Abstract: Background The yellow catfish, Pelteobagrus fulvidraco, belonging to the Siluriformes order, is an economically important freshwater aquaculture fish species in Asia, especially in Southern China. The aquaculture industry has recently been facing tremendous challenges in germplasm degeneration and poor disease resistance. As the yellow catfish exhibits notable sex dimorphism in growth, with adult males about two- to three-fold bigger than females, the way in which the aquaculture industry takes advantage of such sex dimorphism is another challenge. To address these issues, a high-quality reference genome of the yellow catfish would be a very useful resource. Findings To construct a high-quality reference genome for the yellow catfish, we generated 51.2 Gb short reads and 38.9 Gb long reads using Illumina and Pacific Biosciences (PacBio) sequencing platforms, respectively. The sequencing data were assembled into a 732.8 Mb genome assembly with a contig N50 length of 1.1 Mb. Additionally, we applied Hi-C technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with 26 chromosomes and a scaffold N50 length of 25.8 Mb. Using 24,552 protein-coding genes annotated in the yellow catfish genome, the phylogenetic relationships of the yellow catfish with other teleosts showed that yellow catfish separated from the common ancestor of channel catfish ∼81.9 million years ago. We identified 1,717 gene families to be expanded in the yellow catfish, and those gene families are mainly enriched in the immune system, signal transduction, glycosphingolipid biosynthesis, and fatty acid biosynthesis. Conclusions Taking advantage of Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosome-level genome assembly for the yellow catfish P. fulvidraco. The genomic resources generated in this work not only offer a valuable reference genome for functional genomics studies of yellow catfish to decipher the economic traits and sex determination but also provide important chromosome information for genome comparisons in the wider evolutionary research community.

Abstract: The increase of water temperature due to global warming is a great concern of aquaculturists and fishery biologists. In the present study, we examined the effects of high temperature on hematological parameters and blood glucose levels in striped catfish, Pangasianodon hypophthalmus exposed to three temperature conditions (28, 32, and 36 °C) for 7 days. Fish were sacrificed at days 1, 3, and 7. Erythroblasts (Ebs), erythrocytic cellular abnormalities (ECA), and erythrocytic nuclear abnormalities (ENA) were assayed using peripheral erythrocytes of the sampled fishes. Hemoglobin (Hb) and red blood cell (RBC) significantly (P < 0.05) decreased at 36 °C after 3 and 7 days of exposure, whereas white blood cell (WBC) showed opposite scenario. Blood glucose levels significantly (P < 0.05) increased at 36 °C on day 3. Frequencies of Ebs, ECA, and ENA were found to be elevated at increased temperature. Differential leucocytes count showed significant increases in neutrophil and decreases in lymphocytes in the highest temperature (36 °C). Dissolved oxygen decreased and free CO2 increased significantly (P < 0.05) with increasing temperature, while the pH and total alkalinity of the water were almost unchanged throughout the study period. Therefore, the present study demonstrated that striped catfish feel better adaptation at 28 and 32 °C, while high temperature 36 °C is likely stressful to this fish species.

Abstract: Global aquaculture production continue growing in order to meet up with ever increasing fish demand, especially as fish from capture has levelled off and makes an increase in aquaculture production as the only hope to meet the demand for fish. Aquaculture industry involves culture of many fish species of either fresh or brackish water origin and among the important freshwater fish species is North African catfish which is also called African catfish (Clarias gariepinus). Its production is increasing as the total aquaculture production also increases and its culture is spread globally, with Nigeria officially reported as producing the highest annual amount of the fish. There is a substantial culture of the fish in Malaysia, though not a native fish species but its presence in Malaysia is getting closer to over three decades and for almost a decade now, it has been the highest finfish produced in either fresh or brackish water aquaculture in Malaysia. This review discussed African catfish aquaculture in Malaysia and Nigeria, compared the production and prospects of the industry in the two countries.

Abstract: The viability using Lippia alba essential oil as an anesthetic for fish was studied, particularly with respect to physiological effects during recovery. Anesthesia of silver catfish (Rhamdia quelen) using 100 and 300 μL L-1 of two different chemotypes of L. alba essential oil (citral EO-C and linalool EO-L) prevented the increase of plasma cortisol levels caused by handling, but did not avoid alterations in energetic metabolism. Silver catfish did not have increased the levels of thiobarbituric acid reactive species in the kidney and liver during recovery after anesthesia with either EO, avoiding lipid damage. On the other hand, fish anesthetized with EO-C showed higher protein carbonylation levels, superoxide dismutase, catalase, and glutathione S-transferase activities and non-protein thiol group levels in both tissues compared to controls. Our results suggest that both oils show antioxidant capacity, but anesthesia with EO-L does not cause damage to lipids or proteins, only temporary changes, typical of physiological adjustments during recovery from anesthesia. Therefore, EO-L is an effective anesthetic for silver catfish with fewer side effects than EO-C.

