Fish In China Research Articles

Molecular characterisation and histopathological study of Eustrongylides excisus nematode in the northern pike (Esox lucius)

Eustrongylides excisus is a parasitic nematode species whose life cycle requires two intermediate hosts, an aquatic oligochaete and a benthophagous fish. In the present study, 100 specimens of Esox lucius Linnaeus weighing 550-800 g were collected from Freidoonkenar, south of the Caspian Sea (Mazandaran province, Iran) and were examined for the presence of Eustrongylides. The bright red nematode larvae were found in the testes and encapsulated in the body musculature of 90% of E. lucius fish. The larvae were diagnosed as Eustrongylides excisus. Tissue samples were collected from the muscles and testes for histopathological examination of the lesions caused by the parasitic larvae. For molecular analysis, the nematode larvae genomic DNA was extracted and molecular characterisation of Eustrongylides and comparison with the corresponding sequences available in the GenBank was done. The histopathological damages caused by parasites in the muscle included external nodules, inflammation, necrosis, and granulomas. Granulomas containing multi-nucleated giant cells, epithelioid cells, lymphoid cells, macrophages and necrotic debris were observed. Microscopic examination of the testes revealed mild vacuolar degeneration in some Sertoli cells. Molecular analysis confirmed obtained larvae as E. excisus. Comparison of DNA sequences showed that isolated nematodes were very similar to those obtained from freshwater fish in China. The present study reported Eustrongylides nematodes in Esox lucius, and inflammatory lesions caused by E. excisus larvae in the muscle and testis of this species of fish for the first time. In addition, molecular characterization and phylogenic analysis of recovered larvae showed presence of microvarients.

Transcriptome analysis reveals the mechanisms of hepatic injury caused by long-term environmental exposure to atrazine in juvenile common carp (Cyprinus carpio L.).

Atrazine (ATZ) is the second most commonly used herbicide worldwide, resulting in the pollution of water bodies and affecting the economic benefits of aquaculture. ATZ is known to cause liver damage in the common carp, Cyprinus carpio L., one of the most widely cultivated fish in China, but the underlying mechanisms are poorly understood. In this study, juvenile common carp Cyprinus carpio L. were exposed to three different environmental levels (0.4, 0.8, and 1.2μg/L) of ATZ for 12weeks and changes in the liver transcriptomes between the high-dose group and the control group were analyzed. The data showed that different levels of ATZ exposure caused hepatotoxicity in juvenile carp, shown by biochemical parameters and histopathological changes. Comparative transcriptomics showed that high-dose ATZ exposure led to alterations in the expression of various lipid metabolism-related gene changes, including genes associated with metabolic pathways, fatty acid metabolism, and fatty acid elongation. Furthermore, a connection network analysis of the top 100 differentially expressed genes (DEGs) showed a variety of associations between high-dose ATZ-induced liver damage and the principal DEGs, indicating the complexity of hepatotoxicity induced by ATZ. In conclusion, the molecular mechanisms underlying ATZ-triggered hepatotoxicity in juvenile carp are primarily related to impaired lipid metabolism.

Development and applications of chromosome-specific cytogenetic BAC-FISH probes in Larimichthys crocea

Large yellow croaker Larimichthys crocea (Richardson) is an important member in family Sciaenidae, and one of most productive mariculture fishes in China. Fluorescence in situ hybridization is a useful tool for cytogenetics and genomics research. Here, we demonstrated that bacterial artificial chromosome (BAC) clones could be used to identify individual chromosomes in large yellow croaker, and also to study chromosome evolution in the related species. By using BAC paired-end sequencing and sequence alignment, 435 BAC clones were anchored to 24 pseudochromosomes of large yellow croaker genome. Among them, 72 BAC clones with low repeat content were selected and passed PCR test, and then grouped by chromosome for FISH test. As a results, there were 67 BAC clones, 2 to 3 BAC clones per chromosome, generated specific and stable signal at expected position. Then, a dual-color FISH probe cocktail composed of 48 of these BAC clones was formulated and used to hybridize metaphase chromosome spreads, resulting in distinct signal patterns on each chromosome pair, which help to distinguish all chromosomes in the metaphase spreads of large yellow croaker. The chromosome-specific BAC-FISH probes were also applied to a close relative of large yellow croaker, Collichthys lucidus, demonstrating that its Y chromosome originated from the fusion of Chr.1 and Chr.7. Thus, our study provides the first set of chromosome-specific FISH probes in family Sciaenidae, which will play an important role in cytogenetics and genomics research in the family.

