Transcriptome profiling of grass carp (Ctenopharyngodon idellus) infected with Aeromonas hydrophila

Comparative Analysis of mRNA, microRNA of Transcriptome, and Proteomics on CIK Cells Responses to GCRV and Aeromonas hydrophila

Grass Carp Reovirus (GCRV) and Aeromonas hydrophila (Ah) are the causative agents of haemorrhagic disease in grass carp. This study aimed to investigate the molecular mechanisms and immune responses at the miRNA, mRNA, and protein levels in grass carp kidney cells (CIK) infected by Grass Carp Reovirus (GCRV, NV) and Aeromonas hydrophilus (Bacteria, NB) to gain insight into their pathogenesis. Within 48 h of infection with Grass Carp Reovirus (GCRV), 99 differentially expressed microRNA (DEMs), 2132 differentially expressed genes (DEGs), and 627 differentially expressed proteins (DEPs) were identified by sequencing; a total of 92 DEMs, 3162 DEGs, and 712 DEPs were identified within 48 h of infection with Aeromonas hydrophila. It is worth noting that most of the DEGs in the NV group were primarily involved in cellular processes, while most of the DEGs in the NB group were associated with metabolic pathways based on KEGG enrichment analysis. This study revealed that the mechanism of a grass carp haemorrhage caused by GCRV infection differs from that caused by the Aeromonas hydrophila infection. An important miRNA-mRNA-protein regulatory network was established based on comprehensive transcriptome and proteome analysis. Furthermore, 14 DEGs and 6 DEMs were randomly selected for the verification of RNA/small RNA-seq data by RT-qPCR. Our study not only contributes to the understanding of the pathogenesis of grass carp CIK cells infected with GCRV and Aeromonas hydrophila, but also serves as a significant reference value for other aquatic animal haemorrhagic diseases.

Fish arginase constrains excessive production of nitric oxide and limits mitochondrial damage during Aeromonas hydrophila infection

Bacteria-enhanced inducible nitric oxide synthase (iNOS) overproduces nitric oxide (NO) leading to mitochondrial and cellular damage. In mammals, arginase (ARG), the enzyme consuming the same substrate l-arginine with iNOS, was believed to inhibit iNOS activity by competing the substrate. But in fish, this conception has been widely challenged. In this study, the gene expression using real-time quantitative PCR (RT-qPCR) technology showed that when stimulated by Aeromonas hydrophila (A. hydrophila), grass carp (gc) iNOS was up-regulated in head kidney monocytes/macrophages (M0/MФ), and its changes were not detected in the whole tissue of liver or spleen, showing a high degree of cell-specific expression pattern. At the same time, gcARG2 had a high basal expression in tissues and was up-regulated by A. hydrophila stimulation. Next, phthalaldehyde-primaquine reaction was first used in the determination of intracellular urea in fish cells. It was found that the induced gcARG2 led to an increase in the intracellular urea content. Moreover, urea and NO production in M0/MФ were increased in a substrate dose-dependent manner from 30 to 100 μM of l-arginine and reached the highest yield at 300 and 3000 μM of l-arginine, respectively. Furthermore, head kidney M0/MФ was cultured in RPMI1640 medium containing physiological concentration (500 μM) of l-arginine to evaluate the effect of ARG. Under A. hydrophila stimulation, treatment with the arginase inhibitor S-(2-boronoethyl)-l-cysteine (BEC) showed that inhibition of arginase could further enhance the NO production stimulated by A. hydrophila. This in turn led to a cumulation in peroxynitrite (ONOO-) content and an injury of the mitochondrial membrane potential. Our study showed for the first time that fish ARG in head kidney M0/MФ can limit excessive production of NO and harmful products by iNOS to maintain mitochondrial and cellular homeostasis.

Concurrent impacts of polystyrene nanoplastic exposure and Aeromonas hydrophila infection on oxidative stress, immune response and intestinal microbiota of grass carp (Ctenopharyngodon idella)

Research has demonstrated that polystyrene nanoplastics (PS-NPs) can have adverse effects on the immune responses of fish. NPs have the potential to increase the likelihood of infections in fish by pathogenic bacteria, such as the opportunistic pathogen Aeromonas hydrophila, potentially increasing the virulence of pathogenic bacteria infections in fish. The concurrent effects of PS-NPs and A. hydrophila on grass carp intestinal tissues were assessed by exposing grass carp to different concentrations of PS-NPs (10 μg/L, 100 μg/L, 1000 μg/L) after infection with A. hydrophila. As the concentration of PS-NPs in the exposure and the duration of A. hydrophila infection both escalated, intestinal tissues showed damage in the form of disordered breakage of intestinal villi, thinning of the intestinal wall, and reduced necrosis of the cells in the annulus muscle layer. The AHS-PS100 group and AHS-PS1000 group exhibited a substantial rise in the function of CAT, SOD, GST, and MPO, as well as increased MDA content and elevated ROS levels (p < 0.05). In the AHS-PS1000 group, the expression levels of IL-6, IL-8, IL-10, IL-1β, TNF-α, and IFN-γ2 experienced a significant upsurge (p < 0.05). In addition, exposure to PS-NPs and A. hydrophila infection induced modifications in the microbial composition of the grass carp gut, affecting both phylum and genus taxonomic categories. Moreover, an increase in the abundance of Spirochaetota and Bacteroidota was observed not only in the positive control group but also in the AHS-PS100 and AHS-PS1000 groups following A. hydrophila infection. These experimental results indicate that PS-NPs exposure will aggravate the oxidative stress and inflammatory response of grass carp intestinal tissue in response to A. hydrophila infection, and lead to changes in intestinal microbial diversity and abundance. Overall, this study provides valuable hints on the potential concurrent effects of PS-NPs exposure on grass carp's response to A. hydrophila infection.

JunD functions as a transcription factor of IL-10 to regulate bacterial infectious inflammation in grass carp (Ctenopharyngodon idella)

IL-10 is a key anti-inflammatory mediator ensuring the protection of a host from excessive inflammation in response to pathogen infections, whose transcription or expression levels are tightly linked to the onset and progression of infectious diseases. An AP-1 family member called CiJunD was shown to be a transcription factor of IL-10 in grass carp (Ctenopharyngodon idella) in the current study. CiJunD protein harbored the conserved Jun and bZIP domains. Mutant experiments demonstrated that CiJunD bound to three specific sites on IL-10 promoter, i.e., 5'-ATTATTCATA-3', 5'-AGATGAGACATCT-3', and 5'-ATTATTCATC-3', mainly relying on the bZIP domain, and initiated IL-10 transcription. Expression data from the grass carp spleen infected by Aeromonas hydrophila and lipopolysaccharide (LPS) challenged spleen leukocytes indicated that the expressions of CiJunD and IL-10 were positively correlated, while the expression of pro-inflammatory cytokines, such as IL-1β, IL-6, IL-8, IFN-γ, and TNF-α, showed an overall downward trend when CiJunD and IL-10 peaked. The ability of CiJunD to down-regulate the production of pro-inflammatory cytokines and up-regulate the expression of IL-10, both with and without LPS stimulation, was confirmed by overexpression experiments. Meanwhile, the subcellular fractionation assay revealed that the nuclear translocation of CiJunD was significantly enhanced after the LPS challenge. Moreover, in vivo administration of grass carp with Oxamflatin, a potent agonist of JunD activity, could promote IL-10 but suppress the expression of pro-inflammatory cytokines. Intriguingly, tissue inflammation lesions and the survival rates of grass carp infected with A. hydrophila were also significantly improved by Oxamflatin administration. This work sheds light on the regulation mechanism by JunD of IL-10 expression and bacterial infectious inflammation for the first time, and it may present a viable method for preventing infectious diseases in fish by regulating IL-10 expression and inflammatory response.

Comparative transcriptomes reveal different tolerance mechanisms to Streptococcus agalactiae in hybrid tilapia, nile tilapia, and blue tilapia

Tilapia is one of the most economically important freshwater fish farmed in China. Streptococcosis outbreaks have been extensively documented in farmed tilapia species. Hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂) exhibit greater disease resistance than Nile tilapia (O. niloticus) and blue tilapia (O. aureus). However, the molecular mechanism underlying the enhanced tolerance of hybrid tilapia is still poorly understood. In this study, comparative transcriptome analysis was performed to reveal the different tolerance mechanisms to Streptococcus agalactiae in the three tilapia lines. In total, 1982, 2355, and 2076 differentially expressed genes were identified at 48 h post-infection in hybrid tilapia, Nile tilapia, and blue tilapia, respectively. Functional enrichment analysis indicated that numerous metabolic and immune-related pathways were activated in all three tilapia lines. The differential expression of specific genes associated with phagosome, focal adhesion, cytokine-cytokine receptor interaction, and toll-like receptor signaling pathways contributed to the resistance of hybrid tilapia. Notably, immune response genes in hybrid tilapia, such as P38, TLR5, CXCR3, CXCL12, PSTPIP1, and TFR, were generally suppressed under normal conditions but selectively induced following pathogen challenge. These results expand our knowledge of the molecular mechanisms underlying S. agalactiae tolerance in hybrid tilapia and provide valuable insights for tilapia breeding programs.