Abstract: Growth is the most important economic trait in aquaculture. Improvements in growth-related traits can enhance production, reduce costs and time to produce market-size fish. Catfish is the major aquaculture species in the United States, accounting for 65% of the US finfish production. However, the genes underlying growth traits in catfish were not well studied. Currently, the majority of the US catfish industry uses hybrid catfish derived from channel catfish female mated with blue catfish male. Interestingly, channel catfish and blue catfish exhibit differences in growth-related traits, and therefore the backcross progenies provide an efficient system for QTL analysis. In this study, we conducted a genome-wide association study for catfish body weight using the 250 K SNP array with 556 backcross progenies generated from backcross of male F1 hybrid (female channel catfish × male blue catfish) with female channel catfish. A genomic region of approximately 1 Mb on linkage group 5 was found to be significantly associated with body weight. In addition, four suggestively associated QTL regions were identified on linkage groups 1, 2, 23 and 24. Most candidate genes in the associated regions are known to be involved in muscle growth and bone development, some of which were reported to be associated with obesity in humans and pigs, suggesting that the functions of these genes may be evolutionarily conserved in controlling growth. Additional fine mapping or functional studies should allow identification of the causal genes for fast growth in catfish, and elucidation of molecular mechanisms of regulation of growth in fish.

Abstract: Transport procedures usually cause fish stress. The purpose of this study was to investigate the effect of transport stress on blood biochemical profiles, oxidative stress biomarkers, and hepatic heat shock proteins (HSPs) of channel catfish (Ictalurus punctatus). Fish (body weight 55.57 ± 5.13 g) were randomly distributed to two groups, the control, and the treatment. The control group was kept under the normal culture conditions. The treatment group was exposed to the process of transport (3.5 h). Fish samples were collected before transport, after packing and at 0, 1, 6, 24, 72, and 168 h after transport, respectively. Transport caused a significant increase in the serum concentrations of cortisol, glucose, total cholesterol, and triglyceride, as well as, the activity of aspartate aminotransferase at 0 and 1 h after transport compared with non-transported fish and the basal level. Blood total protein content significantly declined in the transported fish. Total antioxidant capacity (T-AOC), malonaldehyde content, and the activities of both glutathione peroxidase and catalase significantly increased in fish within 6 h after transport. The transported fish exhibited a significant higher level in either the concentration of nitric oxide or the mRNA expressions of both hepatic HSP70 and HSP90. It is concluded that transport triggers stress response of I. punctatus, leading to the obvious change in antioxidant capacity. I. punctatus need to be more care after transport to recover from transport stress.

Abstract: Species of two monotypic genera, Ephedrocephalus Diesing, 1850 and Zygobothrium Diesing, 1850 (Cestoda: Proteocephalidae), parasites of one of the most basal members of the catfish family Pimelodidae, the redtail catfish, Phractocephalus hemioliopterus, in the Neotropical Region, are redescribed based on the evaluation of type specimens and newly collected material. Generic diagnoses are amended to provide a robust baseline for the future re-arrangement of the classification of proteocephalid cestodes. Ephedrocephalus is typified by the medullary position of the ovary and uterus, the cortical distribution of vitelline follicles (dispersed throughout almost the entire ventral cortex) and the testes in one dorsal field. Zygobothrium is primarily characterized by its possession of a robust scolex bearing four uniloculate suckers with two openings each and by the tetralobed velum (laciniations) on every proglottid (two on the ventral and two on the dorsal side). The redtail catfish is the definitive host of as many as seven species of proteocephalid cestodes, which, however, do not represent a monophyletic group. Some species, including Z. megacephalum, are among the earliest diverged parasites of Neotropical catfishes, being closely related to African and North American proteocephalids from catfishes, whereas others such as E. microcephalus belong to more recently diverged taxa with uncertain interrelations. Unlike most proteocephalids of the redtail catfish, which almost always infect the anterior parts of the host intestine, E. microcephalus and Z. megacephalum occur exclusively in its posterior third. A key to the identification of the proteocephalid species parasitizing P. hemioliopterus is also presented.