The involvement of oxidative stress mediated endoplasmic reticulum pathway in apoptosis of Golden Pompano (Trachinotus blochii) liver under PS-MPs stress

Globally, microplastics (MPs) are highly prevalent, especially in coastal areas. Unfortunately, golden pompano as a major marine fish in China is typically raised in floating marine cages near coasts, facing these MPs sources. However, toxicological studies on Golden Pompano which farm in coastal areas and face actual microplastic exposure are rare. Therefore, golden pompano were exposed to 10.0 μg/L, 100.0 μg/L, and 1000.0 μg/L polystyrene MPs (PS-MPs) for 14 days to study the potential impact of the microplastics on the Golden Pompano. Fish show slowed growth after 14 days of exposure. Histopathology shows irregular shaped nuclei and nuclear and cytoplasmic vacuolation traits in liver. Oxidative stress-related enzyme activity and gene expression data show that oxidative damage occurs in the high-concentrations (100.0 μg/L and 1000.0 μg/L) of PS-MPs exposures. Up-regulation of Grp78, Xbp-1, Eif-2α and chop gene expression indicates the occurrence of endoplasmic reticulum stress, and the western blot results also confirmed this. Severe oxidative stress also caused ERS, which ultimately increased BAX/Bcl-2 ratios and induces apoptosis. Furthermore, up-regulated anaerobic respiration, altered lipid metabolism, and immune disturbance were exhibited during PS-MPs stress. Therefore, oxidative stress appeared to be the main toxicity issue caused by MPs, while ERS-mediated apoptosis, metabolic alterations, and immune responses were induced by this stress. Notably, endoplasmic reticulum stress and apoptosis are a self-protective mechanism, which may be an intermediate link in the toxicity of microplastics. This study highlights the role of endoplasmic reticulum stress in MPs toxicology and assesses the adverse effects of microplastics on Golden Pompano.

Efficacy of Pneumatophorus japonicus meat as an iron fortificant in whole‐wheat flour in preventing iron deficiency

Iron deficiency anemia (IDA) is a global health concern affecting one-third of the world's population, particularly those dominated by plant-based food. Fortifying staple foods with iron has been an effective strategy for preventing IDA. Pneumatophorus japonicus is an essential economic fish in China. Pneumatophorus japonicus dark meat is usually underutilized as a byproduct, though it contains bounteous nutrients, including heme iron (10.50mg/100g). This study aimed to investigate the iron bioavailability of P. japonicus dark meat and to evaluate its potential as an iron fortifier for whole-wheat flour, a typical staple food, using an in vitro digestion/Caco-2 cell culture system. Our results suggested the excellent iron bioavailability of P. japonicus dark meat in comparison with beef (a heme dietary iron reference), whole-wheat flour (a non-heme dietary iron reference), and FeSO4 (a conventional iron supplement). The addition of P. japonicus dark meat notably enhanced iron solubility, bioavailability, and protein digestibility of whole-wheat flour. The flour-dark meat mixture yielded 1.96 times the iron bioavailability compared to beef per gram. The iron bioavailability was further improved by adding vitamin C, a commonly used dietary factor, at the Vc/iron mass ratio of 2:100-5:100. Our findings reveal the promise of P. japonicus dark meat as a significant source of bioavailable iron, providing a basis for developing fish byproducts as alternatives for iron supplementation. PRACTICAL APPLICATION: This study investigated the iron bioavailability of Pneumatophorus japonicus meat using in vitro digestion/Caco-2 cell culture system. These results could be used to improve the utilization of Pneumatophorus japonicus byproduct (dark meat) and develop the potential of the byproduct asan ironfortifier for whole-wheat flour.

Specificity of DNA Vaccines against the Genogroup J and U Infectious Hematopoietic Necrosis Virus Strains Prevalent in China.