Hemolysin from Aeromonas hydrophila enhances the host's serum enzyme activity and regulates transcriptional responses in the spleen of Cyprinus rubrofuscus

Aeromonas hydrophila is a conditional pathogen impacting public hygiene and safety. Hemolysin is a virulence factor of Aeromonas hydrophila that causes erythrocyte hemolysis, yet its transcriptional response to Cyprinus rubrofuscus remains unknown. Our investigation confirmed the hemolysis of hemolysin from A. hydrophila. Serum enzyme activity was evaluated weekly after C. rubrofuscus were immunized with hemolysin Ahh1. The results showed that the hemolysin enhances the serum superoxide dismutase (SOD), lysozyme (LZM), and catalase (CAT) activity, which reached a maximum on day 14. To elucidate the molecular interaction between hemolysin from A. hydrophila and the host, we performed transcriptome sequencing on the spleen of C. rubrofuscus 14 days post hemolysin infection. The total number of clean reads was 41.37 Gb, resulting in 79,832 unigenes with an N50 length of 1863 bp. There were 1982 significantly differentially expressed genes (DEGs), including 1083 upregulated genes and 899 downregulated genes. Transcript levels of the genes, such as LA6BL, CD2, and NLRC5, were significantly downregulated, while those of IL11, IL1R2, and IL8 were dramatically upregulated. The DEGs were mainly enriched in the immune disease, viral protein interaction with cytokine and cytokine receptor, and toll-like receptor pathways, suggesting that hemolysin stimulation can activate the transcriptional responses. RT-qPCR experiments results of seven genes, IL-8, STAT2, CTSK, PRF1, CXCL9, TLR5, and SACS, showed that their expression was highly concordant with RNA-seq data. We clarified for the first time the key genes and signaling pathways response to hemolysin from A. hydrophila, which offers strategies for treating and preventing diseases.

Effects of Aeromonas hydrophila infection on the intestinal microbiota, transcriptome, and metabolomic of common carp (Cyprinus carpio)

Aeromonas hydrophila frequently has harmful effects on aquatic organisms. The intestine is an important defense against stress. In this study, we investigated the intestinal microbiota and transcriptomic and metabolomic responses of Cyprinus carpio subjected to A. hydrophila infection. The results showed that obvious variation in the intestinal microbiota was observed after infection, with increased levels of Firmicutes and Bacteroidetes and decreased levels of Proteobacteria. Several genera of putatively beneficial microbiota (Cetobacterium, Bacteroides, and Lactobacillus) were abundant, while Demequina, Roseomonas, Rhodobacter, Pseudoxanthomonas, and Cellvibrio were decreased; pathogenic bacteria of the genus Vibrio were increased after microbiota infection. The intestinal transcriptome revealed several immune-related differentially expressed genes associated with the cytokines and oxidative stress. The metabolomic analysis showed that microbiota infection disturbed the metabolic processes of the carp, particularly amino acid metabolism. This study provides insight into the underlying mechanisms associated with the intestinal microbiota, immunity, and metabolism of carp response to A. hydrophila infection; eleven stress-related metabolite markers were identified, including N-acetylglutamic acid, capsidiol, sedoheptulose 7-phosphate, prostaglandin B1, 8,9-DiHETrE, 12,13-DHOME, ADP, cellobiose, 1H-Indole-3-carboxaldehyde, sinapic acid and 5,7-dihydroxyflavone.

IL-4/13 expressing CD3γ/δ+ T cells regulate mucosal immunity in response to Flavobacterium columnare infection in grass carp

Interleukin (IL) 4 and 13 are signature cytokines orchestrating Th2 immune response. Teleost fish have two homologs, termed IL-4/13A and IL-4/13B, and have been functionally characterized. However, what cells express IL-4/13A and IL-4/13B has not been investigated in fish. In this work, the recombinant IL-4/13A and IL-4/13B proteins of grass carp (Ctenopharyngodon idella) were produced in the Escherichia coli (E. coli) cells and purified. Monoclonal antibodies (mAbs) against the recombinant CiIL-4/13A and CiIL-4/13B proteins were prepared and characterized. Western blotting analysis showed that the CiIL-4/13A and CiIL-4/13B mAbs could specifically recognize the recombinant proteins expressed in the E. coli cells and HEK293T cells and did not cross-react with each other. Confocal microscopy revealed that the CiIL-4/13A⁺ and CiIL-4/13B⁺ cells were present in the gills, intestine and spleen and could be upregulated in fish infected with Flavobacterium columnare (F. columnare). Interestingly, the cells expressing CiIL-4/13A and CiIL-4/13B were mostly CD3γ/δ⁺ cells. The CD3γ/δ⁺/IL-4/13A⁺ and CD3γ/δ⁺/IL-4/13B⁺ cells were significantly upregulated in the gill filaments and the intestinal mucosa after F. columnare infection. Our results imply that the CD3γ/δ⁺/IL-4/13A⁺ and CD3γ/δ⁺/IL-4/13B⁺ cells are important for homeostasis and the regulation of mucosal immunity.

Comparative Expression Profiling Reveals the Regulatory Effects of Dietary Mannan Oligosaccharides on the Intestinal Immune Response of Juvenile Megalobrama amblycephala against Aeromonas hydrophila Infection

Mannan oligosaccharides (MOS) are functional oligosaccharides with beneficial effects on the non-specific immunity of Megalobrama amblycephala, but systematic studies on the immunomodulatory mechanisms of MOS are still lacking. To investigate the protective mechanisms of three different levels of dietary MOS supplementation on the intestinal immunity of juvenile M. amblycephala, comparative digital gene expression (DGE) profiling was performed. In this study, 622 differentially expressed genes (DEGs) were identified, while the similar expression tendency of 34 genes by qRT-PCR validated the accuracy of the DGE analyses. Gene Ontology (GO) enrichment revealed that the DEGs were mainly enriched in two functional categories of biological process and molecular function. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs were mainly related to complement and coagulation cascades, coagulation cascades, platelet activation, natural killer cell mediated cytotoxicity, Fc gamma R-mediated phagocytosis and antigen processing and presentation. In addition, the pro-inflammatory, apoptosis and tight junction-related genes were more significantly up-regulated upon infection in the dietary MOS groups to enhance host immune functions and maintain the stability of the intestinal barrier. These results will be helpful to clarify the regulatory mechanism of MOS on the intestinal immunity of M. amblycephala and lay the theoretical foundation for the prevention and protection of fish bacterial diseases.

Transcriptome, intestinal microbiome and histomorphology profiling of differences in the response of Chinese sea bass (Lateolabrax maculatus) to Aeromonas hydrophila infection

The Chinese sea bass (Lateolabrax maculatus) is an important aquaculture fish, but diseases caused by Aeromonas hydrophila have led to severe economic losses to the aquaculture industry in recent years. To date, only a few studies have focused on the relationship between the intestinal immune response and changes in intestinal microbes by A. hydrophila infection. Here, we report the transcriptome and intestinal changes in infected sea bass. Histopathological results showed that severe steatosis and vacuolation occurred in the liver and that the intestinal villi and mesentery were seriously affected after infection. By extracting total RNA from intestinal tissue and studying the transcriptome profile, 1,678 genes (1,013 upregulated and 665 downregulated) were identified as significantly differentially expressed genes (DEGs). These genes are involved in many immune-related signalling pathways, such as the NOD-like receptor, C-type lectin receptor, and Toll-like receptor signalling pathways. Moreover, the intestinal microbes of sea bass changed significantly after infection. Interestingly, at the genus level, there was an increase in Serratia, Candida arthromitus and Faecalibacterium as well as a decrease in Akkermansia and Parabacteroides after infection. The results also indicated that some of the DEGs involved in the immune response were related to the genus level of intestinal microbiota. Finally, there was a relationship between gene expression patterns and the bacterial structure in the host intestine. Our study provides a reference for the study of the immune response and particular functions of intestinal microbes of sea bass after pathogen infection.

