The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis

Genome-wide identification, characterization, and expression analysis of the transient receptor potential gene family in mandarin fish Siniperca chuatsi

BACKGROUND

Temperature is a crucial environmental determinant for the vitality and development of teleost fish, yet the underlying mechanisms by which they sense temperature fluctuations remain largely unexplored. Transient receptor potential (TRP) proteins, renowned for their involvement in temperature sensing, have not been characterized in teleost fish, especially regarding their temperature-sensing capabilities.

RESULTS

In this study, a genome-wide analysis was conducted, identifying a total of 28 TRP genes in the mandarin fish Siniperca chuatsi. These genes were categorized into the families of TRPA, TRPC, TRPP, TRPM, TRPML, and TRPV. Despite notable variations in conserved motifs across different subfamilies, TRP family members shared common structural features, including ankyrin repeats and the TRP domain. Tissue expression analysis showed that each of these TRP genes exhibited a unique expression pattern. Furthermore, examination of the tissue expression patterns of ten selected TRP genes following exposure to both high and low temperature stress indicated the expression of TRP genes were responsive to temperatures changes. Moreover, the expression profiles of TRP genes in response to mandarin fish virus infections showed significant upregulation for most genes after Siniperca chuatsi rhabdovirus, mandarin fish iridovirus and infectious spleen and kidney necrosis virus infection.

CONCLUSIONS

This study characterized the TRP family genes in mandarin fish genome-wide, and explored their expression patterns in response to temperature stress and virus infections. Our work will enhance the overall understanding of fish TRP channels and their possible functions.

TBK1 upregulates the interferon response against virus by the TBK1-IRF3/7 axis in yellow catfish (Pelteobagrus fulvidraco)

Yellow catfish (Pelteobagrus fulvidraco) is an important economic species of freshwater fish, widely distributed in China. Recently, viral diseases of yellow catfish have been identified in Chian (Hubei province), arising more attention to the viral immunity in P. fulvidraco. Tumor necrosis factor (TNF) receptor-associated factor NF-κB activator (TANK)-binding kinase 1 (TBK1) plays an essential role in IFN production and innate antiviral immunity. In the present study, we characterized the P. fulvidraco TBK1 (PfTBK1) and reported its function in interferon response. The full-length open reading frame (ORF) is 2184 bp encoding a protein with 727 amino acids, which is composed of four conserved domains, including KD, ULD, CCD1, and CCD2, similar to TBK1 in other species. Pftbk1 was widely expressed in all detected tissues by qPCR and was not inducible by the spring viremia of carp virus (SVCV), a single-strand RNA virus. In addition, the cellular distribution indicated that PfTBK1 was only located in the cytoplasm. Moreover, PfTBK1 induced strong IFN promoter activities through the Jak-stat pathway, and PfTBK1 interacted with and significantly phosphorylated IFN regulatory factor 3/7 (IRF3/7) in P. fulvidraco, promoting the nuclear translocation of pfIRF3 and PfIRF7, and PfTBK1 upregulated IFN response by PfTBK1-PfIRF3/7 axis. Above all, PfTBK1 triggered IFN response and strongly inhibited the replication of SVCV in EPC cells through induction of IFN downstream IFN-stimulated genes (ISGs). Summarily, this work reveals that PfTBK1 plays a positive regulatory role in IFN induction through the TBK1-IRF3/7 axis, laying a foundation for further exploring the molecular mechanism of the antiviral process in P. fulvidraco.

Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration

Sciaenops ocellatus is among the most important artificially introduced farmed fish across 11 countries and regions. However, the frequent occurrence of extreme weather events and breeding escapes have placed great pressure on local marine biodiversity and ecosystems. We reported the de novo assembly and annotation with a contig N50 of 28.30 Mb using PacBio HiFi sequencing and Hi-C technologies, which resulted in a 283-fold increase in contig N50 length and improvement in continuity and quality in complex repetitive region for S. ocellatus compared to the previous version. In total, 257.36 Mb of repetitive sequences accounted for 35.48% of the genome, and 22,845 protein-coding genes associated with a BUSCO value of 98.32%, were identified by genome annotation. Moreover, 54 hub genes rapidly responding to hypoosmotic stress were identified by WGCNA. The high-quality chromosome-scale S. ocellatus genome and candidate resistance-related gene sets will not only provide a genomic basis for genetic improvement via molecular breeding, but will also lay an important foundation for investigating the molecular regulation of rapid responses to stress.

Muscle transcriptome analysis provides new insights into the growth gap between fast- and slow-growing Sinocyclocheilus grahami