Infectious hematopoietic necrosis virus (IHNV) is the most important pathogen threatening the aquaculture of salmonid fish in China. In addition to the common genogroup J IHNV, genogroup U has been newly discovered in China. However, there is no effective DNA vaccine to fight against this emerging genogroup U IHNV in China. In this study, DNA vaccines encoding the IHNV viral glycoprotein (G) gene of the GS2014 (genogroup J) and BjLL (genogroup U) strains isolated from northern China were successfully developed, which were identified by restriction analysis and IFA. The expression of the Mx-1 gene and G gene in the spleens and muscles of the injection site as well as the titers of the serum antibodies were measured to evaluate the vaccine efficacy by RT-qPCR and ELISA. We found that DNA vaccine immunization could activate Mx1 gene expression and upregulate G gene expression, and the mRNA levels of the Mx1 gene in the muscles were significantly higher than those in the spleens. Notably, DNA vaccine immunization might not promote the serum antibody in fish at the early stage of immunization. Furthermore, the efficacy of the constructed vaccines was tested in intra- and cross-genogroup challenges by a viral challenge in vivo. It seemed that the DNA vaccines were able to provide great immune protection against IHNV infection. In addition, the genogroup J IHNV-G DNA vaccine showed better immune efficacy than the genogroup U IHNV-G or divalent vaccine, which could provide cross-immune protection against the genogroup U IHNV challenge. Therefore, this is the first study to construct an IHNV DNA vaccine using the G gene from an emerging genogroup U IHNV strain in China. The results provide great insight into the advances of new prophylactic strategies to fight both the genogroup J and U IHNV in China.

Nutrient dynamics and coupling with biological processes and physical conditions in the Bohai Sea

The Bohai Sea is a habitat for economically important fish in China, but its ecological environment has changed significantly, and it is necessary to further clarify the dynamics and the internal resupply channels of nutrients in the Bohai Sea. Based on four field observations in the Bohai Sea from May to December 2019, the nutrient dynamics were addressed. The concentration of dissolved inorganic nutrients was depleted throughout the water column in spring and in the euphotic zone in summer and accumulated in the bottom water in summer and in the water column in autumn and winter. Relative phosphorus limitation was present in Laizhou Bay and its surrounding area in all seasons, while relative silicon limitation was evident in spring and relative nitrogen limitation was significant in summer in most other study aeras. The results of end-member mixing model illustrated significant seasonal differences in the nutrient uptake ratios, which may be related to various factors such as different phytoplankton composition and phosphorus turnover rates. Turbulent entrainment was an important nutrient pathway for primary production in the euphotic zone of Central Bohai Sea during the stratification season, with an estimated average nutrient flux of 6.04 ± 9.63, 0.22 ± 0.19 and 6.97 ± 6.61 mmol·m-2·d-1 for DIN, DIP and DSi, respectively.

Comparative study on the gonadal development in the diploid and artificially induced triploid olive flounder Paralichthys olivaceus

Artificial induction and breeding of triploids has been widely performed in fish due to their sterility or low fecundity. However, detailed studies on the gonadal development status, gamete formation, fertilization ability, and molecular mechanism of the induced triploids in marine fish are limited. Olive flounder Paralichthys olivaceus is an important mariculture fish in China, Japan, and Korea. In this study, by observing the gonadal development of the artificially induced triploid and control diploid flounder, the histological structure, sex hormone level, and transcriptome profiles were compared. The fecundity of the male triploid fish was also evaluated. The results showed that the development of the gonads of the triploids was severely inhibited. Apoptosis occurred in both male and female triploid gonads, which may lead to inhibition of germ cell development. At 24 months post hatch (mph), the contents of testosterone (T) and estradiol (E2) in the gonads of the female triploid flounder were lower than those of the diploid ones (P < 0.05), and the contents of E2 in the testes of the male triploid flounder were higher than those of the diploid ones (P < 0.05). Although the triploid flounder could produce sperm, the sperm presented different sizes of the head, deletion of the mitochondrion, and short tail under the scanning electron microscope. Only a few spermatozoa were slightly active. The ploidy of the spermatozoa included haploid, haploid - diploid, triploid, 4-5n aneuploidy, and even higher ploidy. By using sperm from the triploids with the control eggs, very few abnormal embryos and larvae were obtained. Transcriptome data at 18 and 24 mph showed that most of the significantly changed differentially expressed genes between the diploids and triploids were related to cell division and proliferation, energy and metabolism, fertility, and apoptosis. In the triploid testis, many genes related to spermatogenesis, such as mns1, dnah1, and dnah5, were down-regulated; while in the triploid ovary, genes related to testicular development, such as amh, amhr2, and wnt4, were up-regulated, which also provided molecular evidence for the testicular-like gonads observed in the histology of the triploid ovary. These results may help explain the developmental retardation and low fecundity in the gonads of triploid fish that are important for the future application of culture.