miRNA and mRNA expression analysis reveals the effects of continuous heat stress on antibacterial responses to Aeromonas hydrophila lipopolysaccharide (LPS) in grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is the largest economic fish in freshwater culture in China, which is predisposed to infectious diseases under high temperature. Under the background of global warming, the industrialization of the Pearl River Delta region has led to aggravated thermal pollution, which has increasingly serious impacts on the aquatic ecological environment. This will result in more frequent exposure of grass carp to overheated water temperatures. Previous studies have only identified the regulatory genes of fish that respond to pathogens or temperature stress, but the transcriptional response to both is unknown. In this study, the histopathological analysis showed heat stress exacerbated spleen damage induced by Aeromonas hydrophila. The transcriptional responses of the spleens from A. hydrophila lipopolysaccharide (LPS) -injected grass carp undergoing heat stress and at normal temperatures for 6, 24, and 72 h were investigated by mRNA and microRNA sequencing. We identified 28, 20, and 141 differentially expressed (DE) miRNAs and 126, 383, and 4841 DE mRNAs between the two groups after 6, 24, and 72 h, respectively. There were 67 DE genes mainly involved in the cytochrome P450 pathway, antioxidant defense, inflammatory response, pathogen recognition pathway, antigen processing and presentation, and the ubiquitin-proteasome system. There were 5 DE miRNAs involved in regulating apoptosis and inflammation. We further verified 17 DE mRNAs and 5 DE miRNAs using quantitative real-time PCR. Based on miRNAs and mRNAs analysis, continuous heat stress will affect the antibacterial responses of grass carp spleens, resulting in aggravation of spleen injury. Together, these results provide data for further understanding of the decreased tolerance of fish to pathogen infection in persistent high-temperature environments.

Th1-Th2 and M1-M2 interplay sculpt Aeromonas hydrophila pathogenesis in zebrafish (Danio rerio)

Aeromonas hydrophila is an important aquatic zoonotic pathogen that causes septicemia, necrotizing fasciitis and gastroenteritis in various aquatic and non-aquatic animals. However, the pathogenesis of A. hydrophila is not fully understood. Here, we examined the pathogenicity and histopathology of A. hydrophila in the zebrafish (Danio rerio) model system. We found that the intensity of symptoms and mortality is dose-dependent. Bacterial colonization studies demonstrated that A. hydrophila never cleared out from the fish body but stayed in a state of inactivity till it enters a fresh host. Reinfection studies showed that exposure to A. hydrophila provides immunity against future infection and hence improves fish survival. Gene expression studies revealed the crosstalk between T-helper cell and macrophage responses in fish immune system in response to A. hydrophila and infection memory. Histopathological studies showed that symptoms of tissue damage and inflammation lasted for less duration with less intensity in immunized fish when compared to non-immunized fish. Together, our results suggest that the zebrafish model is a useful system in studying the interplay between A. hydrophila pathogenesis, persistence and immunity.

Comparative analysis on the immunoregulatory roles of ferritin M in hybrid fish (Carassius cuvieri ♀ × Carassius auratus red var ♂) and its parental species after bacterial infection

Ferritin M is involved in the regulation of fish immunity. In this study, open reading frame (ORF) sequences of ferritin M from hybrid fish and its parental species were 534 bp. Tissue-specific analysis indicated that the highest level of ferritin M from red crucian carp was observed in kidney, while peaked expressions of ferritin M from white crucian carp and hybrid carp were observed in gill. Elevated levels of ferritin M from hybrid carp and its parental species were detected in immune-related tissues following Aeromonas hydrophila infection or in cultured fish cell lines after lipopolysaccharide (LPS) challenge. Ferritin M overexpression could attenuate NF-κB and TNFα promoter activity in their respective fish cells. Purified ferritin M fusion proteins elicited in vitro binding activity to A. hydrophila and Edwardsiella tarda, lowered bacterial dissemination to tissues and alleviated inflammatory response. Furthermore, treatment with ferritin M fusion proteins could mitigate bacteria-induced liver damage and rescue antioxidant activity. These results suggested that ferritin M in hybrid fish showed a similar immune defense against bacteria infection in comparison with those of its parental species.

Allelically and Differentially Expressed Genes After Infection of Edwardsiella ictaluri in Channel Catfish as Determined by Bulk Segregant RNA-Seq

Identification of genetic markers associated with resistance against enteric septicemia of catfish (ESC) is of great interest for genetic enhancement programs of catfish. In the present study, bulk segregant RNA-Seq analysis was applied to determine differentially expressed genes and alleles after ESC infection. Here we report three genomic regions on LG1, LG12, and LG26, containing significant single-nucleotide polymorphisms (SNPs). These genomic regions aligned well with quantitative trait loci (QTL) previously identified. Within the QTL regions, eleven genes were found to be differentially regulated between phenotypic bulks. Importantly, the QTL on linkage group 1 (LG1) were found to be expressed in the liver, whereas the QTL on LG12 and LG26 were expressed in the intestine, suggesting multiple mechanisms of ESC resistance. It is apparent that apolipoproteins may be important for ESC resistance as the QTL on LG1 included the 14-kDa apolipoprotein genes that are both allelically expressed and differentially expressed between the resistant and susceptible bulks. Traf2 and NCK-interacting protein kinase (TNIK) were found in the QTL on LG12, and it was downregulated in resistant fish, suggesting the importance of NCK downregulation in ESC resistance, as previously reported. In addition, we observed divergent gene expression patterns between the liver and intestine after infection. Immune/inflammatory-related processes were overrepresented from liver DEGs, while those DEGs identified from intestine were enriched for proteolysis and wounding processes. Taken together, the BSR-Seq analysis presented here advanced the knowledge of ESC resistance, providing information of not only positions of QTL but also genes and their differential expression between resistant and susceptible fish, making it one step closer to the identification of the causal genes for ESC resistance.

The Oxidative Injury of Extracellular Hemoglobin Is Associated With Reactive Oxygen Species Generation of Grass Carp (Ctenopharyngodon idella)

Intravascular hemolysis is a fundamental feature of hemorrhagic venereal infection or tissue and releases the endogenous damage-associated molecular pattern hemoglobin (Hb) into the plasma or tissues, which results in systemic inflammation, vasomotor dysfunction, thrombophilia, and proliferative vasculopathy. However, how the cytotoxic Hb affects the tissues of grass carp remains unclear. Here, we established a hemolysis model in grass carp by injecting phenylhydrazine (PHZ). The data revealed that the PHZ-induced hemolysis increased the content of Hb and activated the antioxidant system in plasma. The histopathology analysis data showed that the PHZ-induced hemolysis increased the accumulation of Hb and iron both in the head and middle kidney. The results of quantitative real-time PCR (qRT-PCR) detection suggested that the hemolysis upregulated the expressions of iron metabolism-related genes. In addition, the immunofluorescence and immunohistochemistry data revealed that the hemolysis caused an obvious deposition of collagen fiber, malondialdehyde (MDA), and 4-hydroxynonenal (4-HNE) accumulation and increased the content of oxidative-related enzymes such as β-galactosidase (β-GAL), lipid peroxide (LPO), and MDA in both the head and middle kidney. Furthermore, the PHZ-induced hemolysis significantly increased the production of reactive oxygen species (ROS), which resulted in apoptosis and modulated the expressions of cytokine-related genes. Taken together, excess of Hb released from hemolysis caused tissue oxidative damage, which may be associated with ROS and inflammation generation.

Comparative Study of Bacillus amyloliquefaciens X030 on the Intestinal Flora and Antibacterial Activity Against Aeromonas of Grass Carp

Beneficial microorganisms to control bacterial diseases has been widely used in aquaculture, Bacillus amyloliquefaciens (BaX030) as a probiotic feed additive was a commonly biological control method. Added sucrose promoted the growth of BaX030, and the yield of its antibacterial substance macrolactin A was enhanced by 1.46-fold. A total of 2055 proteins were screened through proteomics, with 143 upregulated and 307 downregulated. Differential protein expression analysis and qRT-PCR verification showed that the pentose phosphate pathway and the fatty acid synthesis pathway were upregulated, thereby providing sufficient energy and precursors for the synthesis of macrolactin A. The influence of some potential regulatory factors (SecG, LiaI, MecG and ComG) on macrolactin A was discovered. After grass carp were fed with BaX030, the abundance of probiotics (Fusobacterium, Proteobacteria, Gemmobacter) were higher than the control group, and the abundance of potential pathogenic bacteria (Planctomycetes, Aeromonas) were significantly lower than the control group. The cell and challenge experiments showed that BaX030 can significantly increase the expression of C3 and IL8 in the liver and kidney, which decreases the risk of immune organ disease. Moreover, BaX030 effectively reduced the mortality of grass carp. The results revealed that BaX030 can significantly improve the structure of the intestinal flora, enhance immunity and it is beneficial to the control of grass carp Aeromonas.

