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

Unravelling the ontogeny and tissue-specific expression profiles of immune-related genes in the near-threatened endemic catfish, Clarias dussumieri

Clarias dussumieri, an air breathing catfish endemic to the Western Ghats in India, is categorized as 'Near Threatened' by the IUCN. This species is of high regional consumer demand and is one of the prioritized candidate species for aquaculture diversification and conservation. Despite its ecological and commercial significance, comprehensive studies on its immune system are lacking. This study elucidates the ontogenetic development and tissue-specific (brain, anterior kidney, gill, spleen, muscle, liver, hindgut and skin) expression profiles of key immune-related genes in C. dussumieri. Larvae were sampled at various developmental stages post-fertilization, and tissues from adult fish were analyzed for expression patterns of genes associated with inflammation (IL-1β, TNF-α, iNOS), antimicrobial defense (LYS, HAMP), stress response (HSP70), complement system (C3), cell-mediated immunity (MHC-IIβ, CD4-1), and adaptive immunity (IgM). The expression of IL-1β was highest at 60 days post-fertilization (60D), while TNF-α expression peaked at 25D before dropping notably by 60D. iNOS showed a peak at 7D, underscoring its importance in early immune defence. LYS exhibited a high expression at 10D, while HAMP peaked at 60D, highlighting their roles in antimicrobial defence. Stress marker HSP70 increased from 15D onwards and complement component C3 was consistently expressed at low levels throughout development. MHC-IIβ and CD4-1 showed significant increase since 10D and 7D respectively, suggesting the establishment of cell-mediated immunity. IgM expression increased notably from 15 days, indicating the development of adaptive immunity. In adult fish tissues, IL-1β, TNF-α, LYS and HSP70 showed highest expression in the hindgut, while C3 was predominantly expressed in the liver. MHC-IIβ and CD4-1 were highly expressed in the spleen and anterior kidney respectively. IgM was abundant in the anterior kidney and spleen. This study provides crucial baseline data on the immune competence of different developmental stages of C. dussumieri, informing strategies for effective vaccination and disease management in aquaculture, and enhancing our understanding of fish immunology for conservation efforts.

Construction of a Full-Length transcriptome resource for the African sharptooth catfish (Clarias gariepinus), a prototypical air-breathing Fish, based on isoform sequencing (Iso-Seq)

The African sharptooth catfish (Clarias gariepinus) assumes significance in aquaculture, given its role as a farmed freshwater species with modified gill structures functioning as an air-breathing organ (ABO). To provide a scientific basis for further elucidating the air-breathing formation mechanism and deeply utilizing the genetic resources of Clarias gariepinus, we utilized the PacBio sequencing platform to acquire a comprehensive full-length transcriptome from five juvenile developmental stages and various adult tissues, including the ABO, gills, liver, skin, and muscle. We generated 25,766,688 high-quality reads, with an average length of 2,006 bp and an N50 of 2,241 bp. Following rigorous quality control, 34,890 (97.7 %) of the high-quality isoforms were mapped to the reference genome for gene and transcript annotation, yielding 387 novel isoforms and 14,614 new isoforms. Additionally, we identified 28,582 open reading frames, 48 SNPs, 5,464 variable splices, and 6,141 variable polyadenylation sites, along with 475 long non-coding RNAs. Many DEGs were involved with low oxygen GO terms and KEGG pathways, such as response to stimulus, biological regulation and catalytic activities. Furthermore, it was found that transcription factors such as zf-C2H2, Homeobox, bHLH, and MYB could underpin the African sharptooth catfish's developmental plasticity and its capacity to adapt its morphology and function to its environment. Through the comprehensive analysis of its genomic characteristics, it was found that the African sharptooth catfish has developed a series of unique respiratory adaptive mechanisms during the evolutionary process, These results not only advances the understanding of genetic adaptations to hypoxia in Clarias fish but also provides a valuable framework for future studies aimed at improving aquaculture practices,besides provide important references and inspirations for the evolution of aquatic organisms.

