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Increasing evidence suggests important roles for long noncoding RNAs (lncRNAs) as new gene modulators involved in various biological processes. However, the function roles of lncRNAs in lower vertebrates are still unknown. Here, we firstly identify a lncRNA, named MAVS antiviral-related lncRNA (MARL), as a key regulator for antiviral immunity in teleost fish. The results indicate that fish MAVS play essential roles in host antiviral responses and inhibition of Siniperca chuatsi rhabdovirus (SCRV) replication. miR-122 reduces MAVS expression and suppress MAVS-mediated antiviral responses, which may help viruses evade host antiviral responses. Further, MARL functions as a competing endogenous RNA (ceRNA) for miR-122 to control protein abundance of MAVS, thereby inhibiting SCRV replication and promoting antiviral responses. Our data not only shed new light on understanding the function role of lncRNA in biological processes in lower vertebrates, but confirmed the hypothesis that ceRNA regulatory networks exist widely in vertebrates.

Large yellow croaker iridovirus (LYCIV) poses a significant threat to the large yellow croaker (Larimichthys crocea) aquaculture industry due to its rapid transmission and high lethality. Galectins, as evolutionarily conserved carbohydrate-binding lectins and pattern recognition receptors (PRRs) in the innate immune system, play crucial roles in immune responses. In this study, we characterized the beta-galactoside-binding lectin from large yellow croaker (LcβLectin) and explored its potential as a disease resistance gene against LYCIV. The full-length cDNA of LcβLectin was cloned and found to contain conserved elements, such as β-galactoside-binding motifs, HNPR, and WCEEHR domains. Using L. crocea head-kidney macrophages (LCM10), we demonstrated that recombinant LcβLectin significantly inhibits LYCIV-induced cytopathic effects and reduces macrophage apoptosis, highlighting its key role in viral defense. Moreover, the overexpression of LcβLectin in LCM10 cells followed by transcriptomic analysis revealed its substantial regulatory effects on key immune-related signaling pathways, including C-type lectin signaling, p53 signaling, and Toll-like receptor signaling pathways. Collectively, our findings suggest that LcβLectin enhances fish resistance to viral diseases by augmenting immune system function and activating immune-related pathways, providing valuable insights into the innate immune mechanisms of aquatic species and potential strategies for disease prevention in aquaculture.

The large yellow croaker iridovirus (LYCIV) poses a significant threat to the aquaculture industry of . Understanding the host defense response to LYCIV infection is crucial for developing effective strategies to mitigate its impact. In this study, an epigenetic approach was employed to investigate dynamic changes in chromatin accessibility using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Additionally, RNA sequencing (RNA-seq) was used to analyze the expression pattern of immune response genes upon LYCIV infection. Substantial alterations in chromatin accessibility were observed, particularly in the regulatory regions of key immune-related genes. Significant changes in the expression of AP-1 transcription factors, including the gene, were noted. CUT&Tag results revealed that AP-1 was significantly enriched in the open chromatin regions of cytokine genes, with potentially regulating the cytokine genes and . These findings suggest that AP-1 may play a crucial role in the defense response against viral infection by modulating inflammatory cytokines and contributing to cellular inflammatory responses. This study provides a comprehensive analysis of the epigenomic landscape and gene expression regulation during iridovirus infection in , offering valuable insights for breeding programs aimed at combating iridovirus infections.

Iridoviruses are an important pathogen of ectothermic vertebrates and are considered a significant threat to aquacultural fish production. Recently, one of the most economically important marine species in China, the large yellow croaker (Larimichthys crocea), has been increasingly reported to be the victim of iridovirus disease. In this study, we isolated and identified a novel iridovirus, LYCIV-ZS-2020, from cage-cultured large yellow croaker farms in Zhoushan island, China. Genome sequencing and subsequent phylogenetic analyses showed that LYCIV-ZS-2020 belongs to the genus Megalocytivirus and is closely related to the Pompano iridoviruses isolated in the Dominican Republic. LYCIV-ZS-2020 enriched from selected tissues of naturally infected large yellow croaker was used in an artificial infection trial and the results proved its pathogenicity in large yellow croaker. This is the first systematic research on the genetic and pathogenic characterization of iridovirus in large yellow croakers, which expanded our knowledge of the iridovirus.

