Intestinal microbiota of gibel carp
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB15495 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1656040.fastq.gz | Fastqsanger.gz | |||
| ERR1656050.fastq.gz | Fastqsanger.gz | |||
| ERR1656060.fastq.gz | Fastqsanger.gz | |||
| ERR1656070.fastq.gz | Fastqsanger.gz | |||
| ERR1656080.fastq.gz | Fastqsanger.gz |
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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:MiRNAs are small non-coding single stranded RNAs that play crucial roles in numerous biological processes. Vertebrate herpesviruses encode multiple viral miRNAs that modulate host and viral genes. However, the roles of viral miRNAs in invertebrates have not been fully determined. Here, we used high-throughput sequencing to analyse miRNA and mRNA expression profiles of Carassius auratus gibelio in response to infection by cyprinid herpesvirus 2 (CyHV-2). RNA sequencing obtained 26,664 assembled transcripts, including 2,978 differentially expressed genes, among which 12 were validated by qRT-PCR. Based on small RNA (sRNA) sequencing and secondary structure predictions, we identified 17 CyHV-2 encoded miRNAs. Target prediction for the viral miRNAs identified >1,109 host and virus gene target pairs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of the viral miRNAs revealed diverse affected immune signalling pathways, including the RIG-I-like receptor, the Toll-like receptor and the JAK-STAT signalling pathways. Finally, we presented a functional analysis of CyHV-2-encoded ORF60 and host gene TLR5, both of which are targeted by CyHV-2 miRNA miR-C1.
2018-01-01 | GSE90626 | GEO
Project description:Proteomic and Phosphoproteomic Analyses Reveal Gibel Carp Responses to Cyprinid Herpesvirus 2 Infection
2022-04-26 | PXD033461 |
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:Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV), is the aetiological agent of an emerging and lethal disease in common and koi carp. In this work we studied the immune response of two genetically different lines of common carp (Polish K and Polish R3) infected with CyHV-3 by immersion. The two carp lines presented a 20% difference in survival rate and, furthermore, significant difference in virus loads measured at day 3 post infection (p.i.). Microarray analysis revealed that 581 genes in line K (330 up-regulated, 251 down-regulated) and 107 genes in line R3 (77 up-regulated, 30 down-regulated), were at least 2-fold differentially expressed at day 3 p.i. compared to day 0. Genes which were at least 4-fold differentially expressed in both lines were selected as potential markers of an infection of common carp by CyHV-3. This group includes 17 up-regulated and only 1 down-regulated genes. In addition, microarray analysis revealed no significant differences in gene expression between line K and R3 at day 0. At day 3 p.i. there were, however, 76 genes that were at least 2-fold differentially expressed between the two lines. The kinetics of expression of T cell markers and selected cytokines indicate for higher activation of immune response in more resistant R3 line. Thus, our study revealed that differences in resistance to CyHV-3 between two carp lines can be correlated with differentially expressed immune-related genes. The experiment included four biological replicates with no dye swaps for (i) each strain (K and R3) and (ii) each condition (day 0 and day 3).
2012-01-05 | E-GEOD-30426 | biostudies-arrayexpress
Project description:Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV), is the aetiological agent of an emerging and lethal disease in common and koi carp. In this work we studied the immune response of two genetically different lines of common carp (Polish K and Polish R3) infected with CyHV-3 by immersion. The two carp lines presented a 20% difference in survival rate and, furthermore, significant difference in virus loads measured at day 3 post infection (p.i.). Microarray analysis revealed that 581 genes in line K (330 up-regulated, 251 down-regulated) and 107 genes in line R3 (77 up-regulated, 30 down-regulated), were at least 2-fold differentially expressed at day 3 p.i. compared to day 0. Genes which were at least 4-fold differentially expressed in both lines were selected as potential markers of an infection of common carp by CyHV-3. This group includes 17 up-regulated and only 1 down-regulated genes. In addition, microarray analysis revealed no significant differences in gene expression between line K and R3 at day 0. At day 3 p.i. there were, however, 76 genes that were at least 2-fold differentially expressed between the two lines. The kinetics of expression of T cell markers and selected cytokines indicate for higher activation of immune response in more resistant R3 line. Thus, our study revealed that differences in resistance to CyHV-3 between two carp lines can be correlated with differentially expressed immune-related genes.
2012-01-05 | GSE30426 | GEO
Project description:Transcriptome of gibel carp (Carassius auratus gibelio)
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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.
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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).
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Project description:Allotetraploid Hybrids of Red Crucian Carp (Carassius auratus red var) (♀) and Common Carp (Cyprinus carpio L) (♂) is a species produced by distant hybridization. In this study, SWATH-MS were applied for quantitative proteomics profiling in gonad tissue of allotetraploid and its parents Red Crucian Carp (♀) and Common Carp (♂) respectively.
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