Population structure, demographic history and local adaptation of the grass carp

Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production

Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.

Mechanisms of persistent hemolysis-induced middle kidney injury in grass carp (Ctenopharyngodon idella)

Infection-induced hemolysis results in intravascular hemolysis, which releases hemoglobin (Hb) into the tissues. Free Hb exhibits cytotoxic, oxidative, and pro-inflammatory effects, leading to systemic inflammation, vascular constriction dysfunction, thrombosis, and proliferative vascular lesions. Currently, the impact of intravascular hemolysis on the middle kidney in fish is unclear. Here, the injection of phenylhydrazine (PHZ) was used to establish a persistent hemolysis model in grass carp. The determination results revealed that the PHZ-induced hemolysis caused conspicuous tissue damage in the kidneys of grass carp, increased the levels of Cr in the serum and the expression indicators of kidney injury-related genes in the middle kidney. Prussian blue staining indicated that PHZ-induced hemolysis significantly increased the deposition of iron ions in the kidneys of grass carp, and activated the expression levels of iron metabolism-related genes. The results of oxidative damage-related experiments indicate that under PHZ treatment, the activity of middle kidney cells decreases, and the production of oxidative damage markers malondialdehyde (MDA) and 4-hydroxynonenal (4-HNE) increases, simultaneously inhibiting the activity of antioxidant enzymes and upregulating the transcription levels of antioxidant enzyme-related genes. Additionally, the analysis of inflammatory factors revealed a significant upregulation of genes associated with inflammation induced by PHZ-induced hemolysis. The transcriptome analysis was performed to further explore the molecular regulatory effects of hemolysis on tissues, the analysis revealed the treatment of PHZ activated various of programmed cell death (PCD) pathways, including ferroptosis, apoptosis, and autophagy. In summary, this study found that sustained hemolysis in fish results in Hb and iron ion deposition in middle kidney, promoting oxidative damage, ultimately inducing various forms of PCD.

Rapid detection of grass carp reovirus type 1 using RPA-based test strips combined with CRISPR Cas13a system

Introduction

Due to the existence of grass carp reovirus (GCRV), grass carp hemorrhagic disease occurs frequently, and its high pathogenicity and infectivity are great challenges to the aquaculture industry. As a highly pathogenic pathogen, the outbreak of hemorrhagic disease often causes tremendous economic losses. Therefore, it is important to rapidly and accurately detect GCRV on site to control timely.

Methods

In this study, recombinant enzyme amplification (RPA) combined with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a system was employed to establish a method to detect the vp7 gene of grass carp reovirus type 1. This method can be adopted for judging the results by collecting fluorescence signal, ultraviolet excitation visual fluorescence and test strip.

Results

Combined with the RPA amplification experiment, the detection limit of the RPA-CRISPR method can reach 7.2 × 101 copies/μL of vp7 gene per reaction, and the detection process can be completed within 1 h. In addition, this method had no cross-reaction with the other 11 common aquatic pathogens. Then, the performance of the RPA-CRISPR/Cas13a detection method was evaluated by comparing it with the real-time fluorescence quantitative PCR detection method of clinical samples. The results of RPA-CRISPR/Cas13a detection were shown to be in consistence with the results obtained from the real-time fluorescence quantitative PCR detection. The coincidence rate of this method with 26 GCRV clinical samples was 92.31%.

Discussion

In summary, this method has high sensitivity, specificity and on-site practicability for detecting GCRV type 1, and has great application potential in on-site GCRV monitoring.

Identification of Genes Related to Resistance to Ichthyophthirius multifiliis Based on Co-expression Network Analysis in Grass Carp

The ciliate protozoan Ichthyophthirius multifiliis is an essential parasite causing white spot disease in grass carp, leading to significant economic losses. Understanding the molecular basis of grass carp's response to I. multifiliis has important scientific and environmental values. The transcriptional network analysis offers a valuable strategy to decipher the changes in gene expression in grass carp infected with I. multifiliis. Our goal was to screen the genes and pathways involved in resistance to I. multifiliis in grass carp. The different traits exhibited by grass carp infected with I. multifiliis may be caused by the differences in gene expression among grass carp individuals. Herein, to reveal those resistance-associated genes against I. multifiliis infection, we performed RNA sequencing using weighted gene co-expression network analysis (WGCNA). The biological function analysis and hub gene annotation for highly relevant modules revealed that different pathogen recognition and clearance responses resulted in different resistance to I. multifiliis infection. Furthermore, gene enrichment analysis revealed that I. multifiliis invasion in the disease-resistant group mainly activated immune pathways, including scavenger receptor activity and kappa B kinase/NF-kappa B signaling. By the annotation of the highly correlated module of the hub gene, we revealed that the apoptosis and ribosome biogenesis-related genes were enriched in the disease-resistant grass carp. The results of the dark grey module showed that several genes were mainly enriched in the two-component system (ko02020) and steroid biosynthesis (ko00100), suggesting that they are resistance-associated and energy metabolism-associated genes. In the disease resistance group, hub genes mainly included Nlrc3, fos, AAP8, HAP2, HAX, cho2, and zgc:113,036. This study revealed the gene network associated with disease resistance after I. multifiliis infection. The disease resistance-related pathways and central genes identified in this study are candidate references for breeders breeding disease-resistant. The results of this study may also provide some references for the development of drugs to antagonize I. multifiliis infection.