The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. To understand the molecular basis for antiviral defense in this species, we used Illumia paired-end sequencing to characterize the spleen transcriptome of polyriboinosinic:polyribocytidylic acid [poly(I:C)]-induced large yellow croakers. The library produced 56,355,728 reads and assembled into 108,237 contigs. As a result, 15,192 unigenes were found from this transcriptome. Gene ontology analysis showed that 4,759 genes were involved in three major functional categories: biological process, cellular component, and molecular function. We further ascertained that numerous consensus sequences were homologous to known immune-relevant genes. Kyoto Encyclopedia of Genes and Genomes orthology mapping annotated 5,389 unigenes and identified numerous immune-relevant pathways. These immune-relevant genes and pathways revealed major antiviral immunity effectors, including but not limited to: pattern recognition receptors, adaptors and signal transducers, the interferons and interferon-stimulated genes, inflammatory cytokines and receptors, complement components, and B-cell and T-cell antigen activation molecules. Moreover, the partial genes of Toll-like receptor signaling pathway, RIG-I-like receptors signaling pathway, Janus kinase-Signal Transducer and Activator of Transcription (JAK-STAT) signaling pathway, and T-cell receptor (TCR) signaling pathway were found to be changed after poly(I:C) induction by real-time polymerase chain reaction (PCR) analysis, suggesting that these signaling pathways may be regulated by poly(I:C), a viral mimic. Overall, the antivirus-related genes and signaling pathways that were identified in response to poly(I:C) challenge provide valuable leads for further investigation of the antiviral defense mechanism in the large yellow croaker.

Background Orange-spotted grouper ( Epinephelus coioides ) is an economically important marine fish cultured in China and Southeast Asian countries. The emergence of infectious viral diseases, including iridovirus and betanodavirus, have severely affected food products based on this species, causing heavy economic losses. Limited available information on the genomics of E. coioides has hampered the understanding of the molecular mechanisms that underlie host-virus interactions. In this study, we used a 454 pyrosequencing method to investigate differentially-expressed genes in the spleen of the E. coioides infected with Singapore grouper iridovirus (SGIV). Results Using 454 pyrosequencing, we obtained abundant high-quality ESTs from two spleen-complementary DNA libraries which were constructed from SGIV-infected (V) and PBS-injected fish (used as a control: C). A total of 407,027 and 421,141 ESTs were produced in control and SGIV infected libraries, respectively. Among the assembled ESTs, 9,616 (C) and 10,426 (V) ESTs were successfully matched against known genes in the NCBI non-redundant (nr) database with a cut-off E-value above 10 -5 . Gene ontology (GO) analysis indicated that \"cell part\", \"cellular process\" and \"binding\" represented the largest category. Among the 25 clusters of orthologous group (COG) categories, the cluster for \"translation, ribosomal structure and biogenesis\" represented the largest group in the control (185 ESTs) and infected (172 ESTs) libraries. Further KEGG analysis revealed that pathways, including cellular metabolism and intracellular immune signaling, existed in the control and infected libraries. Comparative expression analysis indicated that certain genes associated with mitogen-activated protein kinase (MAPK), chemokine, toll-like receptor and RIG-I signaling pathway were alternated in response to SGIV infection. Moreover, changes in the pattern of gene expression were validated by qRT-PCR, including cytokines, cytokine receptors, and transcription factors, apoptosis-associated genes, and interferon related genes. Conclusion This study provided abundant ESTs that could contribute greatly to disclosing novel genes in marine fish. Furthermore, the alterations of predicted gene expression patterns reflected possible responses of these fish to the virus infection. Taken together, our data not only provided new information for identification of novel genes from marine vertebrates, but also shed new light on the understanding of defense mechanisms of marine fish to viral pathogens.

