Chromosome-level genome assembly of Acrossocheilus fasciatus using PacBio sequencing and Hi-C technology.

Acrossocheilus fasciatus (Cypriniformes, Cyprinidae) is emerged as a newly commercial stream fish in the south of China with high economic and ornamental value. In this study, a chromosome-level reference genome of A. fasciatus was assembled using PacBio, Illumina and Hi-C sequencing technologies. As a result, a high-quality genome was generated with a size of 879.52 Mb (accession number: JAVLVS000000000), scaffold N50 of 32.7 Mb, and contig N50 of 32.7 Mb. The largest and smallest scafford was 60.57 Mb and 16 kb, respectively. BUSCO analysis showed a completeness score of 98.3%. Meanwhile, the assembled sequences were anchored to 25 pseudo-chromosomes with an integration efficiency of 96.95%. Additionally, we found approximately 390.91 Mb of repetitive sequences that accounting for 44.45% of the assembled genome, and predicted 24,900 protein-coding genes. The available genome reported in the present study provided a crucial resource to further investigate the regulation mechanism of genetic diversity, sexual dimorphism and evolutionary histories.

Molecular characterization and functional analysis of galectin-1 from silver pomfret (Pampus argenteus).

Galectins, as members of lectin families, exhibit a high affinity for ß-galactosides and play diverse roles in biological processes. They function as pattern recognition receptors (PRRs) with important roles in immune defense. In this study, galectin-1, designated as SpGal-1, was identified and characterized from silver pomfret (Pampus argenteus). The SpGal-1 comprises an open reading frame (ORF) spanning 396 base pairs (bp) and encodes a deduced amino acid (aa) sequence containing a single carbohydrate recognition domain (CRD). Sublocalization analysis revealed that SpGal-1 was mainly expressed in the cytoplasm. The mRNA transcripts of SpGal-1 were ubiquitously detected in various tissues, with a higher expression level in the intestine. In addition, when exposed to Photobacterium damselae subsp. damselae (PDD) infection, both the liver and head kidney exhibited significantly increased SpGal-1 mRNA expression. The recombinant protein of SpGal-1 (named as rSpGal-1) demonstrated hemagglutination against red blood cells (RBCs) from Larimichthys crocea and P. argenteus in a Ca2+ or ß-Mercaptoethanol (ß-ME)-independent manner. Notably, rSpGal-1 could bind with various pathogen-associated molecular patterns (PAMPs) including D-galactose, D-mannose, lipopolysaccharide (LPS), and peptidoglycan (PGN), with highest affinity to PGN. Moreover, rSpGal-1 effectively interacted with an array of bacterial types encompassing Gram-positive bacteria (Staphylococcus aureus and Nocardia seriolae) and Gram-negative bacteria (PDD and Escherichia coli, among others), with the most robust binding affinity towards PDD. Collectively, these findings highlight that SpGal-1 is a crucial PRR with involvement in the host immune defense of silver pomfret.

Identification and functional characterization of Caspase-9 in goldfish (Carassius auratus L.) in response to Aeromonas hydrophila infection.

Apoptosis plays a pivotal role in the immune response to combat pathogen infections. In mammals, caspase-9, abbreviated as Casp9, plays an irreplaceable role in the initiation phase of the apoptotic cascade. To investigate the role of Casp9 in teleosts, we conducted a functional characterization of Casp9 in goldfish (Carassius auratus L.). The open reading frame of GfCasp9 spans 1296 base pairs (bp), encoding a protein composed of 431 amino acids. GfCasp9 was ubiquitously expressed in various tissues, with the spleen and brain showing the highest levels of expression. Subcellular localization analysis revealed that GfCasp9 is distributed in both the cytoplasm and nucleus. Overexpressing of GfCasp9 in HEK293 cells elicits a robust apoptotic response. Additionally, infection with Aeromonas hydrophila significantly increases the mRNA and protein expression of GfCasp9. These findings underscore the critical importance of GfCasp9 in immune responses and apoptosis against bacterial infections.

Identification and functional characterization of Interleukin-11 in goldfish (Carassius auratus L.).