A novel ferritin L (FerL) in hybrid crucian carp could participate in host defense against Aeromonas hydrophila infection and diminish inflammatory signals

FerL, a multifunctional iron-storage polypeptide, not only exhibited a regulatory role in iron metabolism, but also participated in the regulation of fish immunity. In this study, ORF sequence of WR-FerL was 522 bp, encoding 173 amino acid residues. Tissue-specific analysis revealed that the highest expression of WR-FerL was detected in spleen. A. hydrophila challenge and LPS stimulation could sharply enhance WR-FerL mRNA expression in tissues and fish cells, respectively. Purified WR-FerL fusion peptide exhibited in vitro binding activity to A. hydrophila and endotoxin, limited bacterial dissemination to tissues as well as attenuated A. hydrophila-induced production of pro-inflammatory cytokines. Moreover, WR-FerL overexpression could abrogate NF-κB and TNFα promoter activity in fish cells. These results indicated that WR-FerL could play an important role in host defense against A. hydrophila infection.

Effects of Low-dose Mercury Exposure in Newborns on mRNA Expression Profiles

This study was designed to investigate the molecular mechanism of mercury (Hg) toxicity in the newborns by mRNA sequencing (mRNA-seq). A questionnaire survey, routine blood parameters of pregnant women, and umbilical cord blood (UCB) of newborns were collected. The median (25th percentile, 75th percentile) of total Hg (THg) concentrations in UCB of newborns was 3.63 (2.50, 6.19) µg/L. A total of 504 differentially expressed genes of mRNA were revealed between the case and control group, including 456 upregulated and 48 downregulated genes. The Gene Ontology (GO) analysis showed that differentially expressed genes were primarily involved in mitophagy, hemoglobin complex, and oxygen carrier activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the most differentially expressed genes were annotated in Huntington's disease, Parkinson's disease, and Alzheimer's disease. The qRT-PCR was used to validate the results of mRNA-seq. Low-dose Hg exposure could increase blood NE# and WBC in the pregnant women. This study provides scientific evidences on mechanism of Hg toxicity in newborns.

Chimeric ferritin H in hybrid crucian carp exhibits a similar down-regulation in lipopolysaccharide-induced NF-κB inflammatory signal in comparison with Carassius cuvieri and Carassius auratus red var

Ferritin H can participate in the regulation of teleostean immunity. ORF sequences of RCC/WCC/WR-ferritin H were 609 bp, while WR-ferritin H gene possessed chimeric fragments or offspring-specific mutations. In order to elucidate regulation of immune-related signal transduction, three fibroblast-like cell lines derived from caudal fin of red crucian carp (RCC), white crucian carp (WCC) and their hybrid offspring (WR) were characterized and designated as RCCFCs, WCCFCs and WRFCs. A sharp increase of ferritin H mRNA was observed in RCCFCs, WCCFCs and WRFCs following lipopolysaccharide (LPS) challenge. Overexpression of RCC/WCC/WR-ferritin H can decrease MyD88-IRAK4 signal and antagonize NF-κB, TNFα promoter activity in RCCFCs, WCCFCs and WRFCs, respectively. These results indicated that ferritin H in hybrid offspring harbors highly-conserved domains with a close sequence similarity to those of its parents, playing a regulatory role in inflammatory signals.

The Dynamic Immune Response of Yellow Catfish (Pelteobagrus fulvidraco) Infected With Edwardsiella ictaluri Presenting the Inflammation Process

Edwardsiella ictaluri is a highly destructive pathogen in cultured yellow catfish, thus it was very necessary to study the immune response of yellow catfish against bacterial infection. In this study, RNA-Seq technology was used to study the immune response in two distinct tissues of yellow catfish at eight different time points (h) after E. ictaluri infection. The number of differentially expressed genes (DEGs) in the spleen and liver was low at 3 h and 6 h post-infection, respectively. Afterwards, the most number of DEGs in the spleen was detected at 72 h, while the number of DEGs in the liver maintained a high level from 24 h to 120 h. The GO and KEGG enrichment analyses of DEGs at different time points uncovered that cytokines were continuously transcribed at 6 h to 120 h; whereas the liver is the main organ that secretes the components of the complement system, and metabolic regulation was activated from 12 h to 120 h. Moreover, an overview of the inflammation response of yellow catfish was exhibited including pattern-recognition receptors, inflammatory cytokines, chemokines, complements, and inflammation-related signal pathways. The similar expression tendency of nine genes by qRT-PCR validated the accuracy of transcriptome analyses. The different transcriptomic profiles obtained from the spleen and liver will help to better understand the dynamic immune response of fish against bacterial infection, and will provide basic information for establishing effective measures to prevent and control diseases in fish.

A live attenuated Edwardsiella tarda vaccine induces immunological expression pattern in Japanese flounder (Paralichthys olivaceus) in the early phase of immunization

A previous study showed that an attenuated Edwardsiella tarda strain, TXhfq, as a live vaccine could elicit protective immune effects in fish against E. tarda infection. In the current study, in order to clarify the molecular mechanism of fish immune response at the early stage after TXhfq vaccination, RNA-Seq technology was used to compare the transcriptomes of skin, intestine, and spleen between bath-vaccinated and unvaccinated Japanese flounder (Paralichthys olivaceus). An average of 46.6 million clean reads per library was obtained, ~88.04% of which were successfully mapped to the reference genome, and approximately 24,600 genes were detected in each sample. A total of 565, 878, and 1258 differential expression genes (DEGs) were found in skin, intestine, and spleen, respectively, including 1263 up-regulated genes and 1438 down-regulated genes. The DEGs exhibited different characteristics in each tissue. One hundred and sixteen DEGs belonging to six immune related categories were scrutinized, i.e., inflammatory factors, cytokines, complement and coagulation system, mucins, phagocytosis, and antigen processing and presentation. A protein-protein interaction network was constructed to get the interaction network between immune genes during the early stage of immunization. The top six hub genes highly regulated by TXhfq formed complicated interaction relationship with each other, which were involved in immune processes, notably inflammation and phagocytosis. Our results provide valuable information for the understanding of the immune mechanism underlying the protection of live attenuated vaccines in fish.

Integrated transcriptomic and proteomic analyses of grass carp intestines after vaccination with a double-targeted DNA vaccine of Vibrio mimicus

Intestinal mucosal immunity plays a vital role against Vibrio mimicus infection because it is an enteric pathogen causing serious vibriosis in fish. In the previous studies, we developed an oral double-targeted DNA vaccine of V. mimicus and demonstrated that the vaccine could elicit significantly higher intestinal mucosal immune response than did naked DNA vaccine. But, little is known underlying regulatory molecular mechanisms of the enhanced intestinal mucosal immunity. Here the transcriptome and proteome in the intestines of the grass carps immunized or not with the double-targeted DNA vaccine were investigated by using RNA-seq and iTRAQ-coupled LC-MS/MS. Compared with the control group, a total of 5339 differentially expressed genes (DEGs) and 1173 differentially expressed proteins (DEPs) were identified in the immunized fish intestines. Subsequently, the integrated analysis between transcriptome and proteome data revealed that 250 DEPs were matched with the corresponding DEGs (named associated DEPs/DEGs) at both transcriptome and proteome levels. Fifty of all the associated DEPs/DEGs were immune-related and mainly enriched in phagosome, antigen-processing and presentation, complement and coagulation cascades, NLRs and MAPK signaling pathways via Gene Ontology and KEGG pathway analyses, which suggested the coordination of the five activated pathways was essential to the enhanced intestinal mucosal immune response in the immunized fish. The protein-protein interaction analysis showed that 60 of the 63 immune-related DEPs to form an integrated network. Additionally, randomly selected DEGs and DEPs were respectively validated by quantitative real-time RT-PCR and multiple reaction monitoring (MRM) assay, indicating that the both RNA-Seq and iTRAQ results in the study were reliable. Overall, our comprehensive transcriptome and proteome data provide some key genes and their protein products for further research on the regulatory molecular mechanisms underlying the enhanced intestinal mucosal immunity.