Viral nervous necrosis disease (VNN), caused by nervous necrosis virus (NNV), is one major threat to mariculture. Identifying loci and understanding the mechanisms associated with resistance to VNN are important in selective breeding programs. We performed a genome-wide association study (GWAS) using genotyping-by-sequencing (GBS) to study the genomic architecture of resistance to NNV infection in Asian seabass. We genotyped 986 individuals from 43 families produced by 15 founders with 44498 bi-allelic genetic variants using GBS. The GWAS identified three genome-wide significant loci on chromosomes 16, 19, and 20, respectively, and six suggestive loci on chromosomes 1, 8, 14, 15, 21, and 24, respectively, associated with resistance to NNV infection measured as binary and quantitative traits. Using the 500 most significant markers in combination with a training population of 800 samples could reach a genomic prediction accuracy of 0.7. Candidate genes significantly associated with resistance to NNV, including lysine-specific demethylase 2A, beta-defensin 1, and cystatin-B, which play important roles in immune responses against virus infection, were identified. Almost all the candidate genes were differentially expressed in different tissues against NNV infection. The significant genetic variants can be used in genomic selection and help understand the mechanism of resistance to VNN. Future studies should use populations of large effective size and whole genome resequencing to identify more useful genetic variants.

A novel lymphocystivirus causing typical signs of lymphocystis virus disease in whitemouth croaker (Micropogonias furnieri) on the coast of Uruguay was detected and described recently. Based on genetic analysis of some partially sequenced core genes, the virus seemed to differ from previously described members of the genus Lymphocystivirus. In this study, using next-generation sequencing, the whole genome of this virus was sequenced and analysed. The complete genome was found to be 211,086 bp in size, containing 148 predicted protein-coding regions, including the 26 core genes that seem to have a homologue in every iridovirus genome sequenced to date. Considering the current species demarcation criteria for the family Iridoviridae (genome organization, G+C content, amino acid sequence similarity, and phylogenetic relatedness of the core genes), the establishment of a novel species (“Lymphocystis disease virus 4”) in the genus Lymphocystivirus is suggested.

Infectious spleen and kidney necrosis virus (ISKNV) is an emerging viral pathogen with an expanding host range, posing a significant threat to economically important fish species. In this study, we isolated the ISKNV strain responsible for disease outbreaks in Asian seabass (Lates calcarifer) and analyzed the transcriptomic profile of spleen tissues from experimentally infected fish. The phylogenetic analysis confirmed that the virus belongs to clade I of ISKNV. Next-generation sequencing identified differentially expressed genes, providing a comprehensive overview of the transcriptional landscape in the spleen of ISKNV-infected fish. The pathway analysis revealed complex host–virus interactions, impacting immune regulation, endocytosis, cell communication, cell cycle arrest, and programmed cell death. To further investigate these interactions, we analyzed relevant pathways in the Reactome database for Asian seabass, humans, and zebrafish, constructed a protein–protein interaction (PPI) network using STRING database, and identified hub genes using six different algorithms. This analysis revealed 69 key genes, including 41 hub genes and 28 key genes that connect different pathways or clusters within the PPI network. These findings provide new insights into the molecular mechanisms driving ISKNV infection in Asian seabass. Future research should focus on elucidating the regulatory functions of these key genes and their roles in ISKNV pathogenesis.

Tripartite Motif-Containing 44 (TRIM44) is responsible for cancers, neurodegenerative diseases, and viral infections. However, the role of Siniperca chuatsi TRIM44 (scTRIM44) during viral infection remains unclear. In the present study, we analyzed the molecular characteristics of scTRIM44 and its role in infectious spleen and kidney necrosis virus (ISKNV), largemouth bass virus (LMBV), and Siniperca chuatsi rhabdovirus (SCRV) infection. ScTRIM44 contained one B-box domain (B, 166–207 aa) and a coiled-coil domain (CC, 279–309 aa), but lacked the canonical RING domain of E3 ubiquitin ligases. The scTRIM44 mRNA was expressed relatively high in immune-related tissues. The mRNA expression of scTRIM44 significantly decreased in vivo and vitro post-ISKNV and -LMBV infection. However, the expression of scTRIM44 mRNA showed significant up-regulation post-SCRV infection. ScTRIM44 positively regulated SCRV infection in CPB cells, but copies of ISKNV and LMBV showed no significant alteration in over-expressed or knocked-down scTRIM44 cells. Moreover, scTRIM44 positively regulated RIG-I- and MDA5-mediated interferon molecule signaling. These data suggested that scTRIM44 promoted SCRV infection by positively regulating RIG-I- and MDA5-mediated interferon molecule signaling, but didn’t regulate ISKNV and LMBV infection. This research provided a comprehensive insight into the antiviral activity of scTRIM44.