Ontology highlight
ABSTRACT:
PROVIDER: PRJNA690125 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13374872_1.fastq.gz | Fastqsanger.gz | |||
| SRR13374872_2.fastq.gz | Fastqsanger.gz | |||
| SRR13374873_1.fastq.gz | Fastqsanger.gz | |||
| SRR13374873_2.fastq.gz | Fastqsanger.gz | |||
| SRR13374874_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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: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: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:Triploid oysters have poor gonadal development, which can not only bring higher economic benefits but also have a potential application in the genetic containment for aquaculture. However, the key factors that influence germ cell development in triploid oysters remain unclear. In this study, data-independent acquisition was applied to identify proteins related to sterility in triploid Crassostrea gigas.
2021-08-22 | PXD028056 |
Project description:Transcriptomic profiling of gametogenesis in triploid oysters
| PRJNA175118 | ENA
Project description:The interplay between phenotypic plasticity and adaptive evolution has long been an important topic of evolutionary biology. This process is critical to our understanding of a species evolutionary potential in light of rapid climate changes. Despite recent theoretical work, empirical studies of natural populations, especially in marine invertebrates, are scarce. In this study, we investigated the relationship between adaptive divergence and plasticity by integrating genetic and phenotypic variation in Pacific oysters from its natural range in China. Genome resequencing of 371 oysters revealed unexpected fine-scale genetic structure that is largely consistent with phenotypic divergence in growth, physiology, thermal tolerance and gene expression across environmental gradient. These findings suggest that selection and local adaptation are pervasive and together with limited gene flow shape adaptive divergence. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and likely favored by selection in organisms facing dynamic environments such as oysters. Divergence in heat response and tolerance implies that the evolutionary potential to a warming climate differs among oyster populations. We suggest that trade-offs in energy allocation are important to adaptive divergence with acetylation playing a role in energy depression under thermal stress.
2018-07-27 | PXD008057 | Pride