A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus)

Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.     

Selenium nanoparticles are required for the optimum growth behavior,antioxidative capacity,and liver wellbeing of Striped catfish (Pangasianodon hypophthalmus)

Selenium (Se) is a multifunctional trace element required in specific amounts for the optimal growth of aquatic finfish species. For this reason, this study investigated the effect of Se nanoparticles on the growth behavior, antioxidative capacity, and liver wellbeing of Striped catfish (Pangasianodon hypophthalmus). Striped catfish fed varying Se nanoparticles levels (0. 0.5, 1, and 2 mg/kg) in triplicate units and kept for 60 days. Striped catfish delivered dietary Se nanoparticles had markedly increased growth performance, specific growth rate (SGR), consumed feed, and protein efficiency ratio but reduced feed conversion ratio (FCR). The whole body, liver, muscle, and gills have higher Se accumulation levels in fish that received Se nanoparticles than the control with the highest level in fish fed 2 mg/kg. The carcass composition showed higher protein content in fish fed 1 and 2 mg/kg (p = 0.001 and 0.001) and higher ash content (p = 0.001 and 0.002) in fish fed 2 mg/kg than the remaining groups. Superoxide dismutase was meaningfully activated in Striped catfish delivered 1 and 2 mg Se nanoparticles/kg compared with the control (p < 0.05). Also, catalase and glutathione peroxidase activities were higher, and malondialdehyde level was lower in Striped catfish fed Se nanoparticles at 0.5, 1, and 2 mg/kg than the control (p < 0.05). The villi exhibited a visible increase in both height and branching with an increased level of Se nanoparticles in addition to the increased number of goblet cells. The Se nanoparticles-treated fish revealed dose-dependent modifications fluctuated from diffuse fatty vacuolization in hepatocytes with eccentric pyknotic hepatocytes nuclei. In conclusion, Se nanoparticles are required for the optimum growth behavior, antioxidative capacity, and liver wellbeing of Striped catfish. Based on SGR and FCR data's regression analysis, Se nanoparticles are recommended at 1.02–1.11 mg/kg diet.     

Quality of Antimicrobial Products Used in Striped Catfish (Pangasianodon hypophthalmus) Aquaculture in Vietnam

Antimicrobial usage is common in Asian aquaculture. This study aimed to determine the quality of antimicrobial products used by Vietnamese striped catfish (Pangasianodon hypophthalmus) farmers. Twenty one antimicrobial products (11 products contained a single antimicrobial and 10 products contained a mixture of two different antimicrobials) commonly used by catfish farmers were obtained from so-called chemical shops located in the Mekong Delta, Vietnam. Ultra High Performance Liquid Chromatography Mass Spectrometry was used to analyze concentration of sulfonamides, trimethoprim, amoxicillin, cefalexin and ciprofloxacin whereas concentrations of florfenicol and doxycycline were analyzed by High Performance Liquid Chromatography with UV detection. Results revealed that only 4/11 products with a single antimicrobial and 2/10 products with a mixture of antimicrobials contained active substances within ±10% of the concentration declared on the product label. Two products with antimicrobial mixtures did not contain any of the declared antimicrobials. Comparing two batches, analysis of 11 products revealed that only one product contained a concentration of active compound that varied with less than 10% in both batches. Several product labels provided inadequate information on how to calculate therapeutic dosage and further stated withdrawal time despite lack of pharmacokinetic data on the antimicrobials in catfish. There is an urgent need to strengthen approval procedures and in particular regularly to monitor the quality of antimicrobials used in Vietnamese aquaculture.     

Hypoxia tolerance and partitioning of bimodal respiration in the striped catfish (Pangasianodon hypophthalmus)

Air-breathing fish are common in the tropics, and their importance in Asian aquaculture is increasing, but the respiratory physiology of some of the key species such as the striped catfish, Pangasianodon hypophthalmus Sauvage 1878 is unstudied. P. hypophthalmus is an interesting species as it appears to possess both well-developed gills and a modified swim bladder that functions as an air-breathing organ indicating a high capacity for both aquatic and aerial respiration. Using newly developed bimodal intermittent-closed respirometry, the partitioning of oxygen consumption in normoxia and hypoxia was investigated in P. hypophthalmus. In addition the capacity for aquatic breathing was studied through measurements of oxygen consumption when access to air was denied, both in normoxia and hypoxia, and the critical oxygen tension, Pcrit, was also determined during these experiments. Finally, gill ventilation and air-breathing frequency were measured in a separate experiment with pressure measurements from the buccal cavity. The data showed that P. hypophthalmus is able to maintain standard metabolic rate (SMR) through aquatic breathing alone in normoxia, but that air-breathing is important during hypoxia. Gill ventilation was reduced during air-breathing, which occurred at oxygen levels below 8 kPa, coinciding with the measured Pcrit of 7.7 kPa. The findings in this study indicate that the introduction of aeration into the aquaculture of P. hypophthalmus could potentially reduce the need to air-breathe. The possibility of reducing air-breathing frequency may be energetically beneficial for the fish, leaving more of the aerobic scope for growth and other activities, due to the proposed energetic costs of surfacing behavior.     