Transcriptome and DNA Methylation Responses in the Liver of Yellowfin Seabream Under Starvation Stress.

Fish suffer from starvation due to environmental risks such as extreme weather in the wild and due to insufficient feedings in farms. Nutrient problems from short-term or long-term starvation conditions can result in stress-related health problems for fish. Yellowfin seabream (Acanthopagrus latus) is an important marine economic fish in China. Understanding the molecular responses to starvation stress is vital for propagation and culturing yellowfin seabream. In this study, the transcriptome and genome-wide DNA methylation levels in the livers of yellowfin seabream under 14-days starvation stress were analyzed. One hundred sixty differentially expressed genes (DEGs) by RNA-Seq analysis and 737 differentially methylated-related genes by whole genome bisulfite sequencing analysis were identified. GO and KEGG pathway enrichment analysis found that energy metabolism-related pathways such as glucose metabolism and lipid metabolism were in response to starvation. Using bisulfite sequencing PCR, we confirmed the presence of CpG methylation differences within the regulatory region of a DEG ppargc1a in response to 14-days starvation stress. This study revealed the molecular responses of livers in response to starvation stress at the transcriptomic and whole genome DNA methylation levels in yellowfin seabream.

Asymmetric Price Transmission and Market Power: A Case of the Aquaculture Product Market in China

In the aquaculture product market, the efficiency of vertical price transmission is an important manifestation, representing the marketization level of aquatic products. When the price of any sector in the aquatic product industry chain fluctuates slightly, the welfare of each sector will be affected accordingly. This study focuses on carp, the main freshwater fish in China, to explore the relationship between asymmetric price transmission and market power. We use the nonlinear autoregressive distributed lag model to simultaneously describe the short- and long-term asymmetric effects of wholesale-to-retail prices for carp, and apply the asymmetric autoregressive conditional heteroskedasticity model to analyze the differences in market power between wholesalers and retailers. The results confirm the evidence of a nonlinear cointegration between wholesale and retail prices in the carp market. There are also significant asymmetric effects in both the short- and long-term transmission speed and degree of price transmission from the wholesale to the retail market. It is evident that carp wholesalers have strong control over the price, resulting in an asymmetric effect in vertical price transmission, indicating a need to improve the development level and integration degree in the Chinese aquatic products market. Subsequently, the government should develop effective systems for aquatic product circulation, strengthen supervision over the aquatic product wholesale market, and establish a public aquatic product price platform to promote the healthy and stable development of China’s aquatic product market.

Distribution Pattern of Coral Reef Fishes in China

Coral reefs are known as “tropical rain forests” in the ocean. Fish diversity is extremely high, accounting for one-third of marine fishes. To better protect and manage coral reef fishes, this study systematically compiled documents and databases published in China. We counted 2855 species of coral reef fishes in China, which belong to 3 classes, 41 orders, 252 families, and 1017 genera. Among these, Perciformes was the dominant order, accounting for 57.31% of the total species. Gobiidae (7.43%), Labridae (5.36%), Pomacentridae (4.52%), and Serranidae (4.38%) were the main families, while other families accounted for less than 4%. Furthermore, 5.56% of coral reef fish species have entered the IUCN Red List. The present study found that coral reef fishes can be divided into nearshore and offshore. This was mainly because the nearshore coral reef fishes were more affected by human disturbance and runoff from the mainland, whereas offshore coral reef fishes were in areas with high salinity and temperature far from the mainland, where human disturbance was less. Coral reef fish species’ diversity had a significant positive correlation with coral species diversity (p &lt; 0.05), mainly because corals provide habitat and shelter. This study is the first systematic compilation and analysis of coral reef fishes in China and provides a basic reference for global protection management and biological geographical analysis.