Immune Response and Transcriptome Analysis of the Head Kidney to Different Concentrations of Aeromonas veronii in Common Carp (Cyprinus carpio)

The common carp (Cyprinus carpio), a major economic freshwater fish, is suffering from a variety of bacterial infectious diseases because of its high-density, factory and intensive farming patterns. Aeromonas veronii is the causative agent of high mortality in common carp, causing severe economic losses in aquaculture. However, the regulatory mechanisms involved in the response of common carp to this bacterial infection remain poorly understood. In this study, we compared mortality, blood serum LZM (Lysozyme) and IgM (Immunoglobulin M) levels and transcriptome patterns of head kidney tissues after infection with different concentrations of Aeromonas veronii. We observed that mortality increased progressively with an increasing pathogen concentration. The concentrations of blood serum LZM and IgM significantly increased after infection. A total of 13 and 925 differentially expressed genes (DEGs) were identified after infection with low (T4) and high (T9) concentrations of bacterial suspension, respectively. KEGG and GO analyses of the DEGs highlighted multiple immune-related signaling pathways. Weighted gene co-expression network analysis (WGCNA) revealed that 136 and 83 hub genes were related to blood serum LZM and IgM, respectively. Finally, the gene expression in the head kidney was validated via RT-qPCR to be consistent with the transcriptome. These results provide insights into the mechanisms of the immune response to infection with different concentrations of Aeromonas veronii and offer useful information for further studies on immune defense mechanisms in common carp.

Impact of gonadotropin on certain testis-related genes identified through testicular transcriptome analysis in the Asian and the African catfish

Induction of spawning in catfish is well demonstrated in females while stimulation of spermiation in males seems difficult. This has led to least understanding of gene profile changes during testicular maturation. Expression of the factors after hormonal induction that control reproductive processes has become an intense research area in fish endocrinology. In view of this, de novo assemblies of testicular transcriptomes of the Asian catfish, Clarias batrachus and the African catfish, C. gariepinus, were performed to identify genes/factors involved in testicular maturation. For testicular induction, human chorionic gonadotropin (hCG) was administered in vivo to both the catfish species during active phase of reproduction. 1,68,071 and 1,26,232 assembled transcripts were obtained from C. batrachus and C. gariepinus testicular transcriptomes and were annotated using different databases. Further, in silico analysis suggested the presence of several transcripts that were involved in steroidogenesis and male reproduction. Comparison of transcriptomes of both species revealed the presence of certain unique genes related to reproduction differentially. Expression profiles after hCG induction in testis showed higher expression of certain steroidogenesis related genes such as star, cyp11b1, cyp17a and cyp21a in both the species. Further, expression levels of crucial factors related to testis, such as dmrt1/2/3, were also found to be significantly higher after gonadotropin induction. However, amh, tgfα and dmrt4/5 expression levels were significantly low. Factors related to male reproduction i.e., tekt1, tekt2, sox9, spag1, spata2 and spata7 were found to be differentially upregulated in hCG treated testicular tissues of both the species. Histology analysis indicated that the gonadotropin induction either short or long term is a better strategy to highlight expression profile changes during testicular maturation in teleost.

Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus)

Airbreathing catfish are stenohaline freshwater fish capable of withstanding various environmental conditions and farming practices, including breathing atmospheric oxygen. This unique ability has enabled them to thrive in semi-terrestrial habitats. However, the genomic mechanisms underlying their adaptation to adverse ecological environments remain largely unexplored, primarily due to the limited availability of high-quality genomic resources. Here, we present a haplotype-resolved and near telomere-to-telomere (T2T) genome assembly of the African catfish (Clarias gariepinus), utilizing Oxford Nanopore, PacBio HiFi, Illumina and Hi-C sequencing technologies. The primary assembly spans 969.62 Mb with only 47 contigs, achieving a contig N50 of 33.71 Mb. Terminal telomeric signals were detected in 22 of 47 contigs, suggesting T2T assembled chromosomes. BUSCO analysis confirmed gene space completeness of 99% against the Actinopterygii dataset, highlighting the high quality of the assembly. Genome annotation identified 25,655 protein-coding genes and estimated 43.94% genome-wide repetitive elements. This data provides valuable genomic resources to advance aquaculture practices and to explore the genomic underpinnings of the ecological resilience of airbreathing catfish and related teleosts.