Interleukin-11 (IL-11) is a versatile cytokine that modulates cellular differentiation and proliferation in various cell types and tissues. In this study, IL-11 gene from goldfish (Carassius auratus L.) has been identified and characterized. Goldfish IL-11 (gfIL-11) has an open reading frame (ORF) that spans 591 base pairs (bp). The ORF encodes a precursor protein consisting of 196 amino acids (aa), which includes a 26 aa signal peptide and a conserved domain belonging to the IL-11 superfamily. Based on phylogenetic analysis, gfIL-11 was found to be closely related to other IL-11 homologues identified in various fish species. The gfIL-11 transcript exhibited varied expression levels across all the analyzed tissues, with the highest expression observed in the gill and spleen. Treatment of goldfish head kidney leukocytes (HKLs) with LPS and live Aeromonas hydrophila, increased gfIL-11 mRNA expression level. Recombinant gfIL-11 protein (rgIL-11) induced a dose-dependent production of TNF-α and IFNγ from goldfish HKLs. Furthermore, the administration of rgIL-11 to goldfish HKLs triggered an increase in the expression of various transcription factors such as MafB, cJun, GATA2, and Egr1, which play a vital role in the differentiation of myeloid precursors into macrophages and monocytes. Our findings provide evidence that IL-11 is a crucial cytokine that promotes cell proliferation, immune response, and differentiation across various hematopoietic lineages and stages of goldfish.

Molecular characterization, gene expression and functional analysis of goldfish (Carassius auratus L.) macrophage colony stimulating factor 2.

Background: Macrophage colony-stimulating factor 2 (MCSF-2) is an important cytokine that controls how cells of the monocyte/macrophage lineage proliferate, differentiate, and survive in vertebrates. Two isoforms of MCSF have been identified in fish, each exhibiting distinct gene organization and expression patterns. In this study, we investigated a goldfish MCSF-2 gene in terms of its immunomodulatory and functional properties. Methods: In this study, goldfish were acclimated for 3 weeks and sedated with TMS prior to handling. Two groups of fish were used for infection experiments, and tissues from healthy goldfish were collected for RNA isolation. cDNA synthesis was performed, and primers were designed based on transcriptome database sequences. Analysis of gfMCSF-2 sequences, including nucleotide and amino acid analysis, molecular mass prediction, and signal peptide prediction, was conducted. Real-time quantitative PCR (qPCR) was used to analyze gene expression levels, while goldfish head kidney leukocytes (HKLs) were isolated using standard protocols. The expression of gfMCSF-2 in activated HKLs was investigated, and recombinant goldfish MCSF-2 was expressed and purified. Western blot analysis, cell proliferation assays, and flow cytometric analysis of HKLs were performed. Gene expression analysis of transcription factors and pro-inflammatory cytokines in goldfish head kidney leukocytes exposed to rgMCSF-2 was conducted. Statistical analysis using one-way ANOVA and Dunnett's post hoc test was applied. Results: We performed a comparative analysis of MCSF-1 and MCSF-2 at the protein and nucleotide levels using the Needleman-Wunsch algorithm. The results revealed significant differences between the two sequences, supporting the notion that they represent distinct genes rather than isoforms of the same gene. Sequence alignment demonstrated high sequence identity with MCSF-2 homologs from fish species, particularly C. carpio, which was supported by phylogenetic analysis. Expression analysis in various goldfish tissues demonstrated differential expression levels, with the spleen exhibiting the highest expression. In goldfish head kidney leukocytes, gfMCSF-2 expression was modulated by chemical stimuli and bacterial infection, with upregulation observed in response to lipopolysaccharide (LPS) and live Aeromonas hydrophila. Recombinant gfMCSF-2 (rgMCSF-2) was successfully expressed and purified, showing the ability to stimulate cell proliferation in HKLs. Flow cytometric analysis revealed that rgMCSF-2 induced differentiation of sorted leukocytes at a specific concentration. Moreover, rgMCSF-2 treatment upregulated TNFα and IL-1ß mRNA levels and influenced the expression of transcription factors, such as MafB, GATA2, and cMyb, in a time-dependent manner. Conclusion: Collectively, by elucidating the effects of rgMCSF-2 on cell proliferation, differentiation, and the modulation of pro-inflammatory cytokines and transcription factors, our findings provided a comprehensive understanding of the potential mechanisms underlying gfMCSF-2-mediated immune regulation. These results contribute to the fundamental knowledge of MCSF-2 in teleosts and establish a foundation for further investigations on the role of gfMCSF-2 in fish immune responses.

