Cloning and expression analysis of interferon regulatory factor 7 in the Pacific cod, Gadus macrocephalus.

Interferon regulatory factor 7 (IRF7) plays an important role in regulating the response of type I interferon (IFN) to viral infection. To understand the mechanisms underlying immune reactions in the Pacific cod, Gadus macrocephalus, the gene encoding G. macrocephalus IRF7 was cloned and characterized. The cDNA of G. macrocephalus IRF7 was also cloned and sequenced. A cDNA sequence of 2032 bp was assembled using polymerase chain reaction (PCR) products. It contains an open reading frame of 1323 bp in length, which encoded a 440-amino acid polypeptide that comprised a DNA-binding domain (DBD), an IRF association domain (IAD), and a serine-rich domain (SRD). In the DBD, the tryptophan cluster consisted of only four tryptophans, which is a unique characteristic in fish IRF7. The mRNA of IRF7 was detected in various tissues, including in the spleen, thymus, kidney, intestine, and gills, using relative quantification PCR (R-qPCR). Dynamic expression of IRF7 was observed in larvae throughout post-hatching (ph) development, with the highest level detected at day of ph (dph) 25. Response to immune stimulation was examined by challenging larvae with polyriboinosinic polyribocytidylic acid (pIC) to mimic viral infection and elicit an immune reaction. R-qPCR revealed that the expression of IRF7 significantly increased in pIC-treated groups relative to that in the control groups, in a time-dependent manner, with peak responses at 48 and 72 h after pIC-treatment. These results show that IRF7 is expressed in various tissues of adult fish and larvae and is sensitive to viral infection, suggesting that it plays a role in antiviral immune defense in G. macrocephalus.

Transcriptomic features associated with energy production in the muscles of Pacific bluefin tuna and Pacific cod.

Bluefin tuna are high-performance swimmers and top predators in the open ocean. Their swimming is grounded by unique features including an exceptional glycolytic potential in white muscle, which is supported by high enzymatic activities. Here we performed high-throughput RNA sequencing (RNA-Seq) in muscles of the Pacific bluefin tuna (Thunnus orientalis) and Pacific cod (Gadus macrocephalus) and conducted a comparative transcriptomic analysis of genes related to energy production. We found that the total expression of glycolytic genes was much higher in the white muscle of tuna than in the other muscles, and that the expression of only six genes for glycolytic enzymes accounted for 83.4% of the total. These expression patterns were in good agreement with the patterns of enzyme activity previously reported. The findings suggest that the mRNA expression of glycolytic genes may contribute directly to the enzymatic activities in the muscles of tuna.

Transcriptomic analysis and biomarkers (Rag1 and Igµ) for probing the immune system development in Pacific cod, Gadus macrocephalus.

Mortality (>90%) is a big concern in larval rearing facilities of Pacific cod, Gadus macrocephalus, limiting its culture presently still in the experimental stages. Understanding the immune system development of G. macrocephalus is crucial to optimize the aquaculture of this species, to improve the use of economic resources and to avoid abuse of antibiotics. For the transcriptome analysis, using an Illumina sequencing platform, 61,775,698 raw reads were acquired. After a de novo assembly, 77,561 unigenes were obtained. We have classified functionally these transcripts by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). 27 genes mainly related to hematopoietic or lymphoid organ development and somatic diversification of immune receptors have been reported for the first time in Pacific cod, and 14 Ig heavy chain (µ chain) locuses were assembled using Trinity. Based on our previous achievement, we have chosen Rag1 and Igµ as immune system development biomarkers. Full length cDNA of Rag1 and Igµ as biomarkers were obtained respectively using RACE PCR. Concerning Rag1, the deduced amino acid of Rag1 and protein immunodetection revealed a Rag1 isoform of 69 kDa, significantly different from other fish orthologs, such as Oncorhynchus mykiss (121 kDa). Phylogenetic analysis reveals a unique immune system for the Gadus genre, not exclusive for Atlantic cod, among vertebrates. Meanwhile, full length cDNA of Igµ included an ORF of 1710 bp and the deduced amino acid was composed of a leader peptide, a variable domain, CH1, CH2, Hinge, CH3, CH4 and C-terminus, which was in accordance with most teleost. Absolute quantification PCR revealed that significant expression of Rag1 appeared earlier than Igµ, 61 and 95 dph compared to 95 dph, respectively. Here we report the first transcriptomic analysis of G. macrocephalus as the starting point for genetic research on immune system development towards improving the Pacific cod aquaculture.

