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Next generation sequencing facilitates quantitative analysis of control samples and nervous necrosis (VNN) virus infection samples orange-spotted grouper transcriptomes

ABSTRACT: Next generation sequencing facilitates quantitative analysis of control samples and nervous necrosis (VNN) virus infection samples orange-spotted grouper transcriptomes

PROVIDER: PRJNA522739 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8582180_1.fastq.gz	Fastqsanger.gz
	SRR8582180_2.fastq.gz	Fastqsanger.gz
	SRR8582181_1.fastq.gz	Fastqsanger.gz
	SRR8582181_2.fastq.gz	Fastqsanger.gz
	SRR8582182_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Next generation sequencing facilitates quantitative analysis of control samples and nervous necrosis (VNN) virus infection samples orange-spotted grouper transcriptomes

Project description:Purpose:To study the molecular mechanism of nerve necrosis (VNN) virus infection, and to provide help for molecular breeding and further development of Marine fishery Results: we found that 17,939 genes are elevated after NNV infection compared with control group, suggesting that NNV infection can strongly induce the expression of immune associated genes. In summary, we obtained high quality transcriptome of orange-spotted grouper and comparative analysis of transcriptome analysis reveals dramatically perturbation of gene expression with NNV infection.

2020-02-14 | GSE126620 | GEO

Profiling transcriptome and proteome of orange-spotted grouper (Epinephelus coioides) after nervous necrosis virus infection

Project description:Grouper is an important commercial maricultural fish, which suffer viral nervous necrosis (VNN) disease at the larval and juvenile stages, but the changes of transcriptomics and proteomics during viral infection remain unknown. In this study, we applied RNA-seq and label-free mass spectrum for the first time to depict the map of transcriptomics and proteomics in non-infected, susceptible-infected and tolerate-infected grouper in larval stage. Further analyses showed that the transcriptome and proteome change dramatically among 3 distinct groups, indicating that different immune response for infected and perststent grouper in larval stage. These valuable transcriptomics and proteomics datasets enable the investigation of molecular mechanism in nervous necrosis (VNN) virus infection, thus helps the further development of molecular breeding and marine fishery

2019-05-15 | PXD012763 | Pride

Epinephelus coioides strain:orange-spotted grouper

Project description:orange-spotted grouper Epinephelus coioides genetic linkage maps construction

| PRJDB1493 | ENA

Complete Genome Sequence of Nervous Necrosis Virus Isolated from Orange-Spotted Grouper (Epinephelus coioides) in Taiwan.

Project description:The genome sequence of nervous necrosis virus strain KS1 isolated from orange-spotted grouper (Epinephelus coioides) was cloned and analyzed. The viral genome is composed of two single-stranded positive-sense RNA molecules, RNA1 and RNA2. Phylogenetic analysis shows that the virus strain KS1 belongs to the red-spotted grouper nervous necrosis virus genotype.

| S-EPMC5597758 | biostudies-literature

Critical Roles of G3BP1 in Red-Spotted Grouper Nervous Necrosis Virus-Induced Stress Granule Formation and Viral Replication in Orange-Spotted Grouper (Epinephelus coioides)

Project description:Viral infection causes changes in the internal environment of host cells, and a series of stress responses are generated to respond to these changes and help the cell survive. Stress granule (SG) formation is a type of cellular stress response that inhibits viral replication. However, the relationship between red-spotted grouper nervous necrosis virus (RGNNV) infection and SGs, and the roles of the SG marker protein RAS GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1) in viral infection remain unclear. In this study, RGNNV infection induced grouper spleen (GS) cells to produce SGs. The SGs particles co-located with the classic SG marker protein eIF3η, and some SGs depolymerized under treatment with the translation inhibitor, cycloheximide (CHX). In addition, when the four kinases of the eukaryotic translation initiation factor 2α (eIF2α)-dependent pathway were inhibited, knockdown of HRI and GCN2 with small interfering RNAs and inhibition of PKR with 2-aminopurine had little effect on the formation of SGs, but the PERK inhibitor significantly inhibited the formation of SGs and decreased the phosphorylation of eIF2α. G3BP1 of Epinephelus coioides (named as EcG3BP1) encodes 495 amino acids with a predicted molecular weight of 54.12 kDa and 65.9% homology with humans. Overexpression of EcG3BP1 inhibited the replication of RGNNV in vitro by up-regulating the interferon and inflammatory response, whereas knockdown of EcG3BP1 promoted the replication of RGNNV. These results provide a better understanding of the relationship between SGs and viral infection in fish.

| S-EPMC9354888 | biostudies-literature

Single-cell RNA sequencing reveals the gonadal dynamic changes of sex differentiation in hermaphroditic protogynous orange-spotted grouper, Epinephelus coioides

Project description:Sex differentiation is a complex process that requires many factors to regulate proliferation, differentiation, development, and organization of the gonads. In teleosts, the molecular mechanisms of sex differentiation are diverse and unclear, especially in hermaphrodite fish. In the present study, 15 cell types, including germ cells, follicle cells, and theca cells, and so on, were identified using single-cell RNA sequencing (scRNA-seq) in the gonads during sex differentiation in a hermaphrodite fish, orange-spotted grouper (Epinephelus coioides). Two pre-follicle cell types were defined, and the differentiating trajectories of the follicle cells were outlined. Notably, both pre-follicle and follicle cells highly expressed male-related genes synchronously, such as amh, sox9, and dmrt3 in pre-follicle cells, as well as dmrt1 in follicle cells. Oocyte possessed two distinct states, with high expression of oocyte development related genes in one state and spermatogenesis related genes in the other state, respectively. Our results provide novel insights into cell types and lineage tracing in the gonads during sex differentiation in hermaphrodite species.