Molecular and functional characterization of two granulocyte colony stimulating factors in goldfish (Carassius auratus L.).

Granulocyte colony-stimulating factor (GCSF) is a member of the hematopoietic growth factor family that acts primarily on neutrophils and neutrophilic precursors to promote cell proliferation and differentiation. Although multiple GCSF genes have been found in teleosts, knowledge of their functions during fish hematopoietic development is still limited. Here, we report for the first time the molecular and functional characterization of two goldfish GCSFs (gfGCSF-a and gfGCSF-b). The open reading frame (ORF) of the gfGCSF-a and gfGCSF-b cDNA transcript consisted respectively of 624 bp and 678 bp with its ORF encoding 207 and 225 amino acids (aa), with a 17 aa signal peptide for each gene and a conserved domain of the IL-6 superfamily. Treatment of goldfish head kidney leukocytes (HKLs) with LPS increased gfGCSF-a and gfGCSF-b mRNA expression levels, also exposure of HKLs to either heat-killed or live A. hydrophila, induced transcriptional upregulation of gfGCSF-a and gfGCSF-b levels. Recombinant gfGCSF-a and gfGCSF-b protein (rgGCSF-a and rgGCSF-b) induced a dose-dependent production of TNFα and IL-1ß from goldfish neutrophils. In vitro experiments showed rgGCSF-a and rgGCSF-b differentially promoted the proliferation and differentiation of leukocytes in goldfish. Furthermore, treatment of HKLs with rgGCSF-a showed significant upregulation of mRNA levels of the hematopoietic transcription factor GATA2, Runx1, MafB, and cMyb, while gfGCSF-b induces not only all four transcriptional factors mentioned above but also CEBPα. Our results indicate that goldfish GCSF-a and GCSF-b are important regulators of neutrophil proliferation and differentiation, which could stimulate different stages and lineages of hematopoiesis.

Transcriptome profiling and differential expression analysis of altered immune-related genes in goldfish (Carassius auratus) infected with Aeromonas hydrophila.

Goldfish (Carassius auratus) have been employed as a model organism to investigate the innate immune system and host-pathogen interactions. A Gram-negative bacterium called Aeromonas hydrophila has been found to cause mass mortality due to infection in a wide variety of fish species in the aquatic system. In this study, damages in Bowman's capsule, inflammatory tubular (proximal and distilled convoluted) structure, and glomerular necrosis were observed in A. hydrophila-infected head kidney of goldfish. To increase the better understanding of immune mechanisms of host defense against A. hydrophila, we performed a transcriptome analysis in head kidney of goldfish at 3 and 7 days of post-infection (dpi). Comparing to the control group, 4638 and 2580 differentially expressed genes (DEGs) were observed at 3 and 7 dpi, respectively. The DEGs were subsequently enriched in multiple immune-related pathways including Protein processing in endoplasmic reticulum, Insulin signaling pathway, and NOD-like receptor signaling pathway. The expression profile of immune-related genes such as TRAIL, CCL19, VDJ recombination-activating protein 1-like, Rag-1, and STING was validated by qRT-PCR. Furthermore, the levels of immune-related enzyme (LZM, AKP, SOD, and CAT) activities were examined at 3 and 7 dpi. The knowledge gained from the current study will be helpful for better understanding of early immune response in goldfish after A. hydrophila challenge, which will aid in future research on prevention strategies in teleost.

Characterization of the pro-inflammatory roles of the goldfish (Carassius auratus L.) M17 protein.