Microsporidian heavy infection in a batch of salted and dried cod.

The aim of this work is the description and characterization of a severe microsporidian infection in a batch of salted and dried cod. Particularly, the case involves a batch of approximately 800 kg obtained from Gadus macrocephalus (Food and Agriculture Organization Zone 61 - Northwest Pacific Ocean), which, after rehydration and sectioning operations, underwent routine company checks before packaging. In about 20% of the samples, the presence of whitish nodules with a diameter ranging from 1 to 2 mm was observed on the surface of the fillets and in cross-section. The lesions ranged from a few units to 10 per cm2. Some samples were subjected to fresh microscopic observation with the stereomicroscope, confirming the nodular nature of the lesions, which were often confluent, alternating with empty spaces, giving the tissue a honeycombing aspect. The histological examination at low magnification allowed us to observe the heavy vacuolization of nodular lesions irregularly surrounded by a spongy-like wall. The observation at higher magnification of other sections allowed us to identify intra-myofibrillar cists containing presumptive microsporidian elements. The tissue damage derived from the technological processes and gravity of lesions did not allow a morphological characterization of presumptive protozoans. The molecular examination of the nodular lesions and the analysis of the sequence of an 897 bp fragment of the small subunit 16S rRNA revealed 100% identity with Microsporidium theragrae (GenBank accession number MT928885-89) first isolated from the skeletal muscles of Gadus chalcogrammus specimens from the Sea of Okhotsk. This finding confirms the importance of selecting suppliers and raw materials in the seafood industry, as well as the usefulness of an effective traceability system.

Early life history affects fish size mainly by indirectly regulating the growth during each stage: a case study in a demersal fish.

The complex life histories of demersal fishes are artificially separated into multiple stages along with changes in morphology and habitat. It is worth exploring whether the phenotypes expressed earlier and later during the life cycle are related or decoupled. The life stages of first year Pacific cod (Gadus macrocephalus) were tracked over different hatch years and regions to test whether the early life history had a long-lasting effect on subsequent growth. We further explored the contribution of growth in the early and subsequent life history stages to body size at the end of each stage. In addition to the accessory growth centre and the first annual ring, the other two checks on the otolith possibly related to settlement and entering deeper waters were identified in 75 Pacific cod individuals. The direct and indirect relationships among the life history stages was interpreted based on path analysis. The results showed that growth prior to the formation of the accessory growth centre had a significant effect on the absolute growth of the fish before and after settlement and migration to deep water. However, there was no or moderate evidence that early growth affected the body size at each stage, which was mainly regulated by growth during the stage. This study supports the lasting effect of early growth and clarifies that it affects size mainly by indirectly regulating staged growth. Quantifying the phenotype relationships and identifying the internal mechanisms form the basis for assessing population dynamics and understanding the processes behind the changes. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-022-00145-y.

Evaluating dried salted cod amino acid signature for nutritional quality assessment and discriminant analysis.