Abstract: The sex-determining genes are found to be variable among different fish species. Yellow catfish (Pelteobagrus fulvidraco) is an important aquaculture fish species in China with XX/XY sex-determining type. Recently, YY super-male yellow catfish has been successfully produced by combining hormonal-induced sex reversal method with sex chromosome-linked markers. Here, we identified a novel PDZ domain-containing gene in yellow catfish designated as pfpdz1, in whose intron the sex-linked marker was located. The coding sequence of pfpdz1 in Y chromosome was identical to that in X chromosome except a missense SNP (A/T) that changes an amino acid (E8V) in the N-terminal region. Pfpdz1 displayed male-specific expression during sex differentiation. Overexpression of pfpdz1 using additive transgenesis induces XX ovary to differentiate into testis-like tissue, while the targeted inactivation of pfpdz1 in Y chromosome using CRISPR/Cas9-mediated mutagenesis triggers ovarian differentiation. Furthermore, we demonstrated that pfpdz1 initiates testicular differentiation through upregulating expression of amh, dmrt1 and sox9a1, as well as downregulating expression of cyp19a1, foxl2 and wnt4. Our data provide functional evidence that pfpdz1 is significant for male differentiation and maintenance in yellow catfish.

Abstract: Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life. Comparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1–2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish. This study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life.

Abstract: The aim of this research is to evaluate the effects of biofloc system application at different fish density on the nursery production performance and the robustness of African catfish Clarias gariepinus (Burchell) against Aeromonas hydrophila and salinity stress. An economic analysis was also performed to determine the most optimum fish density in biofloc‐based African catfish nursery production. African catfish with an average body weight of 0.96 ± 0.04 g and average body length of 4.20 ± 0.46 cm, respectively, were distributed in 12 units of circular plastic‐lined tanks (1,020 L). The experiment consisted of four treatments in triplicates, that is, a control without carbon source addition at a density of 4 fish/L, and three biofloc treatments at different densities, that is, BFT4 (4 fish/L), BFT6 (6 fish/L) and BFT8 (8 fish/L). Tapioca flour was used as the organic carbon source in biofloc systems and was added at an estimated C/N ratio of 10. Housing the fish in biofloc systems resulted in higher fish growth, more efficient feed utilization, higher fish robustness against A. hydrophila infection and salinity stress, as well as higher profitability of nursery production. Increasing the fish density resulted in higher mortality. However, higher number of fish produced and lower feed conversion ratio were observed in the treatments with higher density (6 and 8 fish/L). In conclusion, the application of biofloc technology at a density of 8 fish/L could be recommended to increase the production and profitability of African catfish nursery culture.

Abstract: We aimed to investigate proximate and fatty acid composition of important freshwater fish species in the Czech Republic. Sampled fish include seven species from intensive farming: African catfish, rainbow trout, Wels catfish, Nile tilapia, brook trout, northern whitefish, and pikeperch; eight species from semi-intensive culture systems: common carp, northern pike, pikeperch, grass carp, European perch, tench, silver carp, and catfish; and three species from extensive culture systems: rainbow trout, tench, and common carp. The fat content and fatty acid composition were highly influenced by the culture systems. Simultaneously, we observed a significant dependence of fatty acid composition on the fat content. The content of saturated fatty acids was below 34% in all analyzed fish. Northern pike, pikeperch, and European perch contained with over 50% the highest proportion of polyunsaturated fatty acids. Intensively cultured fish reached the highest content of eicosapentaenoic and docosahexaenoic fatty acid. Nutritional quality was determined by atherogenic and thrombogenic indexes which ranged from 0.27 to 0.63 and 0.20 to 0.61 and by ratios n-3/n-6 (0.54–3.45) and polyunsaturated/saturated fatty acids (0.67–2.01). Results demonstrated that the flesh of all studied species are of high nutritional quality.

Abstract: The Atlantic salmon (Salmo salar) is one of the world's most emblematic freshwater fish. Despite conservation and rehabilitation plans, populations of this species are dramatically declining due to human impacts such as habitat fragmentation, overfishing and water pollution. Owing to their large body size, anadromous adults were historically invulnerable to fish predation during their spawning period migration. This invulnerability has disappeared in Western Europe with the introduction of a new freshwater predator, the European catfish (Silurus glanis). Here we report how adults of Atlantic salmon are predated in the fishway of a large river of SW France, where the delayed and narrow passage created by the structure increases the probability of predator-prey encounter. We assessed predation risk by monitoring salmon and catfish in one fishway of the River Garonne, using video fish-counting from 1993 to 2016. We analysed the predation strategy of catfish using observations made with acoustic camera and RFID telemetry in 2016. Our results demonstrate a high predation rate (35%-14/39 ind.) on salmon inside the fishway during the 2016 spawning period migration. Our results suggest that a few specialized catfish individuals adapted their hunting behaviour to such prey, including their presence synchronized with that of salmon (i.e, more occurrences by the end of the day). Such results suggest that the spread of European catfish will potentially impact migration of anadromous species through anthropized systems.