The interleukin-6 family of cytokines possesses a diversity of roles with significant redundancy. The roles of these molecules have been relatively well characterized in mammals, with limited attention in other species. Progress has been made in the discovery of homologous molecules in fish. Here we report the characterization of pro-inflammatory properties of recombinant goldfish M17. Recombinant goldfish M17 enhanced phagocytosis, primed production of reactive oxygen intermediates, and was chemotactic to macrophages. Treatment of goldfish macrophages with LPS, heat-killed and live Aeromonas hydrophila resulted in higher M17 mRNA levels. Recombinant M17 (RgM17) induced dose-dependent production of IFNγ and IL-1ß1 in goldfish macrophages. Furthermore, treatment of macrophages with rgM17 resulted in upregulation of transcription factors that were important in the differentiation of myeloid progenitors into monocytes/macrophages (Runx1 and GATA2). Our results indicate that goldfish M17 is an essential inflammatory cytokine for proliferation and differentiation of goldfish progenitor cells.

Nigericin treatment activates endoplasmic reticulum apoptosis pathway in goldfish kidney leukocytes.

Nigericin has been reported to induce apoptosis and pyroptosis in mammalian models. However, the effects and mechanism underlying the immune responses of teleost HKLs induced by nigericin remain enigmatic. To decipher the mechanism after nigericin treatment, the transcriptomic profile of goldfish HKLs was analyzed. The results demonstrated that a total of 465 differently expressed genes (DEGs) with 275 up-regulated and 190 down-regulated genes were identified between the control and nigericin treated groups. Among them, the top 20 DEG KEGG enrichment pathways were observed including apoptosis pathways. In addition, the expression level of selected genes (ADP4, ADP5, IRE1, MARCC, ALR1, DDX58) by quantitative real-time PCR showed a significant change after treatment with nigericin, which was generally identical to the expression patterns of the transcriptomic data. Furthermore, the treatment could induce cell death of HKLs, which was confirmed by LDH release and annexin V-FITC/PI assays. Taken together, our results support the idea that nigericin treatment might activate the IRE1-JNK apoptosis pathway in goldfish HKLs, which will provide insights into the mechanisms underlying HKLs immunity towards apoptosis or pyroptosis regulation in teleosts.

Transcriptome profiling and differential expression analysis of the immune-related genes during the acute phase of infection with Photobacterium damselae subsp. damselae in silver pomfret (Pampus argenteus).

Silver pomfret has been widely cultured in China due to its high economic value. Photobacterium damselae subsp. damselae (PDD) is a Gram-negative bacterium that has been shown to infect many fish species. To increase knowledge of the molecular mechanisms of the host defense against PDD, we conducted transcriptome analysis of head kidney in silver pomfret at 24 h and 72 h post-infection (hpi) via Illumina sequencing. The de novo assembly resulted in the identification of 79,063 unigenes, with 59,386 (75.11%) successfully annotated in public databases (NR, NT, KO, Swiss-Prot, Pfam, GO, and KOG databases). Comparison of gene expression profiles between PBS-injected fish (sham control) and PDD-challenged fish revealed 329 and 570 differentially expressed genes (DEGs) were screened at 24 hpi and 72 hpi, respectively. The DEGs were enriched in multiple immune-related pathways such as Hepatitis C, Gastric acid secretion, CAMs and Leukocyte transendothelial migration pathways, Primary immunodeficieny, ECM-receptor interaction, PI3K-Akt signaling pathway. The data obtained in the present study offers valuable information for acute immune response of silver pomfret challenged with PDD, which will facilitate further investigations on strategies against Photobacterium spp. infection in teleosts.

Outbreak of Cryptocaryon irritans infection in silver pomfret Pampus argenteus cultured in China.

