Ontology highlight
ABSTRACT:
PROVIDER: PRJNA655390 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12391135_1.fastq.gz | Fastqsanger.gz | |||
| SRR12391135_2.fastq.gz | Fastqsanger.gz | |||
| SRR12391136_1.fastq.gz | Fastqsanger.gz | |||
| SRR12391136_2.fastq.gz | Fastqsanger.gz | |||
| SRR12391137_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:Changes of the intestinal microbiota of gibel carp (Carassius auratus gibelio) associated with Cyprinid herpesvirus 2 (CyHV-2) infection
| PRJEB15495 | ENA
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
Project description:Proteomic and Phosphoproteomic Analyses Reveal Gibel Carp Responses to Cyprinid Herpesvirus 2 Infection
2022-04-26 | PXD033461 |
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