Abstract: This article summarizes the biology and culture of ictalurid catfish, an important commercial, aquaculture, and sport fish family in the United States The history of the propagation as well as spawning of common catfish species in this family is reviewed, with special emphasis on channel catfish and its hybridization with blue catfish The importance of the channel catfish female×blue catfish male hybrid, including current and future methods of hybrid catfish production, and the potential role it plays in the recovery of the US catfish industry are discussed Recent advances in catfish culture elements, including environment, management, nutrition, feeding, disease control, culture systems, genetic improvement programs, transgenics, and the application of genome-based approaches in catfish production and welfare, are reviewed The current status, needs, and future projections are discussed, as well as genetically modified organism developments that are changing the future

Abstract: The reuse of effluent waters and sediments from African catfish (Clarias gariepinus) recirculation aquaculture systems requires a deeper understanding of the nutrient and energy flows and material pathways. Three semi-commercial systems, differing in stocking density, were sampled for nutritive and pollutant elements of the input- (tap water, feed) and output pathways (fillet, carcass, process water, sediments) by ICP-OES/MS and calorimetry. Highly water-soluble elements, e.g., potassium, accumulated in the water, whereas iron, copper, chromium and uranium where found in the solids. Feed derived phosphorous was accounted for, 58.3–64.2% inside the fish, 9.7–19.3% in sediments, and small amounts 9.6–15.5% in the process waters. A total of 7.1–9.9% of the feed accumulated as dry matter in the sediments, comprising 5.5–8.7% total organic carbon and 3.7–5.2% nitrogen. A total of 44.5–47.1% of the feed energy was found in the fish and 5.7–7.7% in the sediments. For reuse of water and nutrients in hydroponics, the macro-nutrients potassium, nitrate, phosphorus and the micro-nutrient iron were deficient when compared with generalized recommendations for plant nutrition. Low energy contents and C/N-ratio restrict the solely use of African catfish solids for biogas production or vermiculture. Using the outputs both for biogas supplement and general fertilizer in aquaponics farming (s.l.) (combined with additional nutrients) appears possible.

Abstract: The microbiota of teleost fish has gained a great deal of research attention within the past decade, with experiments suggesting that both host-genetics and environment are strong ecological forces shaping the bacterial assemblages of fish microbiomes. Despite representing great commercial and scientific importance, the catfish within the family Ictaluridae, specifically the blue and channel catfish, have received very little research attention directed toward their gut-associated microbiota using 16S rRNA gene sequencing. Within this study we utilize multiple genetically distinct strains of blue and channel catfish, verified via microsatellite genotyping, to further quantify the role of host-genetics in shaping the bacterial communities in the fish gut, while maintaining environmental and husbandry parameters constant. Comparisons of the gut microbiota among the two catfish species showed no differences in bacterial species richness (observed and Chao1) or overall composition (weighted and unweighted UniFrac) and UniFrac distances showed no correlation with host genetic distances (Rst) according to Mantel tests. The microbiota of environmental samples (diet and water) were found to be significantly more diverse than that of the catfish gut associated samples, suggesting that factors within the host were further regulating the bacterial communities, despite the lack of a clear connection between microbiota composition and host genotype. The catfish gut communities were dominated by the phyla Fusobacteria, Proteobacteria, and Firmicutes; however, differential abundance analysis between the two catfish species using analysis of composition of microbiomes detected two differential genera, Cetobacterium and Clostridium XI. The metagenomic pathway features inferred from our dataset suggests the catfish gut bacterial communities possess pathways beneficial to their host such as those involved in nutrient metabolism and antimicrobial biosynthesis, while also containing pathways involved in virulence factors of pathogens. Testing of the inferred KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways by DESeq2 revealed minor difference in microbiota function, with only two metagenomic pathways detected as differentially abundant between the two catfish species. As the first study to characterize the gut microbiota of blue catfish, our study results have direct implications on future ictalurid catfish research. Additionally, our insight into the intrinsic factors driving microbiota structure has basic implications for the future study of fish gut microbiota.

Abstract: Indiscriminate discharge of pharmaceutical waste into the aquatic ecosystem may pose serious health challenges to aquatic biota. The effect of acute exposure to ibuprofen was evaluated using change...