COVID-19's effect on the spatial integration of fish markets: Evidence from carp price in China

While curbing the spread of Coronavirus Disease 2019 (COVID-19), lockdown policies and “stay-at-home” restrictions caused massive supply chain disruptions worldwide. This led to breaks in spatial market integration, which could further lead to market inefficiency and resource misallocation. Taking daily price data from 2016 to 2021, this study investigates COVID-19's effect on the spatial market integration of fish in China using cointegration tests. We find a high degree of spatial market integration for fish in China before the COVID-19 pandemic. Further, our results show that COVID-19's effect on the spatial market integration of fish varies spatially in China. Specifically, COVID-19 reduces the degree of spatial market integration in most provinces, especially those with high infection rates. Meanwhile, the degree of spatial market integration in provinces with low infection rates remains high. Therefore, the government should be regionally specific when formulating market recovery policies.

Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (Acanthopagrus schlegelii).

Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations (p < 0.05) or extremely significant correlations (p < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy-Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process.

Generation of myostatin gene-edited blotched snakehead (Channa maculata) using CRISPR/Cas9 system

Blotched snakehead (Channa maculata) is one of the most important freshwater fish in China. Genome editing is of great potential in generating new snakehead strains with valuable economic traits without integration of exogenous genes. Myostatin (Mstn) inhibits the development and growth of skeletal muscle in vertebrates, including teleosts. Mstn mutations induced by genome editing can stimulate muscle growth and development, therefore Mstn is an appropriate candidate to breed the fast-growing snakehead strain. For this study, one orthologous Mstn gene was characterized in C. maculata, designated as CmMstn, which possessed the relatively conserved gene and protein structure. CmMstn had the highest expression level and sexual dimorphism in muscles. Two CRISPR/Cas9 target sites were designed to generate knockout mutants within the mature mRNA sequence of CmMstn located in Exon I and Exon II. 1 nL mixture solution of 200 pg gRNA and 300 pg Cas9 protein was directly microinjected into each snakehead embryonic yolk at 1⁓4 cell stage. Mstn was efficiently edited by CRISPR/Cas9 system in shakehead, and all designed gRNAs effectively worked at their target sites with high mutagenesis efficiencies, from 40.0% to 53.3%. The majority of mutations were frame-shift and resulted in premature termination of transcription and disruption of the molecular function of CmMstn protein. Furthermore, we obtained four founders (F0) of snakehead with the mutated Mstn gene in their primordial germ cells, and nineteen F1 offspring of the F0 mutants mated with wild-type individuals were displayed to carry Mstn null alleles. It is the first application of genome editing technology in blotched snakehead, and CRISPR/Cas9 system successfully edit the primordial germ cells. Our findings will accelerate our understanding of the role of Mstn gene in snakehead growth, and speed up the cultivation of the fast-growing snakehead strain.

Genetic analysis of hypermelanosis in Chinese tongue sole (Cynoglossus semilaevis)

Chinese tongue sole (Cynoglossus semilaevis) is an economically important marine fish in China. Generally, the eyeless side of the Chinese tongue sole is white and the side with eyes is brown after metamorphosis, hypermelanosis may still occur in the eyeless side in certain individuals after metamorphosis, which greatly decreases consumer acceptance and market price. In order to study the possibility of genetic improvement, we determined genomic markers in Chinese tongue sole using the genotyping-by-sequencing method and analyzed their association with hypermelanosis area. Genetic analysis showed that hypermelanosis was a complicated quantitative trait, and the estimated heritability for hypermelanosis incidence and area ratio were 0.16 and 0.21, respectively. Genomic selection analysis showed that selection based on hypermelanosis incidence and area ratio had similar reliabilities and prediction accuracies, indicating the feasibility of genetic improvement. Nine loci were significantly associated with hypermelanosis, few of which included genes or flanked genes potentially associated with skin disease, indicating the potential complicated genetic mechanisms underlying hypermelanosis in the Chinese tongue sole.