A short-term of starvation improved the antioxidant activity and quality of African catfish (Clarias gariepinus)

Clarias gariepinus is an important freshwater fish with high economic value and breeding potential in China. It is a fast-growing and adaptable catfish, but the main problems facing the current market are its low price and poor taste, although starvation is a good solution to these problems. In this study, the effects of starvation on the physiology, biochemistry, and muscle quality of C. gariepinus were investigated. The results showed that compared with the control group, the weight gain rate and specific growth rate of the starvation group were significantly different. Body weight, visceral weight, condition factor, viscerosomatic index, hepatosomatic index, and viscera fat index all decreased, while visceral weight and hepatosomatic index decreased significantly after starvation for 30 days. The hardness and crude protein of muscle increased significantly and crude lipid decreased significantly. Taste-enhancing amino acids increased slightly, and fatty acids increased significantly. Compared with the control group, starvation led to changes in antioxidant defense parameters. The level of malondialdehyde (MDA) in liver increased significantly; the activities of superoxide dismutase (SOD) increased in serum after 30 days; the activities of glutathione peroxidase (GSH-Px) increased considerably in the serum and liver after 15 days; the activities of alanine aminotransferase (ALT) increased considerably in the serum and liver after 30 days. The in-depth study of changes in physiological, biochemical, and nutritional components of fish under starvation is helpful to understand the ecological strategy of fish to adapt to starvation and of great guiding significance for fishery resource management and aquaculture production.

Silica nanoparticles alleviate the immunosuppression, oxidative stress, biochemical, behavioral, and histopathological alterations induced by Aeromonas veronii infection in African catfish (Clarias gariepinus)

In the aquaculture industry, silica nanoparticles (SiNPs) have great significance, mainly for confronting diseases. Therefore, the present study aims to assess the antibacterial efficiency of SiNPs as a versatile trial against Aeromonas veronii infection in African catfish (Clarias gariepinus). Further, we investigated the influence of SiNPs in palliating the immune-antioxidant stress biochemical, ethological, and histopathological alterations induced by A. veronii. The experiment was conducted for 10 days, and about 120 fish were distributed into four groups at random, with 30 fish each. The first group is a control that was neither exposed to infection nor SiNPs. The second group (SiNPs) was vulnerable to SiNPs at a concentration of 20 mg/L in water. The third group was experimentally infected with A. veronii at a concentration of 1.5 × 107 CFU/mL. The fourth group (A. veronii + SiNPs) was exposed to SiNPs and infected with A. veronii. Results outlined that A. veronii infection induced behavioral alterations and suppression of immune-antioxidant responses that appeared as a clear decline in protein profile indices, complement 3, lysozyme activity, glutathione peroxidase, and total antioxidant capacity. The kidney and liver function biomarkers (creatinine, urea, alkaline phosphatase, and alanine aminotransferase) and lipid peroxide (malondialdehyde) were substantially increased in the A. veronii group, with marked histopathological changes and immunohistochemical alterations in these tissues. Interestingly, the exposure to SiNPs resulted in a clear improvement in all measured biomarkers and a noticeable regeneration of the histopathological changes. Overall, it will establish that SiNPs are a new, successful tool for opposing immunological, antioxidant, physiological, and histopathological alterations induced by A. veronii infection.

Construction and characterization of Aeromonas hydrophila crp and fur deletion mutants and evaluation of its potential as live-attenuated vaccines in crucian carp