2024-07-26 | GSE218835 | GEO

Grouper TRAF4, a Novel, CP-Interacting Protein That Promotes Red-Spotted Grouper Nervous Necrosis Virus Replication.

Project description:Tumor necrosis factor receptor-associated factors (TRAFs) play important roles in the biological processes of immune regulation, the inflammatory response, and apoptosis. TRAF4 belongs to the TRAF family and plays a major role in many biological processes. Compared with other TRAF proteins, the functions of TRAF4 in teleosts have been largely unknown. In the present study, the TRAF4 homologue (EcTRAF4) of the orange-spotted grouper was characterized. EcTRAF4 consisted of 1413 bp encoding a 471-amino-acid protein, and the predicted molecular mass was 54.27 kDa. EcTRAF4 shares 99.79% of its identity with TRAF4 of the giant grouper (E. lanceolatus). EcTRAF4 transcripts were ubiquitously and differentially expressed in all the examined tissues. EcTRAF4 expression in GS cells was significantly upregulated after stimulation with red-spotted grouper nervous necrosis virus (RGNNV). EcTRAF4 protein was distributed in the cytoplasm of GS cells. Overexpressed EcTRAF4 promoted RGNNV replication during viral infection in vitro. Yeast two-hybrid and coimmunoprecipitation assays showed that EcTRAF4 interacted with the coat protein (CP) of RGNNV. EcTRAF4 inhibited the activation of IFN3, IFN-stimulated response element (ISRE), and nuclear factor-κB (NF-κB). Overexpressed EcTRAF4 also reduced the expression of interferon (IFN)-related molecules and pro-inflammatory factors. Together, these results demonstrate that EcTRAF4 plays crucial roles in RGNNV infection.

| S-EPMC8201248 | biostudies-literature

Orange-spotted grouper nervous necrosis virus-encoded protein A induces interferon expression via RIG-I/MDA5-MAVS-TBK1-IRF3 signaling in fish cells.

Project description:ImportanceAs a major pathogen, nervous necrosis virus (NNV) infects more than 120 fish species worldwide and is virulent to larvae and juvenile fish, hampering the development of the fish fry industry. Understanding virus-host interaction and underlying mechanisms is an important but largely unknown issue in fish virus studies. Here, using channel catfish ovary and fathead minnow cells as models for the study of innate immunity signaling, we found that NNV-encoded ProA activated interferon signaling via the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) pathway which was still suppressed by the infection of wild-type NNV. This finding has important implications for the comprehension of NNV protein function and the immune response from different cells. First, RIG-I is the key node for anti-NNV innate immunity. Second, the response intensity of RLR signaling determines the degree of NNV proliferation. This study expands our knowledge regarding the overview of signal pathways affected by NNV-encoded protein and also highlights potential directions for the control of aquatic viruses.

| S-EPMC10783131 | biostudies-literature

Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infection.

Project description:Viral nervous necrosis (VNN) is an acute and serious fish disease caused by nervous necrosis virus (NNV) which has been reported massive mortality in more than fifty teleost species worldwide. VNN causes damage of necrosis and vacuolation to central nervous system (CNS) cells in fish. It is difficult to identify the specific type of cell targeted by NNV, and to decipher the host immune response because of the functional diversity and highly complex anatomical and cellular composition of the CNS. In this study, we found that the red spotted grouper NNV (RGNNV) mainly attacked the midbrain of orange-spotted grouper (Epinephelus coioides). We conducted single-cell RNA-seq analysis of the midbrain of healthy and RGNNV-infected fish and identified 35 transcriptionally distinct cell subtypes, including 28 neuronal and 7 non-neuronal cell types. An evaluation of the subpopulations of immune cells revealed that macrophages were enriched in RGNNV-infected fish, and the transcriptional profiles of macrophages indicated an acute cytokine and inflammatory response. Unsupervised pseudotime analysis of immune cells showed that microglia transformed into M1-type activated macrophages to produce cytokines to reduce the damage to nerve tissue caused by the virus. We also found that RGNNV targeted neuronal cell types was GLU1 and GLU3, and we found that the key genes and pathways by which causes cell cytoplasmic vacuoles and autophagy significant enrichment, this may be the major route viruses cause cell death. These data provided a comprehensive transcriptional perspective of the grouper midbrain and the basis for further research on how viruses infect the teleost CNS.

| S-EPMC8241073 | biostudies-literature

Solexa sequencing of small RNAs in Singapore grouper iridovirus (SGIV)-infected grouper cells

Project description:We applied Solexa sequencing technology to identify Singapore grouper iridovirus (SGIV) encoded microRNAs during its infection. A small RNA library arising from SGIV infected grouper cells (GP) was constructed and sequenced. We recovered 6,802,977 usable reads, of which 34,400 reads represented the small RNA sequences encoded by SGIV. Among them, 16 novel SGIV encoded miRNAs were identified by a computational pipeline. Generally, these 16 miRNAs are dispersed throughout the SGIV genome, while three of them are located within open reading frame 057L (ORF057L) region. Meanwhile, We identified 138 conserved microRNA genes between grouper fish and zebrafish.

2011-01-29 | GSE26909 | GEO

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