Silver pomfret Pampus argenteus is a major cultivated marine fish species with a high market value. In summer 2021, Cryptocaryon irritans, a ciliate parasite, infected the cultured silver pomfret in aquaculture ponds in Ningbo, Zhejiang Province, China. The symptoms of infected fish include white spots on the skin and fins, increased body surface mucus, loss of appetite, irritability, and shedding of scales. After collecting white spots from moribund fish, the 18S ribosomal RNA sequence of the pathogen on the fish skin was amplified by PCR; phylogenetic analysis showed that it was closely related to C. irritans strains from Ningde, Fujian, China. Four groups of silver pomfret were tested in an artificial infection experiment over the course of 72 h, consisting of 3 infected groups (1600, 4000, and 8000 theronts fish-1) and 1 healthy group. White spots were observed on the skin and fins of the infected fish, but not on their gills. Samples were taken from the gills, liver, kidney, and spleen of both infected and healthy fish and were compared to evaluate any significant histopathological differences. As the dose of infection increased, symptoms became more pronounced. At 72 h, mortality rates were 8.3, 50, and 66.7% for the 3 different concentrations, respectively. The median lethal concentration was calculated to be 366 theronts g-1 at 72 h, 298 theronts g-1 at 84 h, and 219 theronts g-1 at 96 h. This study emphasizes the importance of developing early diagnosis methods and appropriate prevention strategies to decrease the impact of C. irritans infection in the silver pomfret aquaculture industry.

Medical Image Recognition Technology in the Effect of Substituting Soybean Meal for Fish Meal on the Diversity of Intestinal Microflora in Channa argus.

Purpose: To study the application of medical image recognition technology based on backpropagation neural network (BPNN) in the effect of soybean meal replacing fish meal on intestinal microbial diversity of Channa argus and to evaluate the application value of this intelligent algorithm, Channa argus was fed with different contents of soybean meal instead of fish meal. Methods: After intestinal samples were collected and bacteria were isolated, microscopic imaging was performed, and the images were classified and identified. BPNN was constructed to perform denoising, smoothing, and segmentation. Results: After BPNN processing, the bacteria were completely separated from the original image background, and the bacteria was in the closed state, which was beneficial to feature extraction and species recognition. If there were 2 hidden layer nodes, the segmentation accuracy of bacterial microscopic images was the highest, up to 97.3%. With the replacement ratio of fish meal increased, the species of intestinal microbiome gradually enriched, and the relative abundance of intestinal microbiome was higher after fish meal was completely replaced by soybean meal (replacement). The intestinal microbial enzyme activities were affected by different fish meal and soybean meal contents in the diet. The glutamate transaminase and adenosine deaminase activities were increased after the replacement and were higher than those before the replacement, with statistically significant differences (P < 0.05). Conclusion: Replacement of fish meal with soybean meal has a significant effect on the intestinal flora diversity of Channa argus, and there is a close relationship between them. The image recognition technology based on BPNN has high recognition rate and segmentation accuracy for microbiological microscopic images.

The effects of extenders, cryoprotectants and conditions in two-step cooling method on Varicorhinus barbatulus sperm.

In this study, we developed an optimal cryopreservation procedure for Varicorhinus barbatulus sperm. To this end, we optimized (1) the types and dilution ratios of extenders; (2) types and final concentration of cryoprotectants; and (3) freezing conditions, including equilibration time, height above the surface of liquid nitrogen (LN), and the cooling times in the two-step cooling method. The optimum result was obtained when the sperm was diluted at a 1:9 ratio in D-17 with 10% methanol, equilibrated at 4 °C for 10 min, held at 7 cm above LN for 2 min, and finally stored in LN. After storage for 12 h in LN, the sperm was thawed in a water bath at 40 °C for 6s, the post-thaw sperm motility was 66.10 ± 7.12%, while the corresponding rate for fresh sperm was 87.08 ± 2.38%. Using computer-assisted sperm analysis, we found a significant decrease in the motility parameters of post-thaw sperm, especially the parameters related to velocity. To evaluate the effects of cryopreservation on the structural integrity of sperm, transmission electron microscopy and scanning electron microscopy were employed, which showed the defects in frozen sperm, including: abnormal heads, damaged plasma membranes, broken tails, and the disappearance of the mitochondrial internal crest. In addition, we determined the mitochondrial membrane potential to assess the functional integrity of frozen sperm. Our results showed a decrease in the mitochondrial function of frozen sperm. This procedure could be used alongside cryopreservation of V. barbatulus and supports its commercial-scale production and species conservation.