Antibacterial and immunoregulatory activity of a novel hepcidin homologue in diploid hybrid fish (Carassius auratus cuvieri ♀ × Carassius auratus red var ♂)

Hepcidin, a multifunctional hormone oligopeptide, not only exhibits a regulatory role in iron metabolism, but also participates in the regulation of teleostean immunity. In this study, ORF sequence of WR-hepcidin was 258 bp and encoded 85 amino acid residues. Tissue-specific analysis revealed that the highest expression of WR-hepcidin was observed in liver. Aeromonas hydrophila challenge can sharply increased WR-hepcidin mRNA expression in liver, trunk kidney and spleen. The purified WR-hepcidin fusion peptide can directly bind to A. hydrophila and Streptococcus agalactiae, reduce the relative bacterial activity, limit bacterial growth and attenuate their dissemination to tissues in vivo. In addition, the treatment of WR-hepcidin fusion protein can diminish the production of pro-inflammatory cytokines. These results indicated that WR-hepcidin can play a negative regulatory role in bacteria-stimulated pro-inflammatory cytokines production and MyD88-IRAK4 activation.

The important role of phagocytosis and interleukins for nile tilapia (Oreochromis niloticus) to defense infection of Aeromonas hydrophila based on transcriptome analysis

Tilapia is an important economic fish worldwide. It is vital to understand the mechanism of immune response for the prevention and treatment the infection of Aeromonas hydrophila. Based on high-throughput sequencing of Illumina HiSeq™, we found differentially expressed genes in the immune-related pathway were classified into phagosome, cytokine-cytokine receptor interaction and toll-like receptor signaling pathway. Gene Ontology terms were divided into three categories of transporting function, DNA replication activity and energy supply activity. The first one was related to phagocytosis and the process or transporting of antigen driven by tubulins; the second one was to differentiation and proliferation of lymphocyte activated by cytokines; and the former two both needed energy provided by the third one. According to colchicine assay, cross-immune assay, ELISA of interleukins and classical phagocytosis assay, phagocytosis and interleukins were verified to be most important to defense the infection of A. hydrophila.

The key differentially expressed genes and proteins related to immune response in the spleen of pufferfish (Takifugu obscurus) infected by Aeromonas hydrophila

The immune mechanism elicited in pufferfish (Takifugu obscurus) against the invasion of Aeromonas hydrophila is still poorly understood. We examined the spleen of pufferfish at the transcriptome and proteome levels by using Illumina-seq and TMT coupled mass spectrometry after 12 h infection by A. hydrophila, respectively. A total of 2,339 genes (1,512 up-regulated and 827 down-regulated) and 537 (237 up-regulated and 300 down-regulated) proteins were identified. GO and KEGG analyses revealed that the responses to stimulus were the main biological processes, intestinal immune network for IgT production and calcium signaling pathway. Fourteen genes (8 up-regulated and 6 down-regulated) and proteins (5 up-regulated and 9 down-regulated) involved immune responses or signal transduction were validated by qRT-PCR and parallel reaction monitoring to confirm the reliability of the transcriptomic and proteomic analyses, respectively. Moreover, qRT-PCR and flow cytometry were used to detect dynamics of the genes in calcium signaling pathway and changes of concentration of cytoplasm Ca²⁺ in spleen cells within a 72 h challenge. This study provides the findings regarding immune response, especially intestinal immune network for IgT production pathway and calcium signaling pathway at the molecular, protein and cellular in pufferfish after infection by A. hydrophila. These results would provide a new insight and molecular targets into the response to pathogenic infection in pufferfish.

The Impact of Chronic Heat Stress on the Growth, Survival, Feeding, and Differential Gene Expression in the Sea Urchin Strongylocentrotus intermedius

To explore the impact of chronic heat stress on commercial echinoderms, the present study assessed the effects of chronic high temperature on the growth, survival, feeding, and differential gene expression in the sea urchin Strongylocentrotus intermedius cultured in northern Yellow Sea in China. One suitable seawater condition (20°C) and one laboratory-controlled high temperature condition (25°C) were set up. After 28 days incubation, our results showed that: (1) The specific growth, survival, and ingestion rates of S. intermedius reared under high temperature (25°C) decreased compared to those reared under optimal temperature (20°C) conditions; (2) comparative transcriptome analysis identified 2,125 differentially expressed genes (DEGs) in S. intermedius reared under high temperature (25°C) compared to those subjected to optimal temperature condition (20°C), which included 1,015 upregulated and 1,100 downregulated genes. The accuracy of the transcriptome profiles was verified by quantitative real-time PCR (qRT-PCR). Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses revealed that these DEGs mainly enriched the functional categories of ribosome, protein processing in endoplasmic reticulum, and prion diseases. A total of 732 temperature-induced expressed genes, such as ATP5, heat shock protein 70, and heat shock protein 90, were identified as candidates that were closely correlated with heat resistance in S. intermedius. Differentially expressed transcription factors (TFs), such as AP-1, Fos, CREB, and ZNF, were also identified as potential regulators that regulate the molecular network that was associated with responses to heat stress in sea urchins. Observations in the present study provide additional information that improves our understanding of the molecular mechanism of temperate echinoid species in response to heat stress, as well as theoretical basis for the molecular-assisted breeding of heat-resistant sea urchins.

Identification and expression analysis of IL-4/13 receptors in grass carp Ctenopharyngodon idella

Interleukin (IL)-4 and IL-13 are T helper 2 (Th2) cytokines with pleiotropic functions. IL-4 interacts with two receptors consisting of IL-4Rα/γ chain receptor (γC) and IL-4Rα/IL-13Rα1. In contrast, IL-13 binds to IL-13Rα2 but also shares the receptor complex containing IL-4Rα/IL-13Rα1. In fish, two IL-4/13 homologs have been identified but their phylogenetic relationships with IL-4 and IL-13 are ambiguous. In this study, we identified six putative IL-4/13 receptor homologs in grass carp, including γC1, γC2, IL-4Rα1, IL-13Rα1, IL-13Rα2 and a soluble form of IL-4Rα2. Comparative sequence analyses revealed that these receptors possess conserved characteristic domains and the genes encoding them share conserved gene synteny with their human counterparts. All six receptors contain a cytokine binding homology domain (CHD) and two fibronectin type Ⅲ (FNⅢ) like domains, with IL-13Rα1 and IL-13Rα2 harbouring an extra Ig-like domain preceding the CHD domain. Interestingly, grass carp IL-13Rα1 and IL-13Rα2 lack the characteristic WSXWS motif, a typical feature of mammalian type I cytokine receptors. The IL-4/13 receptor genes are differentially expressed in tissues and primary leukocytes of head kidney and can be modulated by Flavobacterium cloumnare (F. cloumnare), suggesting they are involved in immune response against F. cloumnare infection.

Transcriptome profiles in the spleen of African catfish (Clarias gariepinus) challenged with Aeromonas veronii

The African catfish, Clarias gariepinus, an important cultured freshwater species in many countries, possess the characteristic of high disease resistance. However, little genomic information for this character of the fish is available up to now. To address the shortfall and to better understand C. gariepinus immune response to pathogen infection at molecular level, C. gariepinus were challenged with potent A. veronii and the high-throughput RNA sequencing (RNA-seq) technology were employed to produce transcriptomes from spleen. In total, an average of 46,073,372 clean reads obtained were de novo assembled into 156,955 unigenes with an average length of 1082 bp. All of unigenes were annotated to seven public databases. Three comparisons were separately conducted between the infected groups at 3 h, 24 h, 48 h post-challenge and control group. A total of 2482 differentially expressed unigenes (DEGs) were identified. Among these, 114 immune-related DEGs were captured, including 88, 42, and 31 genes at 3 h, 24 h and 48 h after infection respectively, for analysis of expression pattern and enrichment. The 114 DEGs displayed four expression patterns by cluster analysis and they were significantly enriched in 38 pathways (q < 0.01) related to the immune or disease, five of which were NF-kappa B, TNF, NLR, TLR and RLR pathways. Finally, the expression levels of twelve selected immune-related DEGs involved in above five pathways were scrutinized. Seven of which were up-regulated at 3 h after infection, afterward, their expression dropped to control level. In summary, this study provides valuable transcriptome resource for understanding the defense mechanisms of C. gariepinus in resistance to pathogens from the gene expression viewpoint, which also open up the possibility to study the immune complexity and to better comprehend the interrelationships between some immune pathways in C. gariepinus.