Sinocyclocheilus grahami is an economically valuable and famous fish in Yunnan Province, China. However, given its slow growth (40 g/2 years) and large growth differences among individuals, its growth performance needs to be improved for sustainable future use, in which molecular breeding technology can play an important role. In the current study, we conducted muscle transcriptomic analysis to investigate the growth gaps among individuals and the mechanism underlying growth within 14 fast- and 14 slow-growth S. grahami. In total, 1,647 differentially expressed genes (DEGs) were obtained, including 947 up-regulated and 700 down-regulated DEGs in fast-growth group. Most DEGs were significantly enriched in ECM-receptor interaction, starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, amino acids biosynthesis and metabolism, peroxisome, and PPAR signaling pathway. Some genes related to glycogen degradation, glucose transport, and glycolysis (e.g., adipoq, prkag1, slc2a1, agl, pygm, pgm1, pfkm, gapdh, aldoa, pgk1, pgam2, bpgm, and eno3) were up-regulated, while some genes related to fatty acid degradation and transport (e.g., acox1, acaa1, fabp1b.1, slc27a1, and slc27a2) and amino acid metabolism (e.g., agxt, shmt1, glula, and cth) were down-regulated in the fast-growth group. Weighted gene co-expression network analysis identified col1a1, col1a2, col5a1, col6a2, col10a1, col26a1, bglap, and krt15 as crucial genes for S. grahami growth. Several genes related to bone and muscle growth (e.g., bmp2, bmp3, tgfb1, tgfb2, gdf10, and myog) were also up-regulated in the fast-growth group. These results suggest that fast-growth fish may uptake adequate energy (e.g., glucose, fatty acid, and amino acids) from fodder, with excess energy substances used to synthesize collagen to accelerate bone and muscle growth after normal life activities are maintained. Moreover, energy uptake may be the root cause, while collagen synthesis may be the direct reason for the growth gap between fast- and slow-growth fish. Hence, improving food intake and collagen synthesis may be crucial for accelerating S. grahami growth, and further research is required to fully understand and confirm these associations.

High-throughput virtual screening of marine algae metabolites as high-affinity inhibitors of ISKNV major capsid protein: An analysis of in-silico models and DFT calculation to find novel drug molecules for fighting infectious spleen and kidney necrosis virus (ISKNV)

Infectious Spleen and Kidney Necrosis Virus (ISKNV) is linked to severe infections that cause significant financial losses in global aquaculture. ISKNV enters the host cell through its major capsid protein (MCP), and the resulting infection can lead to mass mortality of fish. Even though several drugs and vaccines are at various stages of clinical testing, none are currently available. Thus, we sought to assess the potential of seaweed compounds to block viral entrance by inhibiting the MCP. The Seaweed Metabolite Database (1110 compounds) was assessed for potential antiviral activity against ISKNV using high throughput virtual screening. Forty compounds with docking scores of ≥8.0 kcal/mol were screened further. The inhibitory molecules BC012, BC014, BS032, and RC009 were predicted by the docking and MD techniques to bind the MCP protein significantly with binding affinities of -9.2, -9.2, -9.9, and -9.4 kcal/mol, respectively. Also, ADMET characteristics of the compounds indicated drug-likeness. According to this study, marine seaweed compounds may operate as viral entrance inhibitors. For their efficacy to be established, in-vitro and in-vivo testing is required.

Analysis of Alternative Splicing and Long Noncoding RNAs After the Edwardsiella anguillarum Infected the Immunized European Eels (Anguilla anguilla) Revealed the Role of Outer Membrane Protein A in OmpA Subunit Vaccine

Edwardsiella anguillarum is a bacterium that commonly infects cultivated eels. Outer membrane protein A (OmpA) emulsified with Freund's adjuvant has been shown to be an effective fishery vaccine against this pathogen. However, the specific roles of OmpA in the vaccine have not been fully explored. In this study, we performed RNA-seq in the liver of a European eel (Anguilla anguilla) after challenge with E. anguillarum in eels previously immunized with an OmpA subunit vaccine. Our aim was to elucidate the differentially alternative splicing (DAS) and differentially expressed long noncoding RNAs (DE-lncRNAs) using a genome-wide transcriptome. The results showed after that at 28 days post-immunization, eels challenged with E. anguillarum (Con_inf) exhibited severe pathological changes in the liver. In contrast, the OmpA infused eels (OmpA_inf group) showed infiltrated lymphocytes, while Freund's adjuvant-inoculated eels (FCIA_inf group) showed edema of hepatocytes and blood coagulation. The relative percent survival (RPS) was 77.7% and 44.4% for OmpA_inf and FCIA_inf compared to the Con_inf group. We identified 37 DE-lncRNAs and 293 DAS genes between OmpA_inf and FCIA_inf. Interactions between DAS gene-expressed proteins indicated that 66 expressed proteins formed 20 networks. Additionally, 33 DE-lncRNAs interacted with 194 target genes formed 246 and 41 networks in co-expression and co-location. Taken together, our findings demonstrate that the OmpA subunit vaccine elicits a higher RPS and provides novel insights into the role of OmpA through DAS genes and DE-lncRNAs perspective. These results are significant for the development of fishery subunit vaccines.

Analysis of the transcriptomic profiles of Mandarin fish (Siniperca chuatsi) infected with red sea bream iridovirus (RSIV)

Red sea bream iridovirus (RSIV) belongs to the family Iridoviridae, genus Megalocytivirus, which could widely infect marine fish, causing diseases and huge economic losses. Now it has been reported that RSIV was also detected in diseased mandarin fish. Transmission electron microscopy and immunohistochemistry showed that spleen was the main target organ in mandarin fish infected with RSIV. To investigate the immune response mechanism of mandarin fish to RSIV infection, transcriptomics of RSIV-infected mandarin fish was analyzed. A total of 53,040 unigenes were obtained, and there were 21,576 and 17,904 unigenes had significant hit the Nr and SwissProt databases, respectively. In RSIV-infected and non-infected spleen tissues, there were 309 differentially expressed genes (DEGs), including 100 up-regulated genes and 209 down-regulated genes. Gene Ontology database (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were performed to reveal the function information and give a better understanding of the signal transduction pathways of DEGs. Further analysis of the cytokine-cytokine receptor interactions pathway exhibited that the expression of cytokines was widely activated after viral infection. In addition, ten DEGs were randomly selected and verified by quantitative real-time PCR, which revealed a similar expression tendency as the high-throughput sequencing data. These findings present valuable information that will benefit for better understanding of RSIV infection in mandarin fish.