Abstract: Mercury (Hg) is well recognized as a highly toxic substance to fish. Nevertheless, little is known about the toxic effects of Hg on immune organs. In this study, we investigated histology, antioxidant status and immune response of the spleen and head kidney in yellow catfish following 6 weeks of exposure to environmentally relevant concentrations of inorganic Hg (2 and 10 μg l-1 Hg2+ ). As expected, Hg accumulation and histological injury in both tissues were observed. Meanwhile, Hg2+ exposure induced oxidative stress, which increased antioxidant enzyme (superoxide dismutase, catalase and glutathione peroxidase) activities, glutathione content, anti-hydroxyl radical capacity and the expression of genes associated with antioxidant (sod1, cat, gpx1, nrf2 and mt) and stress (hsp70) responses in dose- and tissue-specific manners. In the spleen, the mRNA levels of immune-related genes (il-1β, il-8, tnf-α, il-10, tgf-β, lys and c3) were upregulated by Hg2+ exposure. However, in the head kidney, upregulation of tnf-α, il-10 and tgf-β mRNAs and downregulation of il-1β and lys expressions were observed, while transcriptions of il-8 and c3 were remarkably upregulated only in the 2 μg l-1 group. Overall, our study indicated that Hg2+ exposure could result in Hg accumulation and thereby induced histological impairment, oxidative stress and immunotoxicity in immune organs of yellow catfish, but some enzymes and/or genes involved in antioxidant and immune systems would be activated to resist Hg2+ -induced damage.

Abstract: The complete genome of the channel catfish, Ictalurus punctatus, has been sequenced, leading to greater opportunities for studying channel catfish gene function. Gene knockout has been used to study these gene functions in vivo. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) system is a powerful tool used to edit genomic DNA sequences to alter gene function. While the traditional approach has been to introduce CRISPR/Cas9 mRNA into the single cell embryos through microinjection, this can be a slow and inefficient process in catfish. Here, a detailed protocol for microinjection of channel catfish embryos with CRISPR/Cas9 protein is described. Briefly, eggs and sperm were collected and then artificial fertilization performed. Fertilized eggs were transferred to a Petri dish containing Holtfreter's solution. Injection volume was calibrated and then guide RNAs/Cas9 targeting the toll/interleukin 1 receptor domain-containing adapter molecule (TICAM 1) gene and rhamnose binding lectin (RBL) gene were microinjected into the yolk of one-cell embryos. The gene knockout was successful as indels were confirmed by DNA sequencing. The predicted protein sequence alterations due to these mutations included frameshift and truncated protein due to premature stop codons.

Abstract: Hardi EH, Nugroho RA, Saptiani G, Sarinah R, Anggraidini M, Mawardi M. 2018. Identification of potentially pathogenic bacteria from tilapia (Oreochromis niloticus) and channel catfish (Clarias batrachus) culture in Samarinda, East Kalimantan, Indonesia. Biodiversitas 19: 480-488. This research was conducted to isolate, identify, and characterize pathogenic bacteria from feces and water of tilapia (Oreochromis niloticus) and channel catfish (Clarias batrachus) culture from two selected locations in Samarinda, East Kalimantan, Indonesia. Bacteria were cultured and isolated on NA, TSA, and BHIA media at 30oC for 24 h. Colonies of the isolated bacteria were characterized morphologically in terms of their shape, chromogenesis, edge, and size. Antibiotic sensitivity test on each bacterial isolate was completed using inhibition zone tests. Commercial antibiotics used in this research were nitrofurantoin, ciprofloxacin, oxytetracycline, chloramphenicol, nalidixic acid, gentamicin, and norfloxacin. Koch’s postulates test was done by intraperitoneal injection of bacterial suspension to tilapia (15 g weight) at 103-109 CFU mL-1 in triplicates to determine the pathogenicity of each bacterium. Overall, there were 37 isolates obtained from different sources and growth media that belonged to 14 species: Acinetobacter calcoaceticus (1 isolate), Aerococcus urinae (2 isolates), Aerococcus viridans (1 isolate), Aeromonas hydrophila (1 isolate), Citrobacter freundii (5 isolates), Enterobacter amnigenus (2 isolate), Enterobacter cloacae (4 isolates), Escherichia coli (3 isolates), Listeria sp. (1 isolate), Niseria sp. (4 isolates), Pantoea spp. (1 isolate), Pseudomonas aeruginosa (1 isolate), Staphylococcus aureus (9 isolates), and Streptococcus iniae (2 isolates). Sixteen of the isolates were grown in BHIA medium, 12 isolates in TSA medium and 9 isolates in NA medium. The highest mortality was found in tilapia injected with Enterobacter sp., Listeria sp. and Streptococcus sp. at a density of 109 CFU mL-1. However, the number of bacteria causing mortality in fish was approximately 104-108 CFU mL-1. All bacteria detected in the tilapia and channel catfish cultures were also known as putative pathogens in human.