Comparative Study of Immune Reaction Against Bacterial Infection From Transcriptome Analysis

Transcriptome analysis is a powerful tool that enables a deep understanding of complicated physiological pathways, including immune responses. RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. Rapid developments in these techniques have not only accelerated investigations into the process of pathogenic infection and defense strategies in fish, but also used to identify immunity-related genes in fish. These findings will contribute to fish immunotherapy for the prevention and treatment of bacterial infections through the design of more specific and effective immune stimulants, adjuvants, and vaccines. Until now, there has been little information regarding the universality and diversity of immune reactions against pathogenic infection in fish. Therefore, one of the aims of this paper is to introduce the RNA-Seq technique for examination of immune responses in pathogen-infected fish. This review also aims to highlight comparative studies of immune responses against bacteria, based on our previous findings in largemouth bass (Micropterus salmoides) against Nocardia seriolae, gray mullet (Mugil cephalus) against Lactococcus garvieae, orange-spotted grouper (Epinephelus coioides) against Vibrio harveyi, and koi carp (Cyprinus carpio) against Aeromonas sobria, using RNA-seq techniques. We demonstrated that only 39 differentially expressed genes (DEGs) were present in all species. However, the number of specific DEGs in each species was relatively higher than that of common DEGs; 493 DEGs in largemouth bass against N. seriolae, 819 DEGs in mullets against L. garvieae, 909 in groupers against V. harveyi, and 1471 in carps against A. sobria. The DEGs in different fish species were also representative of specific immune-related pathways. The results of this study will enhance our understanding of the immune responses of fish, and will aid in the development of effective vaccines, therapies, and disease-resistant strains.

Liver transcriptome analysis and de novo annotation of the orange-spotted groupers (Epinephelus coioides) under cold stress

Cold stress has caused great economic loss in fish culture worldwide. Orange-spotted grouper (Epinephelus coioides) is one of the most serious lost aquatic animals in 2016 cold fronts in South China. However, the molecular mechanism of grouper's cold resistance has remained largely unknown. In the present study, HiSeq™2000 (Illumina) was used to analyze the transcriptomic profiles of the liver from grouper under control temperature (CT, 28 °C) and low temperature (LT, 13 °C). Two normalized liver cDNA libraries of CT and LT groups were created. We obtained 51,944,970 and 51,905,036 clean reads from CT and LT groups, respectively. Comparing the LT group to the CT group, a total of 5905 significantly differentially expressed genes (DEGs) were identified, including 2093 up-regulated unigenes and 3812 down-regulated unigenes. GO annotation and functional enrichment analysis indicated that all of the DEGs were classified into three categories: biological process (23 subclasses), cellular component (18 subclasses) and molecular function (13 subclasses). KEGG analysis of the DEGs showed that 2732 DEGs were annotated to 253 signaling pathways. The most highly enriched pathways were cell adhesion molecules, Staphylococcus aureus infection, PPAR signaling pathway, Vibrio cholerae infection, primary immunodeficiency, fatty acid elongation, and we found cold stress mainly affects immunity, metabolic and signal transduction. Thirteen of the DEGs were further validated by qRT-PCR. Our results provide valuable information for further analysis of the mechanisms of groupers response under cold stress.

Changes in gene and genotype frequencies during the development of the grass carp Ctenopharyngodon idella

In this study, a full-sib population of Ctenopharyngodon idella was constructed and approximately 500 C. idella individuals were sampled at four early developmental stages (hatching, first feeding, juvenile fish and young fish). Four DNA pools were constructed and subjected to next-generation sequencing. On the basis of the identification of single nucleotide polymorphisms (SNP), changes in gene and genotype frequencies during the developmental progress of C. idella were revealed, which indicates that death during the early developmental stage is not a random process. These findings will establish the basis for further studies performed for identifying superior alleles or genotypes as target markers for molecular breeding.

Transcriptome analysis and histopathology of black carp (Mylopharyngodon piceus) spleen infected by Aeromonas hydrophila

Aeromonas hydrophila causes serious economic losses to the black carp (Mylopharyngodon piceus) industry. In this study, we analyzed the spleen of disease-resistant and susceptible black carp by RNA-seq. Overall, a total of 5243 terms were enriched in the gene ontology (GO) analysis, and 323 related pathways were found in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. A total of 1935 differentially expressed genes were found and were primarily involved in cell adhesion, pathogen recognition, cellular immunity, cytokines, complement systems, and iron transport. Sixteen of the differently expressed genes involved in the immune response and the accuracy of the transcriptome data were further validated by quantitative real-time PCR (qRT-PCR). We observed Tissue sections of the spleen infected with A. hydrophila and the control group and found that the spleen of the infected group had necrosis.

Molecular cloning, expression and antibacterial activity of goose-type lysozyme gene in Microptenus salmoides

It is well known that lysozymes are key proteins to teleosts in the innate immune system and possess high bactericidal properties. In the present study, a g-type lysozyme gene was cloned from Microptenus salmoides. The g-type sequence consisted of 582 bp, which translated into a 193 amino acid (AA) protein (GenBank accession no: MH087462). The predicted molecular weight and theoretical isoelectric point were 21.36 kDa and 6.91 respectively and no signal peptide was observed. The qRT-PCR analysis showed that the g-type lysozyme gene was differentially expressed in various tissues under normal conditions and the highest g-type lysozyme level was observed in liver, gill and spleen while there seemed to be low expression in the muscle, heart and head-kidney. The expression of g-type lysozyme was differentially upregulated in the spleen, gill and intestine after stimulation with heat stress and Aeromonas hydrophila (A. hydrophila). Under heat stress and A. hydrophila injection, the g-type lysozyme mRNA levels all in spleens, gill and intestine tissues increased significantly (P < 0.05), with the maximum levels attained at 12 h, 24 h (or 12 h) and 24 h. Thereafter, they all decreased significantly (P < 0.01) and the expression in gill returned to nearly the basal value within 72 h. Those results suggested that g-type lysozyme was involved in the immune response to heat stress and bacterial challenge. The cloning and expression analysis of the g-type lysozyme provide theoretical basis to further study the mechanism of anti-adverseness in Microptenus salmoides. The g-type lysozyme gene perhaps also played an important role in the immune responses against bacterial invasion.

A Review of Molecular Responses of Catfish to Bacterial Diseases and Abiotic Stresses

Catfish is one of the major aquaculture species in the United States. However, the catfish industry is threatened by several bacterial diseases such as enteric septicemia of catfish (ESC), columnaris disease and Aeromonas disease, as well as by abiotic stresses such as high temperature and low oxygen. Research has been conducted for several decades to understand the host responses to these diseases and abiotic stresses. With the development of sequencing technologies, and the application of genome-wide association studies in aquaculture species, significant progress has been made. This review article summarizes recent progress in understanding the molecular responses of catfish after bacterial infection and stress challenges, and in understanding of genomic and genetic basis for disease resistance and stress tolerance.

Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish

Disease resistance is one of the most important traits for aquaculture industry. For catfish industry, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the most severe disease, causing enormous economic losses every year. In this study, we used three channel catfish families with 900 individuals (300 fish per family) and the 690K catfish SNP array, and conducted a genome-wide association study to detect the quantitative trait loci (QTL) associated with ESC resistance. Three significant QTL, with two of located on LG1 and one on LG26, and three suggestive QTL located on LG1, LG3, and LG21, respectively, were identified to be associated with ESC resistance. With a well-assembled- and -annotated reference genome sequence, genes around the involved QTL regions were identified. Among these genes, 37 genes had known functions in immunity, which may be involved in ESC resistance. Notably, nlrc3 and nlrp12 identified here were also found in QTL regions of ESC resistance in the channel catfish × blue catfish interspecific hybrid system, suggesting this QTL was operating within both intra-specific channel catfish populations and interspecific hybrid backcross populations. Many of the genes of the Class I MHC pathway, for mediated antigen processing and presentation, were found in the QTL regions. The positional correlation found in this study and the expressional correlation found in previous studies indicated that Class I MHC pathway was significantly associated with ESC resistance. This study validated one QTL previously identified using the second and fourth generation of the interspecific hybrid backcross progenies, and identified five additional QTL among channel catfish families. Taken together, it appears that there are only a few major QTL for ESC disease resistance, making marker-assisted selection an effective approach for genetic improvements of ESC resistance.

Applications of transcriptomics and proteomics in understanding fish immunity

With the development of intensive aquaculture, economic losses increasingly result from fish mortality due to pathogen infection. In recent years, a growing number of researchers have used transcriptomic and proteomic analyses to study fish immune responses to exogenous pathogen infection. Integrating transcriptomic and proteomic analyses provides a better understanding of the fish immune system including gene expression, regulation, and the intricate biological processes underlying immune responses against infection. This review focuses on the recent advances in the fields of transcriptomics and proteomics, which have contributed to our understanding of fish immunity to exogenous pathogens.

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.

