Crassostrea angulata
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA240216 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1183721.fastq.gz | Fastqsanger.gz | |||
| SRR1183722.fastq.gz | Fastqsanger.gz | |||
| SRR1183723.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The systematic deep sequencing analysis provided a comprehensive understanding of the transcriptome complexity of 2n and 3n Fujian oyster. This information broadens our understanding of the mechanisms of C.angulata polyploidization and contributes to molecular and genetic research by enriching the oyster database. This is the first report on genome-wide transcriptional analysis of adductor muscle of diploid and triploid Fujian oyster and has demonstrated triploid oysters are morphologically almost identical to their diploid counterparts, but have faster growth, due to the reorientation of energetic allocation from gametogenesis to somatic investment. This study provides a foundation for further analysis of the gene expression patterns and signaling pathways which regulate the molecular mechanisms of diploid and triploid oyster.
2014-03-06 | GSE55610 | GEO
Project description:The systematic deep sequencing analysis provided a comprehensive understanding of the transcriptome complexity of 2n and 3n Fujian oyster. This information broadens our understanding of the mechanisms of C.angulata polyploidization and contributes to molecular and genetic research by enriching the oyster database. This is the first report on genome-wide transcriptional analysis of adductor muscle of diploid and triploid Fujian oyster and has demonstrated triploid oysters are morphologically almost identical to their diploid counterparts, but have faster growth, due to the reorientation of energetic allocation from gametogenesis to somatic investment. This study provides a foundation for further analysis of the gene expression patterns and signaling pathways which regulate the molecular mechanisms of diploid and triploid oyster. Examination of 3 different samples, including diploid (DF and DM) and triplod(T) oyster.
2014-03-06 | E-GEOD-55610 | biostudies-arrayexpress
Project description:Crassostrea angulata Transcriptome or Gene expression
| PRJNA695413 | ENA
Project description:Crassostrea angulata Transcriptome or Gene expression
| PRJNA80349 | ENA
Project description:The aim of this study was to gain insight into the molecular mechanisms of intraspecies difference of copper accumulation in Crassostrea angulata. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster (gill and mantle). Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden.
2016-06-30 | GSE65653 | GEO
Project description:The aim of this study was to gain insight into the molecular mechanisms of intraspecies difference of copper accumulation in Crassostrea angulata. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster (gill and mantle). Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden. Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden
2016-06-30 | E-GEOD-65653 | biostudies-arrayexpress
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: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: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:The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process. Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 511 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were “carbohydrate metabolic process”, “integral component of membrane” and “chitin binding” for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the “neuroactive ligand receptor interaction”, “endocytosis” and “spliceosome” as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage. The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.
2024-05-17 | GSE246924 | GEO