Establishment of the first cell line from the small yellow croaker (Larimichthys polyactis) and its application in unraveling the mechanism of ROS-induced apoptosis under hypoxia

Cell lines play an important role in studying biological processes in vitro. In this study, we aimed to establish and characterize the first cell line isolated from the small yellow croaker (Larimichthys polyactis), an economically important marine fish in China. The small yellow croaker fry (SYCF) cells proliferated well in Leibovitz's 15 medium containing 2% antibiotics, 0.1 M NaCl, and 10% fetal bovine serum at 27 °C. Sequence analyses of mitochondrial genes confirmed the origin of SYCF cells. Furthermore, we unraveled the mechanism of hypoxia-induced apoptosis, a major threat to aquatic animals using the SYCF cell line. The HIF-PHD pathway of the SYCF cells can be activated under hypoxic stress, suggesting that this cell line is impressible for hypoxia and can serve as a superb model in vitro to study the cell physiology in L. polyactis in a hypoxic setting. We found that hypoxia results in morphological abnormalities, excess reactive oxygen species (ROS) production, and dysfunctional redox homeostasis, indicating the occurrence of oxidative stress in the SYCF cells. In addition, decreased cell viability and severe apoptosis were detected under hypoxic conditions. Through monitoring the indicators of the intrinsic and extrinsic apoptosis pathways, including the mitochondrial membrane potential, the expression of bax, bcl2, bnip3, and fas, Bcl2, and Caspase-3 protein, and activity of Caspases-3/8/9, we found that both pathways are involved. Considering that ROS-induced oxidative stress may be the main reason of apoptosis, we investigated whether the addition of an antioxidant, N-Acetyl-L-cysteine (NAC), will ameliorate the apoptosis. Interestingly, we found that both intrinsic and extrinsic apoptosis indicators were markedly recovered by adding NAC in culture media, significant remissions were also observed in the cell viability and apoptosis rate. These results suggested that hypoxia-induced apoptosis of SYCF cells may be mediated by the overproduction of ROS, and the antioxidant may be a useful material to relieve cell damage under hypoxia in fish. In general, this study established a marine fish cell line of SYCF cells, which can be used as an in vitro research model of L. polyactis and for revealing the mechanisms of ROS-induced apoptosis under hypoxic conditions in this species. This provides important insights into the cellular physiology of marine fish under hypoxia.

Identification and characterization of lncRNAs and the interaction of lncRNA-mRNA in Epinephelus coioides induced with Singapore grouper iridovirus infection

Singapore grouper iridovirus (SGIV) is a highly pathogenic double-stranded DNA virus, and the fatality rate of SGIV-infected grouper is more than 90%. Up to now, there is no effective methods to control the disease. Long non-coding RNAs (lncRNAs) might play an important role in individual growth and development, immune regulation and other life processes. In this study, lncRNAs were identified in Epinephelus coioides, an important economic aquaculture marine fish in China and Southeast Asia, and the regulatory relationships of lncRNAs and mRNA response to SGIV infection were analyzed. A total of 11,678 lncRNAs were identified and classified from the spleen and GS (grouper spleen) cells. 105 differentially expressed lncRNAs (DElncRNAs) were detected during SGIV infection. The lncRNAs and the regulated mRNAs were analyzed using co-expression network, lncRNA target gene annotation and GO enrichment. At 24 and 48 h after SGIV infection, 118 and 339 lncRNA-mRNA pairs in GS cells were detected, and 728 and 688 differentially expressed lncRNA-mRNA pairs in spleen were obtained, respectively. GO and KEGG were used to predict the DE lncRNAs' target genes, and deduce the DE lncRNAs-affected signaling pathways. In GS cells, lncRNAs might participate in cell part, binding and catalytic activity; and lncRNAs might be involved in immune system process and transcription factor activity in spleen. These data demonstrated that lncRNAs could regulate the expression of immune-related genes response to viral infection, and providing a new insight into understanding the complexity of immune regulatory networks mediated by lncRNAs during viral infection in teleost fish.