Genomic and transcriptomic approaches to study immunology in cyprinids: What is next?

Accelerated by the introduction of Next-Generation Sequencing (NGS), a number of genomes of cyprinid fish species have been drafted, leading to a highly valuable collective resource of comparative genome information on cyprinids (Cyprinidae). In addition, NGS-based transcriptome analyses of different developmental stages, organs, or cell types, increasingly contribute to the understanding of complex physiological processes, including immune responses. Cyprinids are a highly interesting family because they comprise one of the most-diversified families of teleosts and because of their variation in ploidy level, with diploid, triploid, tetraploid, hexaploid and sometimes even octoploid species. The wealth of data obtained from NGS technologies provides both challenges and opportunities for immunological research, which will be discussed here. Correct interpretation of ploidy effects on immune responses requires knowledge of the degree of functional divergence between duplicated genes, which can differ even between closely-related cyprinid fish species. We summarize NGS-based progress in analysing immune responses and discuss the importance of respecting the presence of (multiple) duplicated gene sequences when performing transcriptome analyses for detailed understanding of complex physiological processes. Progressively, advances in NGS technology are providing workable methods to further elucidate the implications of gene duplication events and functional divergence of duplicates genes and proteins involved in immune responses in cyprinids. We conclude with discussing how future applications of NGS technologies and analysis methods could enhance immunological research and understanding.

Interleukin 4/13 receptors: An overview of genes, expression and functional role in teleost fish

In superior vertebrates, Interleukin 4 (IL-4) and Interleukin 13 (IL-13) play key and diverse roles to support immune responses acting on cell surface receptors. When stimulated, receptors activate intracellular signalling cascades switching cell phenotypes according to stimuli. In teleost fish, Interleukin 4/13 (IL-4/13) is the ancestral family cytokine related to both IL-4 and IL-13. Every private and common receptor subunit for IL-4/13 have in fish at least two paralogues and, as in mammals, soluble forms are also part of the receptor system. Reports for findings of fish IL-4/13 receptors have covered comparative analysis, transcriptomic profiles and to a lesser extent, functional analysis regarding ligand-receptor interactions and their biological effects. This review addresses available information from fish IL-4/13 receptors and discusses overall implications on teleost immunity, summarized gene induction strategies and pathogen-induced gene modulation, which may be useful tools to enhance immune response. Additionally, we present novel coding sequences for Atlantic salmon (Salmo salar) common gamma chain receptor (γC), Interleukin 13 receptor alpha 1A chain (IL-13Rα1A) and Interleukin 13 receptor alpha 1B chain (IL-13Rα1B).

A Preliminary Study on the Pattern, the Physiological Bases and the Molecular Mechanism of the Adductor Muscle Scar Pigmentation in Pacific Oyster Crassostrea gigas

The melanin pigmentation of the adductor muscle scar and the outer surface of the shell are among attractive features and their pigmentation patterns and mechanism still remains unknown in the Pacific oyster Crassostrea gigas. To study these pigmentation patterns, the colors of the adductor muscle scar vs. the outer surface of the shell on the same side were compared. No relevance was found between the colors of the adductor muscle scars and the corresponding outer surface of the shells, suggesting that their pigmentation processes were independent. Interestingly, a relationship between the color of the adductor muscle scars and the dried soft-body weight of Pacific oysters was found, which could be explained by the high hydroxyl free radical scavenging capacity of the muscle attached to the black adductor muscle scar. After the transcriptomes of pigmented and unpigmented adductor muscles and mantles were studied by RNAseq and compared, it was found that the retinol metabolism pathway were likely to be involved in melanin deposition on the adductor muscle scar and the outer surface of the shell, and that the different members of the tyrosinase or Cytochrome P450 gene families could play a role in the independent pigmentation of different organs.

Integrated analysis of mRNA-seq in the haemocytes of Eriocheir sinensis in response to Spiroplasma eriocheiris infection

The Chinese mitten crab Eriocheir sinensis is an important economic crustacean that has been exposed to various diseases. Spiroplasma eriocheiris, isolated from tremor-diseased E. sinensis, was first identified as a lethal pathogen of freshwater crustaceans. To understand the pathogenesis of S. eriocheiris to E. sinensis, the transcriptomic profiles of haemocytes in the experimental and control groups at 1 d and 7 d post-injection were obtained using Illumina HiSeq 2500. These results showed that 40,358,724, 44,462,112, 45,516,576 and 37,713,728 paired-end clean reads were obtained from the cDNA libraries of DZ1 (the control group at 1 d), DZ7 (the control group at 7 d), SY1 (the experimental group at 1 d) and SY7 (the experimental group at 7 d), respectively. In total, 106,641 unique transcript fragments (unigenes) were assembled, with an average length of 710 bp. On the first day of stimulation, 33,084 up-regulated transcripts and 19,208 down-regulated transcripts were found in the experimental group compared with those in the control group. On the seventh day of stimulation, 40,198 up-regulated transcripts and 12,032 down-regulated transcripts were found in the experimental group compared with those in the control group. Some canonical immune-related pathways were identified via KEGG pathway analysis, including complement and coagulation cascades, the VEGF signalling pathway, the Wnt signalling pathway, natural killer cell-mediated cytotoxicity, the MAPK signalling pathway, neuroactive ligand-receptor interactions, and the Lysosome pathway. We found important immune-related genes (GNPTAB, MASP2, F7, F5, NFATC, TRAF6, MAP3K5, and TRa) in the KEGG pathway, and those genes were confirmed by qRT-PCR analysis. In addition, the significantly enriched neuroactive ligand-receptor interaction pathway was associated with intense paroxysmal tremors of infected crabs. Our results provide valuable information for the further analysis of the mechanisms of E. sinensis defence against S. eriocheiris invasion.

Transcriptome profiling reveals the immune response of goose T cells under selenium stimuli

The goose is an economically important poultry species and a principal natural host of avian viruses. This study aimed to determine the effects of selenium on the immune response of geese. Under selenium stimulation, gene expression profiling was investigated using transcriptome sequencing. The selenoproteins were promoted by selenium stimulation, while the heat shock proteins, interleukin and interferons were mainly down-regulated. After comparison, 2228 differentially expressed genes were primarily involved in immune and environmental response, and infectious disease and genetic information processing related pathways were identified. Specifically, the enzymes of the lysosomes which acted as a safeguard in preventing pathogens were mostly up-regulated and six randomly selected differentially expressed genes were validated by quantitative polymerase chain reaction. In addition, the most proportional increased transcription factor family basic helix-loop-helix (bHLH) located in the 5' flank of selenoprotein P-like protein for selenium metabolism was identified by response to the selenium stimulation in this study. These analyses show that selenium can promote immune function by activating selenoproteins, transcript factors and lysosome pathway related genes, while weakening cytokine content genes in geese.

Transcriptomic variation of locally-infected skin of Epinephelus coioides reveals the mucosal immune mechanism against Cryptocaryon irritans

Fish skin is the largest immunologically active mucosal organ, providing first-line defense against external pathogens. However, the skin-associated immune mechanisms of fish are still unclear. Cryptocaryon irritans is an obligate ectoparasitic ciliated protozoan that infects almost all marine fish, and is believed to be an excellent pathogen model to study fish mucosal immunity. In this study, a de novo transcriptome assembly of Epinephelus coioides skin post C. irritans tail-infection was performed for the first time using the Illumina HiSeq™ 2500 system. Comparative analyses of infected skin (group Isk) and uninfected skin (group Nsk) from the same challenged fish and control skin (group C) from uninfected control fish were conducted. As a result, a total of 91,082 unigenes with an average length of 2880 base pairs were obtained and among them, 38,704 and 48,617 unigenes were annotated based on homology with matches in the non-redundant and zebrafish database, respectively. Pairwise comparison resulted in 10,115 differentially-expressed genes (DEGs) in the Isk/C group comparison (4,983 up-regulated and 5,132 down-regulated), 2,275 DEGs in the Isk/Nsk group comparison (1,319 up-regulated and 956 down-regulated) and 4,566 DEGs in the Nsk/C group comparison (1,534 up-regulated and 3,032 down-regulated). Seven immune-related categories including 91 differentially-expressed immune genes (86 up-regulated and 5 down-regulated) were scrutinized. Both DEGs and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and immune-related gene expression analysis were used, and both analyses showed that the genes were more significantly altered in the locally-infected skin than in the uninfected skin of the same challenged fish. This suggests the skin's local immune response is important for host defense against this ectoparasite infection. Innate immune molecules, including hepcidin, C-type lectin, transferrin, transferrin receptor protein, serum amyloid A, cathepsin and complement components were significantly up-regulated (fold-change ranged from 3.3 to 12,944) in infected skin compared with control skin. The up-regulation of chemokines and chemokine receptors and activation of the leukocyte transendothelial migration pathway suggested that leucocytes intensively migrated to the local infected sites to mount a local immune defense. Toll-like receptors (TLRs) 1, 2, 5 and 5S were most significantly up-regulated in the infected skin, suggesting that these TLRs may be involved in parasite pathogen-associated molecular pattern (PAMPs) recognition. Up-regulation of the dendritic cell markers CD209 and CD83 and other antigen presentation pathway molecules provided evidence for skin local antigen presentation. Up-regulation of the T cell markers CD4 and CD48, B cell markers CD22 and CD81 and B cell receptor signaling kinase Lyn, showed the presence and population expansion of T/B cells at locally-infected sites, which suggested possible activation of a local specific immune response in the skin. Our results will facilitate in-depth understanding of local immune defense mechanisms in fish skin against ectoparasite infection.