Aeromonas hydrophila (A. hydrophila) is a typical zoonotic pathogenic bacterium that infects humans, animals, and fish. It has been reported that the Fur, a Fe2+ regulatory protein, and the Crp, a cAMP receptor protein, play important roles in bacterial virulence in many bacteria, but no research has been investigated on A. hydrophila. In this study, the Δfur and Δcrp mutant strains were constructed by the suicide plasmid method. These two mutant strains exhibited a slightly diminished bacterial growth and also were observed some alterations in the number of outer membrane proteins, and the disappearance of hemolysis in the Δcrp strain. Animal experiments of crucian carp showed that the Δfur and Δcrp mutant strains significantly decreased virulence compared to the wild-type strain, and both mutant strains were able to induce good immune responses by two kinds of administration routes of intraperitoneal immunization (i.p) and immersion immunization, and the protection rates through intraperitoneal injection of Δfur and Δcrp to crucian carp were as high as 83.3 % and 73.3 %, respectively, and immersion immunization route of Δfur and Δcrp to crucian carp provided protection as high as 40 % and 20 %, respectively. These two mutant strains showed abilities to induce changes in enzymatic activities of the non-specific enzymes SOD, LZM, AKP, and ACP in crucian carp. Together, these results indicated the Δfur and Δcrp mutants were safe and effective candidate vaccine strains, showing good protection against the wild-type A. hydrophila challenge.

Hematological, immuno-antioxidant disruptions, and genes down-regulation induced by Aeromonas veronii challenge in Clarias gariepinus: The ameliorative role of silica nanoparticles

Aeromonas veronii is a pathogenic bacterium associated with various diseases in aquaculture. However, few studies address the antibacterial activity using nanoparticles (NPs). Hence, the current study is innovative to evaluate the antibacterial efficacy of silica nanoparticles (SiNPs) against A. veronii infection in-vitro with a trial for treatment in-vivo. Primarily, we assessed the in-vitro antibacterial activity against A. veronii. Further, we investigated the hematological profile, immune-antioxidant response, and gene expression of African catfish (Clarias gariepinus) in response to SiNPs exposure and the A. veronii challenge. Fish (N = 120; weight: 90 ± 6.19 g) were distributed into four groups (30 fish/group) for a ten-days-treatment trial. The first (control) and second (SiNPs) groups were treated with 0 mg/L and 20 mg/L SiNPs in water, respectively. The third (A. veronii) and fourth (SiNPs + A. veronii) groups were treated with 0 mg/L and 20 mg/L SiNPs in water, respectively, and infected with A. veronii (1.5×10⁷ CFU/mL). Results demonstrated that SiNPs displayed an in-vitro antibacterial activity against A. veronii with a 21 mm inhibitory zone. A. veronii infection caused a high mortality rate (56.67%) and substantial reductions in hematological indices and immune indicators [nitric oxide (NO) and immunoglobulin M (IgM)]. Additionally, marked decline in the level of antioxidants [superoxide dismutase (SOD), catalase (CAT), and reduced glutathione content (GSH)] as well as down-regulation in the immune-related genes [interleukins (IL-1β and IL-8) and tumor necrosis factor-alpha (TNF-α)] and antioxidant-related genes [SOD1, glutathione peroxidase (GPx), and glutathione-S-transferase (GST)] were the consequences of A. veronii infection. Surprisingly, treatment of A. veronii-infected fish with SiNPs lessened the mortality rate, enhanced the blood picture, modulated the immune-antioxidant parameters, and resulted in gene up-regulation. Overall, this study encompasses the significant role of SiNPs, a new versatile tool for combating hematological, immuno-antioxidant alterations, and gene down-regulation induced by A. veronii infection and sustainable aquaculture production.

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Silica nanoparticles are novel aqueous additive mitigating heavy metals toxicity and improving the health of African catfish, Clarias gariepinus

