Differential gene expression profilings between diploid and triploid Fujian Oyster
Ontology highlight
ABSTRACT:
ORGANISM(S): Crassostrea angulata
PROVIDER: GSE55610 | GEO | 2014/03/06
SECONDARY ACCESSION(S): PRJNA240216
REPOSITORIES: GEO
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. Examination of 3 different samples, including diploid (DF and DM) and triplod(T) oyster.
2014-03-06 | E-GEOD-55610 | 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: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 Pacific oyster (Crassostrea gigas) is a kind of marine bivalve of great economic and ecological importance and is among the animals possessing the highest level of genome DNA variations. Despite large efforts made for the discovery of Pacific oyster SNPs in many research groups, challenge still remains as how to utilize SNPs in a high-throughput, transferable and economical manner. In the study, we constructed an oyster 190K SNP array with Affymetrix Axiom genotyping technology. A total of 190,420 SNPs were designed on the chip, which were selected from 54 M SNPs identified by re-sequencing of more than 400 Pacific oysters. Genotyping results from 96 wild oysters indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. Carrying 133K polymorphic SNPs, the oyster 190K SNP array is the first high density SNP chip with the largest throughput currently in mollusc and is commercially available to the worldwide research community.
2017-03-22 | GSE94633 | GEO
Project description:Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas Samples of 38 developmental stages from egg to juvenile were analyzed using single-end 49 bp RNA-seq. Two libraries mixed by RNAs from different developmental stages were analyzed using paired-end 90 bp RNA-seq. A total of 11 samples mainly from 8 organs (mantle, gill,adductor muscle, digestive gland, hemocyte, labial palp, female gonad and male gonad) were analyzed using paired-end 90 bp RNA-seq. At the same time, single-end 49 bp RNA-seq was conducted on 61 samples collected from adult oysters subjected to 9 types of environmental stressors (exposure to air, salinity, temperature, and exposure to metals).
2012-09-13 | E-GEOD-31012 | biostudies-arrayexpress
Project description:To elucidate the modulatory participation of miRNAs in mollusk biomineralization, we have employed high-throughput sequencing to identify miRNAs of pearl oyster, Pinctada fucata. Our study focused on the miRNA expression profile of the mantle, an organ responsible for shell formation of the oyster. The pearl oysters were cultured in the tank with the maintaining conditions of temperature 19 ℃, PH 8.1 and salinity 33‰ in recirculating seawater.
2021-05-01 | GSE145993 | GEO
Project description:Summer mortality of the Pacific oyster Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. Heredity appears to be a major factor determining the sensitivity of oysters to summer mortality, allowing resistant (R) and susceptible (S) lines to be produced. We conducted genome-wide expression profiling of R and S gonads during the 3-month period preceding a summer mortality event using a 9K cDNA microarray that we designed. This transcriptional analysis provides new indications to define markers for Quantitative Trait Loci searches and functional studies, and evaluates the potential role of each gene in the resistance to summer mortality
2009-08-15 | GSE16448 | GEO
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:To examain effects of triploidy on gene expression in mouse cells, we have employed whole genome microarray expression profiling. To study the effects of aneuploidy in mouse cells, we isorated diploid, triploid and tetraploid cells from p53-/- mouse embryonic cells Gene expression in diploid cells (RRI2, 15 and 2-1), triploid cells (RRI2-5, 2-12 and 2-15) and tetraploid cells (RRI2-2, 2-4 and 2-6).
2014-03-31 | E-GEOD-32449 | biostudies-arrayexpress
Project description:Plastics are persistent synthetic polymers that accumulate in the marine environment as waste. Microplastic (MP) particles are derived from the breakdown of larger debris or can enter the environment as microscopic fragments. Filter-feeder organisms ingest MP while feeding and are likely to be impacted by MP pollution. To assess the impact of polystyrene microspheres (PS) on the physiology of the Pacific oyster, adult oysters were experimentally exposed to virgin micro-PS (2 and 6 µm in diameter; 32 µg L-1) for two months during a reproductive cycle. Effects were investigated on transcriptomic responses, in digestive gland gonads and oocytes of exposed oysters. Transcriptomic profiles in the tissues of the exposed oyster showed endocrine disrupting signals, notably highlighting alteration in glucocorticoid response, insulin pathway and fatty-acid metabolism in response to micro-PS exposition. In oocytes from exposed females, several transcripts coding for proteins involved in Ca2+ binding were differentially expressed suggesting a disruption of the Ca2+ signaling pathway with crucial consequences on oocyte maturation.
2016-01-15 | GSE71845 | GEO