Optimizing protein and lipid levels in practical diet for juvenile northern snakehead fish (Channa argus).

A 3 × 3 factorial feeding trial was conducted to evaluate the production response of juvenile northern snakehead fish (Channa argus). Nine diets containing 3 protein levels (45%, 48% and 51%) and 3 lipid levels (9%, 12% and 15%) were formulated and fed to triplicate groups of juvenile northern snakehead (15.78 ± 0.09 g/fish) for 8 weeks. The formulated diets were named as P45L9, P45L12, P45L15, P48L9, P48L12, P48L15, P51L9, P51L12 and P51L15 (P-Protein, L-Lipid), respectively. Fish fed diets with the lowest protein and lipid combination (P45L9) had the lowest growth performance. Weight gains (WG) of fish fed the 4 diets P48L12, P48L15, P51L9, and P51L12 were not significantly different (P > 0.05), but significantly higher (P < 0.05) than those of fish fed the other diets. Fish fed diets P48L12 and P48L15 had significantly lower (P < 0.05) feed conversion ratios (FCR) than the rest of the treatments. Protein retentions (PR) among fish fed the diets P45L12, P45L15, P48L12, P48L15, P51L9, and P51L12 were similar and significantly higher (P < 0.05) than those of fish fed the remaining diets. Protein sparing effect was observed in the treatments when fish was fed diets containing 45% or 48% dietary protein levels with dietary lipid increased from 9% to 12%. Fish fed diets with 9% lipid tended to have lower viscerosomatic index (VSI), hepatosomatic index (HSI), and whole-body lipid. Increasing dietary protein level significantly increased (P < 0.05) liver moisture and lipid while dietary lipid level increased liver lipid. Intestinal lipase activity increased significantly (P < 0.05) with increasing dietary lipid and protein levels while intestinal α-amylase and protease activities were not significantly influenced (P > 0.05) by dietary treatments. Based on these results, the diet containing 48% protein with either 12% or 15% lipid is the optimal for supporting growth and feed utilization of juvenile northern snakehead under the current testing conditions.

A histological study of testis development and ultrastructural features of spermatogenesis in cultured Acrossocheilus fasciatus.

Testis development and ultrastructural features of spermatogenesis in Acrossocheilus fasciatus (Cypriniformes, Barbinae), a commercial stream fish, were studied using light and electron microscopy. The reproduction cycle in A. fasciatus testes is classified into six successive stages from Stage I to Stage VI. Based on an analysis of previous results, May to July can be confirmed as the best breeding season for A. fasciatus males. During this time, the A. fasciatus testes are in Stage V and the sperm in males is most abundant. In the first reproductive cycle, sexually mature male testes return to Stage III in October, subsequently overwintering at this stage. In the lobular-type testes of A. fasciatus, cystic type spermatogenesis occurs with restricted spermatogonia. All spermatogenic cells at different stages are distributed along the seminiferous lobules, which contain spermatogonia, spermatocytes, spermatids and spermatozoa. At the end of spermatogenesis, spermatogenic cysts open to release spermatozoa into the lobule lumen. Ultrastructural observation of A. fasciatus spermiogenesis reveals that electron-dense substances appear at the different stages of germ cells, from primary spermatogonia to secondary spermatocytes. We have termed these dense substances as "nuage" when free in the cytoplasm or adjacent to the nuclear envelope, while those close to the mitochondria are called inter-mitochondrial cement. The spermatozoa in A. fasciatus can be classified as type I due to the presence of nuclear rotation. Although the nuclear chromatin in the head of sperm was highly condensed, no acrosome was formed. The cytoplasmic canal, a common ultrastructural feature of Teleostei spermatozoa, was also present in the midpiece. In addition, numerous fused mitochondria were observed. The distal centriole and proximal centriole constituting the centriolar complex were oriented incompletely perpendicular to each other. The flagellum showed a typical 9+2 arrangement pattern. Conversely, our study on A. fasciatus yielded no information concerning the lateral fins although an enlarged saclike area was present at the end of some flagella.