In Vitro Characterization of a Recombinant AHL-Lactonase from Bacillus cereus Isolated from a Striped Catfish (Pangasianodon hypophthalmus) Pond

aiiA gene encoding AHL-lactonase was isolated from Bacillus cereus strain N26.2, originating from a striped catfish (Pangasianodon hypophthalmus) pond in Vietnam. This gene, abbreviated as aiiA(N26.2), was cloned and expressed in a competent Escherichia coli strain BL21(DE3)pLysS. The resulting protein, abbreviated as AiiA_N26.2, was highly active in the pH range of 6–8 and could retain 80 % of the maximum activity under storage for 5 days at 4 °C or for 3 days at 20 °C. These properties of AiiA_N26.2 protein confers its future application via feed supplementation, with the purpose of controlling aquaculture pathogens which regulate the virulence via a quorum sensing system.     

First identification of Flavobacterium columnare infection in farmed freshwater striped catfish Pangasianodon hypophthalmus

The bacterium Flavobacterium columnare was recovered and identified as the aetiological agent causing freshwater columnaris infection in farmed striped catfish Pangasianodon hypophthalmus (Sauvage) fingerlings that had suffered high mortality rates within commercial hatchery ponds in Vietnam. The gross clinical signs were typical of columnaris-infected fish. Histological examination found numerous Gram-negative, filamentous bacteria present on the skin, muscle and gill tissues of affected fish. The yellow-pigmented bacteria were isolated and identified as F. columnare using primary, biochemical and PCR methods. An experimental immersion-challenge study with 2 strains was also performed. It fulfilled Koch's postulates and showed a median lethal concentration (LC50) of 4.27 × 105 and 1.66 × 106 cfu ml-1 for the F. columnare strains FC-HN and FC-CT, respectively. To the best of our knowledge this is the first report of freshwater columnaris infection in P. hypophthalmus.     

Intra-annual genetic variation in the downstream larval drift of sutchi catfish (Pangasianodon hypophthalmus) in the Mekong river

Larvae of the sutchi catfish Pangasianodon hypophthalmus were collected during peak downstream drift in the Lower Mekong river on four occasions over an 8-week period during the 2003 spawning season, and genotyped using seven microsatellite loci. We provide evidence for several heterogeneous groups within and among the temporally discrete larval peak samples. Strong evidence for a significant deficit of heterozygotes was observed for each larval sample and the pooled sample, possibly due to population admixture. Although individual-based assignment tests suggested that each larval peak sample was admixed, significant but low genetic differentiation was observed among larval samples ( F _ST = 0.0052, P  < 0.01). The lack of significant relatedness confirms the multifamily composition of each larval group, excluding family bias to explain the observed genetic heterogeneity. Both the entire larval peak and each temporally separated larval peak originated from spawning groups with heterogeneous allelic composition involving several distinct spawning events. We propose three explanations to account for our findings: (1) the ecological match/mismatch hypothesis; (2) the genetic 'sweepstakes' selection hypothesis; and (3) life-history-specific characteristics of the spawning populations. Finally, an intra-annual shift in the contribution of the spawning populations to the larval drift was detected on successive occasions.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 719–728.     