Aim: Thus, the aim of this study was to answer three scientific questions: (1) Are the protein content and amino acid profile of dried salted cod influenced by species (Gadus morhua and Gadus macrocephalus)? (2) Are the protein content and amino acid profile of dried salted cod influenced by the geographical area of capture (Iceland and Norway)? and (3) Does the amino acid profile have the potential to be used as a discriminator of species and geographical areas of capture? Methods: A total of 45 dried salted cods (2-3 kg of dry weight; n = 15 samples/origin) were used in this study. The Atlantic cod was fished in the Atlantic northeast (FAO 27 area) within the Exclusive Economic zones (EEZ) of Norway (n = 15) and Iceland (n = 15), while the Pacific cod was caught in the Pacific northeast (FAO 67 area) within the Alaska EEZ (n = 15). Total protein content was determined by the Kjeldahl method, in accordance with the AOAC procedures. The amino acid profile was analyzed by HPLC with fluorescence detection (at excitation and emission wavelengths of 338 and 425 nm, respectively). Results: The Atlantic cod presented higher contents of total protein (33.90 versus 33.10 g/100 g of cod edible portion; p = 0.017) and total amino acid contents (32.52 versus 32.04 g/100 g of cod edible portion; p = 0.015) but displayed lower percentage of indispensable amino acids (32.16 versus 32.83 g/100 g of protein; p < 0.001) than Pacific cod. Among the Atlantic cod harvesting locations, the Norwegian cod displayed higher total amino acid contents (96.91 versus 96.81 g/100 g of protein; p = 0.012) and higher percentage of indispensable amino acids (35.38 versus 28.94 g/100 g of protein; p = 0.042) than the Icelandic counterpart. A correct classification of 100% was obtained for the Pacific and Icelandic cod varieties, but the classification accuracy in the Norwegian cod was of just 86.67%, since 2 samples out of 15 were incorrectly classified as Icelandic. Conclusion: The comparison of cod species showed that the Atlantic cod had a significantly lower EAAI than the Pacific cod (p < 0.001; 88.23 versus 88.61). On the other hand, the comparison of the two origins in the Atlantic cod, showed that Norwegian cod displayed a significantly higher EAAI than the Icelandic cod (99.15 versus 77.32). The assessment of the EAAI allows the classification of the protein's nutritional quality, allowing us to classify both cod species as a good protein source to human diet. However, within the Atlantic cod, the Norwegian cod's protein is classified as high quality, while the Icelandic cod attain the classification of useful quality. Regarding the amino acid profile discriminatory potential to classify cod samples. The results show that the AA profile has 100% accuracy in the separation of cod species, but was not globally efficient in the differentiation of the Norwegian from the Icelandic cod.

The Effect of the Species and Harvesting Location on Dried Salted Cod Fatty Acid Signatures and Nutritional Quality.

The Atlantic cod was listed as 'vulnerable' by the International Union for Conservation of Nature, a condition that persists today. Fishing pressure on the Atlantic cod could be partially transferred to the Pacific cod, since the two cod species share genetic and phenotypic similarities. The aim of this study is to expand knowledge of the composition of dried salted cod obtained from Atlantic and Pacific cod species, with the Atlantic cod being from two different harvesting locations. The comparison of these cod species revealed the existence of nine significant differences among individual FAs (accountable for 63.2% of total FAs), which was at a similar level to that observed between different harvesting locations for the Atlantic cod (ten significant differences among individual FAs, accountable for 61.6% of total FAs). Canonical discriminant analysis and cross-validation achieved full discrimination of the cod's origin and 100% accuracy in the cod's origin classification. The amount of EPA plus DHA in dried salted cod reached its higher value among the Pacific cod (302.3 mg/100 g), while the Atlantic cod averaged 284.1 g/100 g of edible portion. The Pacific cod presented a higher α-tocopherol content than its Atlantic counterpart (8.04 vs. 4.94 µg/g).

Purification, structural characterization, and anticoagulant activity evaluation of chondroitin sulfate from codfish (Gadus macrocephalus) bones.

Chondroitin sulfate (CCS) was purified from discarded codfish (Gadus macrocephalus) bones, and its chemical structure and anticoagulant activity were assessed. CCS was obtained via enzymatic lysis and ion-exchange column chromatography, with a yield of approximately 0.15%. High-performance gel performance chromatography revealed CCS to be a largely homogeneous polysaccharide with a relatively low molecular weight of 12.3 kDa. FT-IR spectroscopy, NMR spectroscopy, and SAX-HPLC indicated that CCS was composed of monosulfated disaccharides (ΔDi4S 73.85% and ΔDi6S 19.06%) and nonsulfated disaccharides (ΔDi0S 7.09%). In vitro anticoagulation analyses revealed that CCS was able to significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT) (p < 0.05). At a CCS concentration of 5 µg/mL and 25 µg/mL, APTT and TT were approximately 1.08 and 1.12 times higher, respectively, compared to the negative control group. The results indicated that CCS might offer value as a dietary fiber supplement with the potential to prevent the incidence of coagulation-related thrombosis.

Whole-genome survey and phylogenetic analysis of Gadus macrocephalus.