Silica nanoparticles (SiNPs) are among the non-toxic nanoparticles (NPs) that have magnetic capabilities. It is hypothesized that SiNPs may be able to reduce toxic effects exerted by a mixture of lead (Pb) and mercury (Hg) in African catfish Clarias gariepinus. The in vitro magnetic potential of SiNPs to absorb Pb and Hg was tested. Fish (N = 240) were divided into four groups in triplicates for 30 days. The first group served as control and the second group (SiNPs) was exposed to 1/10 of 96 h LC50 of SiNPs (14.45 mg/L). The third group (HMM) was exposed to 1/10 of 96-h LC50 of a mixture of mercury chloride (HgCl₂) and lead chloride (PbCl₂) equal to 0.04 mg/ L and 23.1 mg/L. The fourth group (SiNPs+ HMM) was exposed to a suspension composed of SiNPs, HgCl₂, and PbCl₂ at the same concentrations as the third group. Results showed that fish exposed to heavy metals revealed the following consequences; a significant decrease in hematological, immunological (complement-3 and nitric oxide), and antioxidants (total antioxidant capacity, glutathione peroxidase, superoxide dismutase, and catalase) indices, down-regulation of IL-1β, IL-8, TGF-β, NF-κβ, HSP70, and Hepcidin genes, the highest mortality rate (48.33%), higher values of alkaline phosphatase, alanine, and aspartate aminotransferases, urea, creatinine, and branchial malondialdehyde, marked up-regulation of CC chemokine and CXC chemokines, and high HMs residues levels in muscles. Extensive pathology showed degeneration with diffuse vacuolation of hepatopancreatic cells and hemorrhage in the HMM group. Interestingly, the exposed group to SiNPs and HMM demonstrated a decline of HMs concentration in fish muscles and modulated the abovementioned parameters with the regeneration of histological alterations of liver and gills. Based on the study outcomes, we highlight the importance and the safety of SiNPs as a novel aqueous additive to alleviate HMs toxicity and recommend using SiNPs for enhancing fish performance for sustaining aquaculture without adverting safety of human health by their little accumulation in muscular tissue.

Recurrent expansions of B30.2-associated immune receptor families in fish

B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.

PACAP modulates the transcription of TLR-1/TLR-5/MyD88 pathway genes and boosts antimicrobial defenses in Clarias gariepinus

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a multifunctional neuropeptide that belongs to the secretin/glucagon/GHRH/VIP superfamily. Some of these molecules have antimicrobial activity and they are capable of stimulating the immune system. The present work studied the antibacterial and immunostimulatory activity of PACAP-38 from African catfish Clarias gariepinus against the Gram-negative bacterium Pseudomonas aeruginosa in an in vivo test. PACAP-38 improved antimicrobial activity of skin mucus molecules against P. aeruginosa. The peptide modulates the gene expression profile of TLR-1, TLR-5, MyD88, IL-1β, TNF-ɑ, IL-8, pardaxin, hepcidin and G/C-type lysozymes in skin, spleen and head kidney. The influenced exerted depended on the time after infection and tissue analyzed. This study provides the first evidence of a link between PACAP and antimicrobial peptides hepcidin and pardaxin. Our results suggest further use of PACAP as antimicrobial agent that could potentially be used to control disease in aquaculture.

Congenital asplenia due to a tlx1 mutation reduces resistance to Aeromonas hydrophila infection in zebrafish

It is documented that tlx1, an orphan homeobox gene, plays critical roles in the regulation of early spleen developmental in mammalian species. However, there is no direct evidence supporting the functions of tlx1 in non-mammalian species, especially in fish. In this study, we demonstrated that tlx1 is expressed in the splenic primordia as early as 52 hours post-fertilization (hpf) in zebrafish. A tlx1^-/- homozygous mutant line was generated via CRISPR/Cas9 to elucidate the roles of tlx1 in spleen development in zebrafish. In the tlx1^-/- background, tlx1^-/- cells persisted in the splenic primordia until 52 hpf but were no longer detectable after 53 hpf, suggesting perturbation of early spleen development. The zebrafish also exhibited congenital asplenia caused by the tlx1 mutation. Asplenic zebrafish can survive and breed normally under standard laboratory conditions, but the survival rate of animals infected with Aeromonas hydrophila was significantly lower than that of wild-type (WT) zebrafish. In asplenic zebrafish, the mononuclear phagocyte system was partially impaired, as demonstrated by retarded b7r expression and reduced ccr2 expression after injection with an inactivated A. hydrophila vaccine. Furthermore, the expression of MHCII/IgM was significantly reduced in the congenitally asplenic fish compared with that of the WT zebrafish. Taken together, our data suggest that tlx1 is a crucial regulator of spleen development in fish, as it is in mammals. We have also provided a new perspective for studying the role of the spleen during pathogen challenge in fish.