Immune responses and intestinal morphology of striped catfish,Pangasianodon hypophthalmus (Sauvage, 1878), fed dietary nucleotides

The present study was conducted to evaluate the effects of dietary nucleotides (NT) on growth performance, immune responses, and intestinal morphology of striped catfish, Pangasianodon hypophthalmus. Different levels of NT (0, 0.25. 0.5, 0.75, and 1% weight per weight, WW^?1) were used in the basal diet and then randomly allocated to triplicate groups of fish with an average initial weight of 1.52 ± 0.11 g for 10 weeks. Nucleotide supplementation did not improve growth parameters significantly (P > 0.05). Feeding fish with a NT‐containing diet significantly improved ACH₅₀ activity and IgM levels in comparison to the control group (P < 0.05). The dietary NT (P < 0.05) affected the intestinal morphology, whereby the folds and enterocyte heights in the mid‐intestine were significantly increased compared to the control group (P < 0.05), while the microvilli length was not affected. The results indicate that feeding striped catfish with commercial NT have significant effects on the immune parameters and intestinal morphology of catfish and that the best NT levels are 0.25 and 0.5%.     

Partitioning of oxygen uptake and cost of surfacing during swimming in the air-breathing catfish Pangasianodon hypophthalmus

Though air-breathing has probably evolved mainly as a response to hypoxia, it may provide an important oxygen supplement when metabolism is elevated, as for example during swimming. Due to the increased travelling distance involved when an air-breathing fish swims to and from the surface, and the increased drag when the surface is breached, it can be proposed that air-breathing results in a rise in the apparent cost of transport. In order to investigate this hypothesis, it is necessary to use a fish that is able to swim equally well with and without access to air. The striped catfish Pangasianodon hypophthalmus has been shown to have a sufficiently high capacity for aquatic oxygen uptake in normoxia, to allow for such a comparison. Here, we measured the partitioning of oxygen uptake ( $ \dot{M}{\text{O}}_{2} $ ) during swimming and recovery, and calculated the apparent cost of transport with and without access to air, under normoxic conditions. Aerial $ \dot{M}{\text{O}}_{2} $ constituted 25–40 % of the total $ \dot{M}{\text{O}}_{2} $ during swimming and less than 15 % during recovery. The net cost of transport was 25 % lower in fish that did not air-breathe compared to fish that did, showing that the cost of surfacing can be substantial. This is the first study to measure partitioning in an air-breathing fish during swimming at velocities close to the critical swimming speed.     

In vivo effects of Escherichia coli lipopolysaccharide on regulation of immune response and protein expression in striped catfish (Pangasianodon hypophthalmus)

Lipolysaccharide (LPS), a component of outer membrane protein of gram-negative bacteria, reportedly stimulates fish immune system. However, mechanisms driving this immunomodulatory effect are yet unknown. To determine effects of Escherichia coli lipopolysaccharide on regulation of immune response and protein expression of striped catfish (Pangasianodon hypophthalmus), juvenile fish (20–25 g) were injected with 3, 15 or 45 mg E.coli LPS/kg and challenged with Edwardsiella ictaluri. Plasma cortisol and glucose were rather low and did not differ (p < 0.05) among treatments. All LPS treatments differed regarding blood cell count and immune variables such as plasma and spleen lysozyme, complement activity and antibody titer, 3 mg LPS/kg yielding best results; red blood cell count was not affected by LPS treatment. Accumulated mortalities after bacterial challenge were 23.4, 32.8, 37.7 and 52.5% for treatment 3, 15, 45 mg LPS/kg fish and control respectively. Proteomic analysis of peripheral blood mononuclear cells (PBMC) confirmed that LPS induced differentially over-expressed immune proteins such as complement component C3 and lysozyme C2 precursor. Regulation of other proteins such as Wap65, alpha-2 macroglobulin-3 and transferrin precursor was also demonstrated. Striped catfish injected with E.coli LPS enhanced innate immune responses.     

High genetic diversity in cryptic populations of the migratory sutchi catfish Pangasianodon hypophthalmus in the Mekong River

The detection and conservation of spawning units is of crucial importance in highly migratory species. The sutchi catfish Pangasianodon hypophthalmus (Pangasiidae; Teleostei) is a common large-sized tropical fish, which migrates annually to several upstream spawning sites on the Lower Mekong River and feeds on the huge floodplain of the Lower Mekong and Tonle Sap for the other half of the year. We hypothesised that because of the relative size of the feeding and spawning habitat, genetic variability would be high and homogeneous in foraging populations, but that spawning stocks would be distinct in space and time. To test these predictions, 567 individuals from 10 geographic locations separated by up to 1230 km along the Lower Mekong River were genotyped at seven microsatellite loci. The level of genetic diversity was much higher than other freshwater fish and reached values comparable to marine species (mean H(e)=0.757). All samples collected at the potential spawning sites deviated from Hardy-Weinberg expectations, suggesting admixture. Individual-based clustering methods revealed genetic heterogeneity and enabled the detection of three genetically distinct sympatric populations. There was no evidence of recent reduction in effective population size in any population. Contrasting with the vast extent of the feeding grounds, the shortage of spawning grounds seems to have moved sutchi catfish towards diachronous spawning. Hence the sustainable exploitation of this natural resource hinges on the conservation of the limited spawning grounds and open migration routes between the spawning and feeding grounds.     