Gadus macrocephalus (Pacific cod) is an economically important species on the northern coast of the Pacific. Although numerous studies on G. macrocephalus exist, there are few reports on its genomic data. Here, we used whole-genome sequencing data to elucidate the genomic characteristics and phylogenetic relationship of G. macrocephalus. From the 19-mer frequency distribution, the genome size was estimated to be 658.22 Mb. The heterozygosity, repetitive sequence content and GC content were approximately 0.62%, 27.50% and 44.73%, respectively. The draft genome sequences were initially assembled, yielding a total of 500,760 scaffolds (N50 = 3565 bp). A total of 789,860 microsatellite motifs were identified from the genomic data, and dinucleotide repeat was the most dominant simple sequence repeat motif. As a byproduct of whole-genome sequencing, the mitochondrial genome was assembled to investigate the evolutionary relationships between G. macrocephalus and its relatives. On the basis of 13 protein-coding gene sequences of the mitochondrial genome of Gadidae species, the maximum likelihood phylogenetic tree showed that complicated relationships and divergence times among Gadidae species. Demographic history analysis revealed changes in the G. macrocephalus population during the Pleistocene by using the pairwise sequentially Markovian coalescent model. These findings supplement the genomic data of G. macrocephalus, and make a valuable contribution to the whole-genome studies on G. macrocephalus.

Cloning, Exogenous Expression and Function Analysis of Interferon-γ from Gadus macrocephalus.

Interferon γ (IFN-γ) is now considered to be one of the key molecules in the regulation of innate and adaptive immunity. The function of IFN-γ is best described in humans, but less of IFN-γ in fish species has been described at protein level. In the present study, IFN-γ from Gadus macrocephalus (GmIFN-γ) has been examined in terms of bioinformatics, prokaryotic expression, yeast expression, antiviral activity and immune regulatory function. The cDNA of GmIFN-γ contains an open reading frame of 570 nucleotides, coding 189 amino acids. The mature protein contains a nuclear localization signal motif and an obvious IFN-γ signature sequence at the C-terminal. GmIFN-γ is very similar to that of Atlantic cod, with homology up to 89.89%, but less than 32% to other species. GmIFN-γ can be detected in the gills, spleen, intestine, brain and kidney. Interestingly, during early development, a strong signal of GmIFN-γ was not detected until 40 days post hatching. Prokaryotic expression plasmid pET-32a-GmIFN-γ was constructed, and the expression products in BL21 were confirmed by Mass Spectrometry. Meanwhile, the plasmid pGAPZA-GmIFN-γ with Myc tag was constructed and transmitted into Pichia pastoris yeast GS115, and the products were tested using Western blot. The purified GmIFN-γ from either BL21 or yeast has a strong antivirus (Spring viremia of carp virus) effect. The vector of pcDNA3.1-GmIFN-γ was expressed in EPC cell lines; high transcript levels of MHC class I chain-related protein A (MICA) gene were detected; and the exogenous GmIFN-γ protein could also induce MICA expression, indicating that GmIFN-γ could stimulate immune response. The yeast GS115 with GmIFN-γ protein, which is an inclusion body, was given to zebrafish orally, and the transcript of zebrafish IFN-γ was upregulated significantly; however, genes of the interferon type-I signal pathway were not well stimulated.

Fas/FasL of pacific cod mediated apoptosis.

Fas and Fas ligand (FasL) pathway plays important roles in virus defense and cell apoptosis. In our previous work, nervous necrosis virus (NNV) was discovered in Pacific cod (Gadus macrocephalus), and the Fas ligand (PcFasL) was up-regulated when NNV outbreak, however, signal transmission of Fas/FasL in fish are still unclear. In the present study, Pacific cod Fas (PcFas), PcFasL and Fas-associating protein with a novel death domain (PcFADD) were characterized. The predicted protein of PcFas, PcFasL and PcFADD includes 333 aa, 90 aa and 93 aa, separately. 3-D models of PcFas, PcFasL and PcFADD were well constructed based on reported templates, respectively, even though the sequence homology with other fish is very low. The transcript levels of PcFas increased gradually from 15 day-post hatching (dph) to 75dph. PcFas was significantly up-regulated when cod larvae had NNV symptoms at 24dph, 37dph, 46dph, 69dph, and 77dph. Subcellular localization revealed that PcFasL was located in the cytoplasm, while PcFas was mainly located in the cell membrane. Exogenous expressed PcFasL of 900 µg/mL could kill the Epithelioma papulosum cyprinid (EPC) cells by MTT test, but low concentration has no effect on the cells. qPCR analysis showed that overexpression of PcFas could significantly up-regulate the expression of genes related to Fas/FasL signaling pathway, including bcl-2, bax, and RIP3, while overexpression of PcFasL significantly up-regulate the expression of caspase-3, caspase-9, and MLKL. Overexpression of PcFas or PcFasL could induce EPC apoptosis significantly by flow cytometry, which was consistent with the results of caspase-3 mRNA level increasing. The results indicated that NNV could induce apoptosis through Fas/FasL signal pathway.