Transcriptome data analysis of grass carp (Ctenopharyngodon idella) infected by reovirus provides insights into two immune-related genes

Grass carp (Ctenopharyngodon idella) was one of the economically important freshwater fish in China. However, hemorrhagic disease caused by grass carp reovirus (GCRV) results in a tremendous loss in the process of grass carp cultivation. Transcriptome analysis could provide a comprehensive understanding of the molecular mechanisms involved in specific biological processes and diseases for the resistance to reovirus infection of grass carp. In this study, the raw data from NCBI (accession number: SRA099702) were analyzed, in which, 50 significant differentially expressed genes by routine transcriptome analysis and 84 notably differentially expressed genes by co-expression network method. KEGG analysis revealed that the pathway in hemorrhagic diseases in grass carp was similar to the influenza A induced pathway. The interferon-stimulated gene ISG15 and sacsin-like gene, which were up-regulated in data (SRA099702), were also up-regulated in data (SRP049081) from a similar assay. QPCR experiment was performed to validate these up-regulated genes. The ISG15 gene was shown to be the core gene in the co-expression network. The results would enhance our understanding of the antivirus system of grass carp infected by reovirus.

Transcriptome Analysis Reveals Comprehensive Insights into the Early Immune Response of Large Yellow Croaker (Larimichthys crocea) Induced by Trivalent Bacterial Vaccine

Vaccination is an effective and safe strategy for combating bacterial diseases in fish, but the mechanisms underlying the early immune response after vaccination remain to be elucidated. In the present study, we used RNA-seq technology to perform transcriptome analysis of spleens from large yellow croaker (Larimichthys crocea) induced by inactivated trivalent bacterial vaccine (Vibrio parahaemolyticus, Vibrio alginolyticus and Aeromonas hydrophila). A total of 2,789 or 1,511 differentially expressed genes (DEGs) were obtained at 24 or 72 h after vaccination, including 1,132 or 842 remarkably up-regulated genes and 1,657 or 669 remarkably down-regulated genes, respectively. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichments revealed that numerous DEGs belong to immune-relevant genes, involved in many immune-relevant pathways. Most of the strongly up-regulated DEGs are innate defense molecules, such as antimicrobial peptides, complement components, lectins, and transferrins. Trivalent bacterial vaccine affected the expressions of many components associated with bacterial ligand-depending Toll-like receptor signaling pathways and inflammasome formation, indicating that multiple innate immune processes were activated at the early period of vaccination in large yellow croaker. Moreover, the expression levels of genes involved in antigen processing were also up-regulated by bacterial vaccine. However, the expression levels of several T cell receptors and related CD molecules and signal transducers were down-regulated, suggesting that the T cell receptor signaling pathway was rapidly suppressed after vaccination. These results provide the comprehensive insights into the early immune response of large yellow croaker to vaccination and valuable information for developing a highly immunogenic vaccine against bacterial infection in teleosts.

A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila

Inflammation is a protective response that is implicated in bacterial enteritis and other fish diseases. The inflammatory mechanisms behind Aeromonas hydrophila infections in fish remain poorly understood. In this study, we performed a de novo grass carp transcriptome assembly using Illumina's Solexa sequencing technique. On this basis we carried out a comparative analysis of intestinal transcriptomes from A. hydrophila-challenged and physiological saline solution (PSS/mock) -challenged fish, and 315 genes were up-regulated and 234 were down-regulated in the intestines infected with A. hydrophila. The GO enrichment analysis indicated that the differentially expressed genes were enriched to 12, 4, and 8 GO terms in biological process, molecular function, and cellular component, respectively. A KEGG analysis showed that 549 DEGs were involved in 165 pathways. Moreover, 15 DEGs were selected for quantitative real-time PCR analysis to validate the RNA-seq data. The results confirmed the consistency of the expression levels between RNA-seq and qPCR data. In addition, a time-course analysis of the mRNA expression of 12 inflammatory genes further demonstrated that the intestinal inflammatory responses to A. hydrophila infection simultaneously modulated gene expression variations. The present study provides intestine-specific transcriptome data, allowing us to unravel the mechanisms of intestinal inflammation triggered by bacterial pathogens.

Effect of high temperature on immune response of grass carp (Ctenopharyngodon idellus) by transcriptome analysis

Exposure to high temperature is an inherent feature of grass carp culture in southern China and juvenile grass carps are predisposed to infectious disease in this condition. To understand how high temperature impacts the immune response to pathogens in grass carp, the transcriptomic profiles of the spleens from immune injected grass carp groups undergoing heat stress and normal temperature were investigated. An average of 72 million clean reads per library was obtained, and approximate 80% of these genes were successfully mapped to the reference genome. A total of 2287 up-regulated and 1068 down-regulated genes were identified. 10 immune-related categories involving 90 differently expressed genes were scrutinized. Expression patterns of 18 differentially expressed genes involving in immune response were validated by quantitative real-time RT-PCR. These results provide further significant insights into the influence mechanism of high temperature to immune response in grass carp.

Dietary choline deficiency and excess induced intestinal inflammation and alteration of intestinal tight junction protein transcription potentially by modulating NF-κB, STAT and p38 MAPK signaling molecules in juvenile Jian carp

This study investigated the effects of choline on intestinal mucosal immune and the possible mechanisms in fish by feeding juvenile Jian carp (Cyprinus carpio var. Jian) with graded levels of dietary choline (165-1820 mg/kg diet) for 65 days. The results firstly showed that choline deficiency induced inflammatory infiltration in the proximal intestine (PI), mid intestine (MI) and distal intestine (DI) of fish. Meanwhile, compared with the optimal choline group, choline deficiency decreased the activities of lysozyme and acid phosphatase, contents of complement 3 and IgM in the intestine, downregulated the mRNA levels of antimicrobial peptides (liver-expressed antimicrobial peptide (LEAP) 2A and defensin-3 in the PI and MI, LEAP-2B and hepcidin in the PI, MI and DI), anti-inflammatory cytokines (interleukin (IL) 10 and transforming growth factor β2 in the PI, MI and DI), and signaling molecule IκB in the PI, MI and DI; while upregulated the mRNA levels of pro-inflammatory cytokines (IL-6a and tumor necrosis factor α in the MI and DI, interferon γ2b in the PI and MI, IL-1β and IL-6b in the PI, MI and DI), and signaling molecules (Toll-like receptor 4 in the MI, myeloid differentiation primary response 88 in the PI and MI, Janus kinase 3 and tyrosine kinase 2 in the MI and DI, nuclear factor kappa B (NF-κB), signal transducers and activators of transcription (STAT) 4 and STAT5 in the PI, MI and DI) of juvenile Jian carp, further indicating that choline deficiency caused inflammation and immunity depression in the intestine of fish. But choline deficiency decreased the PI IL-6a mRNA level, and increased the DI LEAP-2A and defensin-3 mRNA levels with unknown reasons. Furthermore, dietary choline deficiency downregulated mRNA levels of tight junction (TJ) proteins (claudin 3c in the PI and MI, claudin 7, claudin 11 and occludin in the PI, MI and DI) and signaling molecule mitogen-activated protein kinases p38 in the PI, MI and DI of juvenile Jian carp, whereas upregulated the mRNA levels of claudin 3b in the MI and DI, and claudin 3c in the DI. Moreover, the excessive choline exhibited negative effects on intestinal immunity and TJ proteins that were similar to the choline deficiency. In summary, dietary choline deficiency or excess caused the depression of intestinal mucosal immune by inducing inflammation and dysfunction of the intestinal physical barrier, and regulating related signaling molecules of fish.