Isolation and characterization of SAP and CRP,two pentraxins from Pangasianodon (Pangasius) hypophthalmus

From the serum of Pangasianodon hypophthalmus, two proteins were isolated by affinity chromatography on Sepharose and phosphorylcholine–Sepharose. Their binding on the affinity matrices critically depends on the presence of Ca²⁺ ions. N-terminal sequencing and sequencing of internal tryptic peptides identified the proteins as pentraxins and from their binding properties they are identified as SAP (serum amyloid P component) and CRP (C-reactive protein). Per ml serum, 36 μg SAP and 56 μg CRP was purified. Upon gel filtration, both the SAP and CRP elute as trimers of respectively 24 kDa and 28 kDa subunits. Both proteins are devoid of inter-chain disulfide bonds. Both SAP and CRP are glycosylated and agglutinate rabbit erythrocytes and pathogenic bacteria Edwardsiella ictaluri and Aeromonas hydrophila, but not Micrococcus lysodeikticus or Escherichia coli. Haemagglutination of SAP and CRP is inhibited by galactose (MIC = 1 mM) and by phosphorylcholine (MIC = 1–2 mM), respectively. Circular dichroism studies revealed that antiparallel β-pleated sheets are dominating the secondary structure. Upon removing the Ca²⁺ ions by EDTA, slight structural changes are observed by CD spectroscopy in the near-UV region. Immunodiffusion shows that P. hypophthalmus SAP and CRP do not cross-react.     

Production of a biologically active growth hormone from giant catfish (Pangasianodon gigas) in Escherichia coli

Giant catfish growth hormone (gcGH) cDNA was cloned and expressed in E. coli. The expected 20.5 kDa protein corresponded to the mature gcGH and was efficiently expressed. This protein was produced as inclusion bodies and comprised about 20% of total cellular proteins. The recombinant hormone promoted growth when injected intramuscularly or intraperitoneally into goldfish (Carassius auratus) at 0.1 or 1 microg soluble gcGH per g fish body wt per week. In addition, the recombinant gcGH inclusions had growth-promoting activity similar to that of the soluble form when the fish was received either by intraperitoneal injection or by oral administration.     

MtDNA diversity of the critically endangered Mekong giant catfish (Pangasianodon gigas Chevey, 1913) and closely related species: implications for conservation

Catfishes of the family Pangasiidae are an important group that contributes significantly to the fisheries of the Mekong River basin. In recent times the populations of several catfish species have declined, thought to be due to overfishing and habitat changes brought about by anthropogenic influences. The Mekong giant catfish Pangasianodon gigas Chevey, 1913 is listed as Critically Endangered on the IUCN Red List. In the present study, we assessed the level of genetic diversity of nine catfish species using sequences of the large subunit of mitochondrial DNA (16S rRNA). Approximately 570 base pairs (bp) were sequenced from 672 individuals of nine species. In all species studied, haplotype diversity and nucleotide diversity ranged from 0.118±0.101 to 0.667±0.141 and from 0.0002±0.0003 to 0.0016±0.0013, respectively. Four haplotypes were detected among 16 samples from natural populations of the critically endangered Mekong giant catfish. The results, in spite of the limited sample size for some species investigated, indicated that the level of genetic variation observed in wild populations of the Mekong giant catfish (haplotype diversity=0.350±0.148, nucleotide diversity=0.0009±0.0008) is commensurate with that of some other related species. This finding indicates that (1) wild populations of the Mekong giant catfish might be more robust than currently thought or (2) present wild populations of this species carry a genetic signature of the historically larger population(s). Findings from this study also have important implications for conservation of the Mekong giant catfish, especially in designing and implementing artificial breeding programme for restocking purposes.     

Effects of temperature on sound production and auditory abilities in the Striped Raphael catfish Platydoras armatulus (Family Doradidae)

Background

Sound production and hearing sensitivity of ectothermic animals are affected by the ambient temperature. This is the first study investigating the influence of temperature on both sound production and on hearing abilities in a fish species, namely the neotropical Striped Raphael catfish Platydoras armatulus.

