Ontology highlight
ABSTRACT:
PROVIDER: PRJNA818789 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18466000_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR18466001_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR18466002_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR18466003_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR18466004_subreads.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries), and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allow for their stable coexistence, integrating the evolutionary and ecological advantages and disadvantages of the two reproductive forms. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.
2024-05-17 | GSE254010 | GEO
Project description:Parasite-mediated selection is considered one of the potential mechanisms contributing to the coexistence of asexual-sexual complexes. Gibel carp (Carassius gibelio), an invasive fish species in Europe, often forms populations composed of gynogenetic and sexual specimens. In the present study, experimental infection was induced in gynogenetic and sexual gibel carp using eye-fluke Diplostomum pseudospathaceum (Trematoda), and the transcriptome profile of the spleen as a major immune organ in fish was analyzed to reveal the differentially expressed immunity-associated genes related to D. pseudospathaceum infection differing between gynogenetic and sexual gibel carp. High parasite infection was found in gynogenetic fish when compared to genetically diverse sexuals. Although metacercariae of D. pseudospathaceum are situated in an immune-privileged organ, our results show that eye trematodes may induce a host immune response. We found differential gene expression induced by eye-fluke infection, with various impacts on gynogenetic and sexual hosts, documenting for the majority of DEGs upregulation in sexuals, and downregulation in asexuals. Differences in gene regulation between gynogenetic and sexual gibel carp were evidenced in many immunity-associated genes. GO analyses revealed the importance of genes assigned to the GO terms: immune function, the Notch signaling pathway, MAP kinase tyrosine/threonine/phosphatase activity, and chemokine receptor activity. KEGG analyses revealed the importance of the genes involved in 12 immunity-associated pathways – specifically, FoxO signaling, adipocytokine signaling, TGF-beta signaling, apoptosis, Notch signaling, C-type lectin receptor signaling, efferocytosis, intestinal immune network for IgA production, insulin signaling, virion - human immunodeficiency virus, Toll-like receptor signaling, and phosphatidylinositol signaling system. Our study indicates the limited potential of asexual fish to cope with higher parasite infection (likely a loss of capacity to induce an effective immune response) and highlights the important role of molecular mechanisms associated with immunity for the coexistence of gynogenetic and sexual gibel carp, potentially contributing to its invasiveness.
2024-07-17 | GSE256052 | GEO
Project description:Transcriptome of gibel carp (Carassius auratus gibelio)
| PRJNA1056495 | ENA
Project description:Here we provide dataset from a proteomic experiment, using trypsin digestion, and reversed-phase chromatography (RPC) with tandem mass spectrometr (RPC-MS/MS), in order to relatively quantify the protein composition of skin mucus of Prussian carp Carassius gibelio. The main aim of the project is to identify the proteins specifically assotiated with fish inhabits euthophic shallow lakes lake Chany Lake (West Siberia).
2021-05-27 | PXD025974 | Pride
Project description:This study was conducted to investigate the effects of the rapeseed meal (RM) on two strains of gibel carp (A strain and F strain) and to explore whether two strains show the different molecular mechanisms to the fishmeal (FM) and rapeseed meal (RM). Transcriptomic analysis showed that amino acid metabolism, lipid metabolism and digestive system were three main biological processes affected by RM diet in both strains. The differentially expressed genes between strains were involved in amino acid metabolism, immune responses and lipid metabolism.
2020-01-01 | GSE106551 | GEO
Project description:Physiological and transcriptomic responses to fishmeal-based diet and rapeseed meal-based diet in two strains of gibel carp (Carassius gibelio)
| PRJNA417239 | ENA
Project description:More and more evidence prove that deltamethrin (Del) exposure induced the adverse effect and damaged immune function to the aquatic animals in the parasite killing process with increasing insecticide application. However, little is currently known of the negative effect on mucosal immunity, especially in gills tissue. In this study, the LC50 of deltamethrin on gibel carp at 96h was determined to be 6.194 μg/L, and then juvenile gibel carp (Carassius auratus gibelio) (8.8 ± 1.0 g) were exposed to four Del exposure groups (0.61, 1.22, 2.44, and 4.88 μg/L) for 12h and 24h. To evaluate the innate immune-related enzymes in gills tissue, we measured the lysozyme (LYZ) and myeloperoxidase (MPO) contents and found that with increased concentration of Del exposure, the LYZ content was found to increase in the 1.22 μg/L Del group initially significantly and then gradually significantly decrease in the 4.88 μg/L Del group. And the activity of MPO was significantly lifted in a dose-dependent manner. The histological analysis showed that Del exposure serious desquamation and necrosis in the surface of epithelial cells are often found, accompanied by interlamellar cellular mass degenerative. In addition, the mucous cells were significantly decreased in the high Del concentration group (2.44 μg/L and 4.88 μg/L Del group) by AB-PAS staining. Importantly, totally 2857 DEGs (including 1624 up-regulated and 1233 down-regulated genes) were identified in the gill between the control group and 4.88μg/L Del exposure group using comparative transcriptional analysis. Among these, some genes involved in innate immune molecules, complement activation, apoptosis-related molecules, cytokine, and adaptive immune molecules, were also down-regulated. Importantly, we found several signal pathways related to immune response were downregulated, such as immune system process and tumor necrosis factor receptor (superfamily) binding pathways based on the GO and KEGG enrichment analysis. Consistently, we detect the expression of pro-inflammatory cytokines (TNF-α, IFN-γ, IL-1β, and IL-8), anti-inflammatory cytokines (TGF-β), LYZ, IgM, and Hsp70 in the gills tissue at 12h and 24h after Del exposure, which were consistent with our sequencing results. Collectively, these results demonstrated that the gills mucosa injury and immunotoxicity was induced by Del exposure and provided novel insight for explaining to some extent why Del-exposure fish and are more susceptible to concurrent or secondary viral or bacterial infections.
2023-03-01 | GSE197741 | GEO
Project description:Whilst the hybrids of F1 generations usually experience heterosis for fitness-related traits (including the resistance to parasites), post-F1 generations, due to Dobzhansky–Muller genetic incompatibilities, express numerous disadvantageous traits (including susceptibility to parasites). Genetic disruption in hybrids may also result from the broken system of cyto-nuclear coadaptation. Maternal backcrosses (each parent having with the same mtDNA of parents) and paternal backcrosses (each parent having with different mtDNA of parents) have the same nuclear genetic compositions, but differ in cytoplasmic genetic elements, affecting their viability and survival. Spring viraemia of the carp virus (SVCV), a disease with a serious economic impact in aquacultures, affects almost exclusively cyprinids, primarily common carp, and causes high mortality, whilst gibel carp is a less susceptible species. Our study was focused on the transcriptome profile analysis of head kidney to reveal differential gene expression in highly susceptible common carp, weakly susceptible gibel carp, and hybrid lines, hypothetizing that the patterns of differential gene expression will reflect hybrid heterosis in F1 generations and hybrid breakdown in backcrosses and F2 generations. We expected the differences in differential gene expression between maternal and paternal backcrosses to be in line with the hypothesis of broken cyto-nuclear coadaptation.
2023-09-12 | GSE240031 | GEO