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.     

Striped catfish (Pangasianodon hypophthalmus) could be suitable for coastal aquaculture

Salinity intrusion in the coastal freshwater rivers due to climate change and construction of the dam in the upstream rivers are alarming in aquaculture. Hence, an experiment was conducted to know the effects of salinity on growth performance, hemato‐biochemical parameters and erythrocytes structure in a commercially cultivable catfish species, striped catfish (Pangasianodon hypophthalmus). Firstly, median lethal concentration (LC₅₀) of salinity for striped catfish was determined and then the fish were exposed to three salinity conditions (4, 8 and 12‰) and a control (0‰). Fish were sacrificed at day 7, 14, 28 and 56 after the start of salinity exposure. The 96 hr LC₅₀ value was found to be 14.87‰. Salinity levels from freshwater to 8‰ showed optimal conditions with high survival rate and good growth performances of fish in terms of weight gain and specific growth rate (SGR). Interestingly, the lowest food conversion ratio (FCR) was found in 4‰ group. The hemoglobin (Hb) level and number of red blood cells (RBCs) were found to be decreased significantly in 8 and 12‰ compared to 0 and 4‰ at the initial days of exposure, while number of white blood cells (WBCs) and glucose level showed opposite scenario. Frequencies of ENA (erythrocytic nuclear abnormalities) and ECA (erythrocytic cellular abnormalities) were significantly increased with increasing salinities in the initial days of exposure. Overall, findings of the present study revealed that striped catfish might be suitable fish species for culture in the brackish water containing salinity up to 10‰.     

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.     

Isolation and characterization of polymorphic microsatellite loci in yellowtail catfish, Pangasius pangasius (Hamilton, 1822)

A total of nine polymorphic microsatellite loci were obtained from a genomic library of Pangasius pangasius (order Siluriformes, family Pangasiidae). Samples from rivers Bhagirathi (n = 22) and Mahanadi (n = 20) were genotyped for each of the nine microsatellite loci to determine genetic variation. The mean number of alleles per locus was 5.22 in Bhagirathi and 5.78 in Mahanadi; and expected heterozygosity ranged from 0.567 (Bhagirathi) to 0.578 (Bhagirathi). Significant deviation (P < 0.003) from Hardy–Weinberg expectations was evident at three loci, Ppa2 (Bhagirathi), Ppa14 (Mahanadi) and Ppa28 (Bhagirathi and Mahanadi). The identified microsatellite loci were found to be promising for population genetics studies of P. pangasius.     

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.     

Jeltraxin, a frog egg jelly glycoprotein, has calcium-dependent lectin properties and is related to human serum pentraxins CRP and SAP

The egg jelly that encapsulates amphibian eggs is essential for fertilization, but its molecular composition and roles remain largely unknown. We identified a calcium-dependent lectin from the pentraxin superfamily in the egg jelly coat from the South American burrowing frog, Lepidobatrachus laevis. This lectin, jeltraxin, was related to the host-response acute phase serum proteins C-reactive P component (CRP) and serum amyloid P component (SAP). The amino acid sequence of jeltraxin is 44% identical to that of Xenopus laevis CRP, 31-35% identical to those of mammalian CRP and SAP, and 21-27% identical to those of the large fusion pentraxins. Expression of jeltraxin mRNA was restricted to the oviduct, which distinguishes it as the first serum-related pentraxin not expressed in the liver. Purified jeltraxin was previously shown to exist in an oligomeric complex of approximately 250 kDa comprised of self-associating subunits. We have demonstrated by MALDI-TOF that this configuration is due to a decameric complex of 27.7 kDa subunits. Biotinylated jeltraxin bound to the high-molecular mass components of the egg jelly in a calcium-dependent manner with specificity for beta-galactose residues. On the basis of homology modeling, we predict that jeltraxin will coordinate two calcium ions. The function of jeltraxin will likely be related to its calcium-dependent lectin properties.     

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.     