Quick detection of Carassius auratus herpesvirus (CaHV) by recombinase-aid amplification lateral flow dipstick (RAA-LFD) method.

Crucian carp (Carassius auratus) is one of the major freshwater species and is also a common food fish in China. Recently, Carassius auratus herpesvirus (CaHV) could induce fatal viral disease with high mortality of crucian carp, which had caused huge economic losses. In this study, we described a rapid and simple recombinase-aid amplification (RAA) assay coupled with lateral flow dipstick (LFD), which could achieve sensitive diagnosis of tumor necrosis factor receptor (TNFR) of CaHV within 35 min at 40°C. Our RAA-LFD method had a satisfactory detection limit of 100 gene copies per reaction, which was 100-fold more sensitive than traditional PCR. In addition, no cross-reaction was observed with other viral pathogens, including koi herpesvirus (KHV), cyprinid herpesvirus 2 (CyHV-2), infectious hematopoietic necrosis virus (IHNV), spring viremia of carp virus (SVCV) and grass carp reovirus (GCRV). Furthermore, the overall cost of the method was cut in half compared to previous studies. In conclusion, RAA-LFD assay is therefore, a promising alternative for point-of-care testing (POCT) of CaHV, which is feasible and of certain value in application of aquatic disease control.

Genome-wide characterization of three IGFs in hybrid yellow catfish (Pseudobagrus fulvidraco ♀× Pseudobagrus vachellii ♂) and the association of IGF2 allelic variants with growth traits

“Huangyou No. 1”, a new hybrid yellow catfish (Pseudobagrus fulvidraco ♀× Pseudobagrus vachellii ♂) with heterosis in growth traits, is an economically important freshwater fish in China. Among genes related to growth traits, Insulin-like growth factors (IGFs) are recognized as key factors during embryonic development and growth period. Thus, we identified and characterized IGF1, IGF2 and IGF3 gene from hybrid yellow catfish. Phylogenetic analysis showed that the IGF genes were evolutionarily-constrained and their function was conserved. Transcriptional studies indicated that three IGF mRNA expression were most abundant in liver, despite the ubiquitous expression in nine tested tissues. Further, two opposite temporal expression patterns were observed in these three IGF genes during 16 embryogenesis and larval development stages of hybrid yellow catfish, of which IGF2 and IGF3 shared the similar profile highly expressed after gastrula. Finally, single nucleotide polymorphisms (SNPs) of IGF2 were screened and genotyped in 264 hybrid yellow catfish by Sanger sequencing. Only a non-synonymous mutation (SNP 97 T > C) obeyed Hardy-Weinberg equilibrium. Association analysis indicated SNP 97 T > C significantly associated with nine growth traits (body length, full length, head length, body height, caudal peduncle height, caudal peduncle length, body width, body weight and fatness; P < 0.05). This association was also validated in a second population with 183 individuals. Overall, results from our studies highlight the importance of IGF system in mediating growth development of hybrid yellow catfish, and provide a potential marker for “Huangyou No. 1” breeding.

A chromosome-level genome assembly of the redfin culter (Chanodichthys erythropterus)

Chanodichthys erythropterus is a fierce carnivorous fish widely found in East Asian waters. It is not only a popular food fish in China, it is also a representative victim of overfishing. Genetic breeding programs launched to meet market demands urgently require high-quality genomes to facilitate genomic selection and genetic research. In this study, we constructed a chromosome-level reference genome of C. erythropterus by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. The 1.085 Gb C. erythropterus genome was assembled from 132 Gb of Nanopore sequence. The assembled genome represents 98.5% completeness (BUSCO) with a contig N50 length of 23.29 Mb. The contigs were clustered and ordered onto 24 chromosomes covering roughly 99.49% of the genome assembly with Hi-C data. Additionally, 33,041 (98.0%) genes were functionally annotated from a total of 33,706 predicted protein-coding sequences by combining transcriptome data from seven tissues. This high-quality assembled genome will be a precious resource for future molecular breeding and functional genomics research of C. erythropterus.