. Among them, ten are related to “Immune Response”. The kinetics of their mRNA levels appeared clearly different between lines and suggests that in environment, R oysters had the capacity to modulate signaling in innate immunity whereas S oysters did not. This study enhances our understanding of the complex summer mortality syndrome and provides candidates of interest for further functional and genetics studies.
2011-04-22 | GSE25614 | GEO
Project description:There are 18 ready-to-eat food samples (8 ready-to-eat meat, 7 ready-to-eat vegetables and 3 ready-to-eat fruit) and 6 human faecal samples. The samples were sequenced on the Illumina, NovaSeq PE150.
| PRJEB33440 | ENA
Project description:Background Triploidy can occur in all species but is often lethal in birds and mammals. In amphibian, invertebrates and numerous species of fishes, triploid animals are viable and undistinguishable from diploid individuals. Gametogenesis is often affected and most animals are sterile for at least one sex, and gametes for the other sex are often unfertile. Although the majority of triploid oysters are sterile (beta individuals, 3nb), a low but persistent proportion of male and female animals produce gametes (alpha individuals, 3na). Thus, oysters constitute a unique model to study the effect of triploidy on germ cells development of both male and females. In this study, we used microarray to study the consequences of polyploidy on triploid oyster germ cells mitosis and meiosis. Results We compared the transcriptome of gonads of 3na and 3nb oyster gonads over the course of gametogenesis to the transcriptome of diploid (2n) oyster gonads. This study allowed us to reveal an increase in DNA repair and apoptosis through the NF-kappaB pathway, and a decrease in actin remodeling and chromatin remodeling in all 3n oysters. The comparison of 3na and 3nb individuals with 2n revealed that a pachytene checkpoints may be responsible for the success in gametogenesis of 3na individuals and for the observed delay in gametogenesis. However, the sterility of 3nb individuals can be explained by a disruption of sex determinism mechanisms. Indeed 3nb females express male-specific genes including enkurin and an Elav-like gene, and 3nb males express female-specific genes including Forkhead box L2 and beta-catenin. Conclusions Our results bring back to the front of the research field the questions of genetic sex determinism, mitosis/meiosis control, pachytene checkpoint, and cell type specific DNA damage pathways. Furthermore, this study identifies numerous new candidate genes which function should now be studied in details in oysters and in other triploid animals in order to elucidate the complex mechanisms involved in the regulation of triploid cells division. Triploid spats were obtained by crossing tetraploid males and diploid females in the ifremer experimental hatchery (La tremblade, Charente Maritime, France). We performed microarray analysis on a total of 35 individual triploid gonads that can be grouped as follow: 3n stage 0 (4 individuals), 3n alpha Stage 1 (8 individuals), 3n beta Stage 1 (8 individuals), 3n alpha Stage 3 male (4 individuals), 3n beta Stage 3 male (3 individuals), 3n alpha Stage 3 female (4 individuals), and 3n beta stage 3 female (4 individuals).
2015-03-26 | E-GEOD-40855 | biostudies-arrayexpress
Project description:This experiment was designed to enable the identification of field mortality sensitive Pacific oysters while also permitting the repetitive, non-lethal sampling of tissue from identifiable individual oysters. These samples have been difficult to obtain because pre-mortality phenotypes are obscured by the presence of an outer shell which occludes all views of body tissues. Additionally, mortality triggers have not been identified and there is need to better characterize the pathophysiology preceding mortality. 300 three year old oysters were sampled on 6 dates from May to October, 2008 from their grow out site at Totten Inlet, WA, USA. 100-200ul of hemolymph was withdrawn from the adductor muscle and preserved for possible mRNA analysis by microarray. At the end of the summer, mortality phenotypes were assigned to individuals (alive vs. dead/mortality). Gene expression profiles from screened mortality individuals showed up-regulation of a set of 124/11904 ESTs within one month of death that were not usually found in the alive individuals. This indicates that the path to death in oysters occurs over several days and maybe weeks, and is a molecularly coordinated response in which the hemolymph is involved. Gene expression predictors of survival fate could be developed from this data set.
2011-03-16 | E-MTAB-548 | biostudies-arrayexpress
Project description:Illumina RNA sequencing to assmeble a transcriptome for the oyster Ostrea lurida and identify genes signficantly differentially expressed among three populations of oysters that differ in their tolerance of low salinity. Our new transcripmotme provides an important genomic resource for future work in this species of conservation concern. Genes differentially expressed between oyster populations provide insight into mechanisms underlying different low salinity tolerances.
2018-04-28 | GSE98355 | GEO