Growth and morphological development of laboratory-reared larval and juvenile Pangasianodon hypophthalmus

The morphological development, including the fins, body proportions and pigmentation, of laboratory-reared larval and juvenile Pangasianodon hypophthalmus was described and their behavioral features were observed under rearing conditions. Body lengths (BL) of larvae and juveniles were 3.0 ± 0.2 (mean ± SD) mm just after hatching, and 12.9 ± 1.1 mm on day 13, reaching 23.4 ± 1.8 mm on day 25 after hatching. Aggregate fin ray numbers (for caudal fin, principal soft ray number) attained their full complements in specimens larger than 12.8 mm BL. Notochord flexion began in yolksac larvae on day 0 (10.5 h after hatching), with teeth buds and barbels appearing with jaw formation in yolksac flexion larvae on day 1. Melanophores on the body increased with growth, with a broad vertical band forming on the lateral line and an oblique band extending from above the pectoral fin base towards the forepart of the anal fin during the postflexion larval and juvenile stages. Body proportions became relatively constant in juveniles, except for maxillary barbel length (MBL), which continued to decrease. Yolksac flexion larvae started feeding on day 2 with the onset of intense cannibalism. Yolks were completely absorbed by day 3, and cannibalism ended by day 6. Subsequently, fish displayed a schooling behavior with growth, preferring relatively dark areas during the juvenile stage.     

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%.     

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.     

Monogeneans from Pangasiidae (Siluriformes) in Southeast Asia: III. Five new species of Thaparocleidus Jain, 1952 (Ancylodiscoididae) from Pangasius bocourti,P. djambal and P. hypophthalmus

The examination of gill parasites from Pangasius bocourti Sauvage, 1880; P. djambal Bleeker, 1846; P. hypophthalmus (Sauvage, 1878) and P. gigas Chevey, 1930 (Siluriformes, Pangasiidae) revealed the presence of seven species of Monogenea among which five are considered new species. They all belong to Thaparocleidus Jain, 1952 (Ancylodiscoididae) as defined by Lim (1996) and Lim et al. (2001). P. bocourti: T. combesi n. sp., T. komarudini n. sp. and T. vietnamensis n. sp. P. djambal: T. caecus (Mizelle & Kritsky, 1969), T. combesi n. sp., T. euzeti n. sp., T. komarudini n. sp. and T. sadilii n. sp. P. hypophthalmus: T. caecus, T. siamensis (Lim, 1990) and T. vietnamensis n. sp. P. gigas: no Monogenea were found on this host species.     

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.     

Isolation and characterization of microsatellite loci from two inbreeding bark beetle species (Coccotrypes)

We developed 14 microsatellite markers in Coccotrypes carpophagus and 14 in C. dactyliperda. These loci will be used for studying genetic structure and the level of inbreeding in populations in the Canary Islands and Madeira. As a result of long‐term inbreeding, genetic variability is relatively low in these bark beetle species. We found one to five alleles per locus in 29 C. carpophagus and 41 C. dactyliperda from various localities. Eleven of the markers developed for C. carpophagus amplified in C. dactyliperda and seven of the markers developed for C. dactyliperda amplified in C. carpophagus.     

Polymorphic microsatellite primers developed from DNA of the endangered Mekong giant catfish,Pangasianodon gigas (Chevey) and cross‐species amplification in three species of Pangasius

The critically endangered Pangasianodon gigas is endemic to the Mekong River. Despite its importance, little is known about its genetic diversity and conservation efforts are hampered. Ten polymorphic dinucleotide microsatellite primer pairs were developed from DNA of P. gigas. The analysis of 20 individuals from hatchery stocks using these primers resulted in two to six alleles/locus; H_O = 0.05–0.95; H_E = 0.05–0.81. All but one locus (Pg‐3) conformed to Hardy–Weinberg expectation. Eight, six and seven primer pairs were amplified with the DNA from Pangasianodon hypophthalmus, Pangasius larnaudii and Pangasius sanitwongsei, respectively. These markers will be useful for genetic monitoring of wild and hatchery stocks of these pangasiids.     

Isolation and biochemical characterization of two soluble iron(III) reductases from Paracoccus denitrificans.

Two soluble enzymes (FerA and FerB) catalyzing the reduction of a number of iron(III) complexes by NADH, were purified to near homogeneity from the aerobically grown iron-limited culture of Paracoccus denitrificans using a combination of anion-exchange chromatography (Sepharose Q), chromatofocusing (Mono P), and gel permeation chromatography (Superose 12). FerA is a monomer with a molecular mass of 19 kDa, whereas FerB exhibited a molecular mass of about 55 kDa and consists of probably two identical subunits. FerA can be classified as an NADH:flavin oxidoreductase with a sequential reaction mechanism. It requires the addition of FMN or riboflavin for activity on Fe(III) substrates. In these reactions, the apparent substrate specificity of FerA seems to stem exclusively from different chemical reactivities of Fe(III) compounds with the free reduced flavin produced by the enzyme. Observations on reducibility of Fe(III) chelated by vicinal dihydroxy ligands support the view that FerA takes part in releasing iron from the catechol type siderophores synthesized by P. denitrificans. Contrary to FerA, the purified FerB contains a noncovalently bound redox-active FAD coenzyme, can utilize NADPH in place of NADH, does not reduce free FMN at an appreciable rate, and gives a ping-pong type kinetic pattern with NADH and Fe(III)-nitrilotriacetate as substrates. FerB is able to reduce chromate, in agreement with the fact that its N-terminus bears a homology to the previously described chromate reductase from Pseudomonas putida. Besides this, it also readily reduces quinones like ubiquinone-0 (Q0) or unsubstituted p-benzoquinone.     