Methodology/Principal Findings

Doradid catfishes produce stridulation sounds by rubbing the pectoral spines in the shoulder girdle and drumming sounds by an elastic spring mechanism which vibrates the swimbladder. Eight fish were acclimated for at least three weeks to 22°, then to 30° and again to 22°C. Sounds were recorded in distress situations when fish were hand-held. The stridulation sounds became shorter at the higher temperature, whereas pulse number, maximum pulse period and sound pressure level did not change with temperature. The dominant frequency increased when the temperature was raised to 30°C and the minimum pulse period became longer when the temperature decreased again. The fundamental frequency of drumming sounds increased at the higher temperature. Using the auditory evoked potential (AEP) recording technique, the hearing thresholds were tested at six different frequencies from 0.1 to 4 kHz. The temporal resolution was determined by analyzing the minimum resolvable click period (0.3–5 ms). The hearing sensitivity was higher at the higher temperature and differences were more pronounced at higher frequencies. In general, latencies of AEPs in response to single clicks became shorter at the higher temperature, whereas temporal resolution in response to double-clicks did not change.

Conclusions/Significance

These data indicate that sound characteristics as well as hearing abilities are affected by temperatures in fishes. Constraints imposed on hearing sensitivity at different temperatures cannot be compensated even by longer acclimation periods. These changes in sound production and detection suggest that acoustic orientation and communication are affected by temperature changes in the neotropical catfish P. armatulus.     

刺参对浅海筏式贝类养殖系统的修复潜力

浅海筏式养殖滤食性贝类产生大量的粪便和假粪（总称生物沉积物）,对海水养殖环境产生一系列影响;而沉积食性海参能够有效清除颗粒有机物,在海水养殖系统中扮演“清道夫”的生态角色.为评估刺参在浅海筏式贝类养殖系统中的生物修复潜力,本文在不同季节现场研究了贝 参混养模式下刺参对贝类生物沉积物的摄食及生长和排泄特征.结果表明: 刺参能够在新设计的养殖设施中与滤食性贝类混养,最大生长率达0.34%·d^-1; 并可通过摄食有效清除贝类生物沉积物, 摄食率为0.1746 g·g^-1·d^-1（夏季,21.2 ℃）、0.0989 g·g^-1·d^-1（秋季,19.2 ℃）和0.0050 g·g^-1·d^-1（冬季,7.7 ℃）;刺参主要通过排泄溶解形态的NH₄⁺N和PO₄^3- -P来促进沉积物中营养盐的再生,其排泄率也呈现明显的季节变化.基于现场试验数据,估算了刺参在桑沟湾的生物修复潜力, 刺参与贝类混养可摄食4.5～159.6 kg·hm^-2·d^-1生物沉积物、排泄1 382.5～3 678.1 mmol·hm^-2·d^-1NH₄⁺ -N及74.6～335.7 mmol·hm^-2·d^-1PO₄^3--P.表明刺参对浅海筏式贝类养殖系统具有较大的生物修复潜力,贝-参混养模式不仅能够取得较大的生态效益,而且能显著增加养殖生产的经济效益.     

Planktonic bacteria in white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) aquaculture ponds in a salt-alkaline region

Aquaculture in salt-alkaline regions is encouraged in China, and culture of many aquatic species has been introduced into these areas. In this study, we cultured two species, white shrimp (Litopenaeus vannamei) and channel catfish (Letalurus punetaus) separately in aquaculture ponds in a salt-alkaline region in northwest China and assessed the impacts of the aquaculture operations on the planktonic bacterial community in the culture ponds. Culture of both species decreased the planktonic bacterial diversity and altered the bacterial community structure in the aquaculture ponds compared with the source water. Among the 10 dominant bacterial phyla, 8 were significantly correlated with environmental parameters; the exception was Actinobacteriota, the most dominant phylum, and Firmicutes. Proteobacteria and Bacteroidota abundances showed significant positive correlations with alkalinity, whereas Patescibacteria, Cyanobacteria, Planctomycetota, and Verrucomicrobiota abundance were positively correlated with salinity. Linear regression analysis showed that alkalinity was positively correlated with bacterial beta diversity and salinity was negatively correlated with that. In addition, white shrimp aquaculture significantly lowered the alkalinity, which suggests that culture of this species in inland salt-alkaline regions is a potential dealkalization solution.