Multiple ice-age refugia in Pacific cod, Gadus macrocephalus.

Pleistocene ice-ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (FST = 0.028, r(2) = 0.33) and mtDNA (FST = 0.027, r(2) = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice-age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice-age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14-15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre-date the last glacial maximum.

Transcriptome from Pacific cod liver reveals types of apolipoproteins and expression analysis of AFP-IV, structural analogue with mammalian ApoA-I.

Apolipoproteins (Apos), transporting the lipids through the lymphatic and circulatory systems, are associated with kinds of diseases. Additionally, type IV antifreeze protein (AFP-IV) was related evolutionarily with apolipoproteins. However, the information of Apos in fish was limited. In this study, ApoA-I, ApoA-I-2, ApoA-IV, Apo E, ApoB-100-like and AFP-IV were sequenced from Pacific cod (Gadus macrocephalus) liver transcriptome using Illumina HiSeq 2000, and their 3-D models were constructed based on the most confidence templates ever reported in mammals. Interestingly, the model of G. macrocephalus AFP-IV, named GmAFPIV, is quite similar to the structure of ApoA-I. GmAFPIV includes 689 bases with a complete open reading frame encoding 125 amino acids. Sequence alignment of GmAFPIV showed 30% to 50% similarity with that of other species except Gadus sp. Expression levels of GmAFPIV were found in a decreasing manner in liver, intestine, gill, brain and gonad. Heterologously expression of the GmAFPIV protein was expressed in Escherichia coli and purified to immunize New Zealand rabbits. The survivors of E. coli in 60 µg/mL of GmAFPIV are more than that in the 30 µg/mL group after stored in -20 °C and -80 °C, indicating high concentration of GmAFPIV could protect E. coli avoiding the damage from ice crystal. The subcellular localization of GmAFPIV showed that the green fluorescence was mainly observed in the cytoplasm, indicating GmAFPIV play roles in the cytoplasm. It was concluded that GmAFPIV may function not only as an antifreeze protein but also as an apolipoprotein transporting lipids in fish.

A new method for the rapid detection of Atlantic cod (Gadus morhua), Pacific cod (Gadus macrocephalus), Alaska pollock (Gadus chalcogrammus) and ling (Molva molva) using a lateral flow dipstick assay.

Species-specific lateral flow dipstick (LFD) assays for the identification of Atlantic cod (Gadus morhua), Pacific cod (Gadus macrocephalus), Alaska pollock (Gadus chalcogrammus) and ling (Molva molva) in food products were developed. The method comprises a PCR system with four sets of specific primers, for each target species. This step was also devised to dual-labeling of PCR products with biotin and 6-FAM, which are then easily read on a lateral flow dipstick, upon which these products are immobilized by a fixed biotin-ligand and visualized with anti-FAM antibody-coated gold nanoparticles. Sensitivity and selectivity were determined for each of the developed assays. Validation of the assays was performed with DNA extracted from commercial fish products, the identification of all samples by PCR-LFD was coherent with the results found with DNA sequencing. Target species were successfully detected in analyzed commercial samples, demonstrating the applicability of this method to the rapid analysis of food products.

Complete mitochondrial genome of the Pacific cod, Gadus macrocephalus (Gadiformes, Gadidae).

The Pacific cod Gadus macrocephalus is a commercially important species belonging to the family Gadidae. In this study, we performed the first sequencing and assembly of the complete mitochondrial genome of G. macrocephalus. The complete mitochondrial genome is 16,567 bp long, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using the mitochondrial genomes of 15 species showed that G. macrocephalus clusters with G. ogac. This mitochondrial genome provides potentially important resources for performing population genetic analysis and addressing phylogenetic issues.