Isolation and partial characterization of two antigenic glycoproteins from rye-grass (Lolium perenne) pollen.

Two glycoproteins have been purified from a buffer extract of rye-grass (Lolium perenne) pollen. Both migrated as single bands on sodium dodecyl sulphate/polyacrylamide gels. Glycoprotein 1 (0.8 mg/g of pollen) had a apparent mol.wt. of 33 000 and contained 95% protein and 5% carbohydrate. The monosaccharides glucose, galactose, mannose, arabinose and N-acetylglucosamine were present in the proportions 3:3:1:2:1. Glycoprotein 2 (0.4 mg/g of pollen) had an apparent mol. wt. of 68000 and contained 88% protein and 12% carbohydrate. The monosaccharides glucose, galactose, mannose, fucose, xylose, arabinose and N-acetylglucosamine were present in the proportions 4:7:13:5:8:6:6. This glycoprotein bound concanavalin A and Lotus tetragonolobus (asparagus pea) lectin. Radioallergosorbent (RAST) inhibition tests showed that Glycoprotein 1 is an effective allergen, whereas Glycoprotein 2 has less allergenic activity. A method for performing both lectin-binding assays and RAST inhibition tests using microtitre trays is described.     

Carcass traits of two marketable size classes of Pangasius pangasius (Hamilton, 1822)

Carcass and commercial yield traits of Pangasius pangasius were evaluated and morphometric parameters measured along with carcass traits in two marketable weight classes (average ± SD) 1603 ± 49.5 g and 1985.6 ± 56.6 g. The Pangas fish head yield was 14.80% and 15.1% for the 2000 g and 1600 g weight classes, respectively. The offal percentage varied from 8.6 to 8.8 in both weight classes. Pangasius had a significant accumulation of fat deposits in mesenteric tissue and on the lining of the abdominal cavity. Headless (73.2%), head and skinless (68.7%), head, skin and boneless (57.7%) dressing yields were significantly higher in 1600 g than in the 2000 g weight class. The 2000 g weight class category exhibited mesenteric fat (4.3%), dissected subcutaneous and intramuscular fat (10.1%) which was significantly higher than in the 1600 g weight class. The yields of dressing stages were affected mostly by skin (8.3–4.5%) and mesenteric fat (4.3–3.7%), and dissected subcutaneous and intramuscular fat (10.1–6.8%), which is significantly higher in the 2000 g than in the 1600 g category. The later weight class category resulted in more meat yield, and less bone, skin and fat yields.     

Isolation, purification and characterization of hemerythrin from Methylococcus capsulatus (Bath)

Earlier work from our laboratory has indicated that a hemerythrin-like protein was over-produced together with the particulate methane monooxygenase (pMMO) when Methylococcus capsulatus (Bath) was grown under high copper concentrations. A homologue of hemerythrin had not previously been found in any prokaryote. To confirm its identity as a hemerythrin, we have isolated and purified this protein by ion-exchange, gel-filtration and hydrophobic interaction chromatography, and characterized it by mass spectrometry, UV-visible, CD, EPR and resonance Raman spectroscopy. On the basis of biophysical and multiple sequence alignment analysis, the protein isolated from M. capsulatus (Bath) is in accord with hemerythrins previously reported from higher organisms. Determination of the Fe content in conjunction with molecular-weight estimation and mass analysis indicates that the native hemerythrin in M. capsulatus (Bath) is a monomer with molecular mass 14.8 kDa, in contrast to hemerythrins from other eukaryotic organisms, where they typically exist as a tetramer or higher oligomers.     

Isolation and characterization of two rubredoxins from Clostridium thermoaceticum

Two rubredoxins with similar molecular weights (about 6000) have been purified from Clostridium thermoaceticum, a thermophile and strict anaerobe. They exhibit minor differences in several properties like elution pattern from DEAE-cellulose column, isoelectric point, amino acid composition, absorption and EPR spectra and redox potential. Their chemical and physical properties are similar to those of other rubredoxins from anaerobic microorganisms.