Transcriptome Analysis of the Spleen Provides Insight into the Immune Regulation of GCRV Resistance in Grass Carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is one of the most economically important fish in China, and its production is commonly lost due to GCRV infection. To understand the molecular mechanism of GCRV resistance in grass carp, we compared the spleen transcriptome of the GCRV-resistant and susceptible individuals under GCRV infection (Res-Sus) and the GCRV-resistant individuals under different conditions of injection with GCRV and PBS (Res-Ctl). A total of 87.56 GB of clean data were obtained from 12 transcriptomic libraries of spleen tissues. A total of 379 DEGs (156 upregulated genes and 223 downregulated genes) were identified in the comparison group Res-Ctl. A total of 1207 DEGs (633 upregulated genes and 574 downregulated genes) were identified in the comparison group Res-Sus. And 54 DEGs were shared including immune-related genes of stc2 (stanniocalcin 2), plxna1 (plexin A1), ifnα (interferon alpha), cxcl 11 (C-X-C motif chemokine ligand 11), ngfr (nerve growth factor receptor), mx (MX dynamin-like GTPase), crim1 (cysteine-rich transmembrane BMP regulator 1), plxnb2 (plexin B2), and slit2 (slit guidance ligand 2). KEGG pathway analysis revealed significant differences in the expression of genes mainly involved in immune system and signal transduction, including antigen processing and presentation, Toll-like receptor signaling pathway, natural killer cell-mediated cytotoxicity, and Hippo signaling pathway. This study investigates the immune mechanism of the resistance to GCRV infection in grass carp and provides useful information for the development of methods to control the spread of the GCRV infection.

miR-130a targets CiGadd45bb to modulate the inflammatory response to bacterial infection in Ctenopharyngodon idella kidney (CIK) cells

Septicemia is a systemic inflammatory response to bacterial infection that results in a hyper-inflammatory state, which could lead to septic shock and death in grass carp (Ctenopharyngodon idella). The aim of this study was to determine the underlying mechanism of microRNA (miR-130a) in bacteria-infected grass carp. Expression levels of miR-130a against Aeromonas hydrophila (A. hydrophila) infection in Ctenopharyngodon idella kidney cells (CIK) were analyzed. Luciferase reporter assay, quantitative reverse transcription-polymerase chain reaction were performed to explore whether Ctenopharyngodon idella growth arrest and DNA damage-inducible 45 (CiGadd45bb) was a target of miR-130a. MiR-130a mimic, inhibitor and miR-control were transfected to CIK respectively. After transfection, the expression levels of proinflammatory genes were determined. Here we show that CiGadd45bb as a target of miR-130a. We also confirmed that miR-130a levels were significantly higher after being stimulated for 4 h and lower after 12 h (P < 0.01). Overexpressing miR-130a strikingly inhibited p38, JNK, ERK and TNF-a genes (P < 0.01) and silencing miR-130a activated p38, JNK, ERK, TNF-a, IFN and IL-8 (P < 0.01). Our results provide a theoretical basis for studying the molecular mechanism underlying the regulation of inflammation by miR-130a in grass carp.

Genome-wide DNA methylation reveals potential epigenetic mechanism of age-dependent viral susceptibility in grass carp

Background

Grass carp are an important farmed fish in China that are infected by many pathogens, especially grass carp reovirus (GCRV). Notably, grass carp showed age-dependent susceptibility to GCRV; that is, grass carp not older than one year were sensitive to GCRV, while those over three years old were resistant to this virus. However, the underlying mechanism remains unclear. Herein, whole genome-wide DNA methylation and gene expression variations between susceptible five-month-old (FMO) and resistant three-year-old (TYO) grass carp were investigated aiming to uncover potential epigenetic mechanisms.

Results

Colorimetric quantification revealed that the global methylation level in TYO fish was higher than that in FMO fish. Whole-genome bisulfite sequencing (WGBS) of the two groups revealed 6214 differentially methylated regions (DMRs) and 4052 differentially methylated genes (DMGs), with most DMRs and DMGs showing hypermethylation patterns in TYO fish. Correlation analysis revealed that DNA hypomethylation in promoter regions and DNA hypermethylation in gene body regions were associated with gene expression. Enrichment analysis revealed that promoter hypo-DMGs in TYO fish were significantly enriched in typical immune response pathways, whereas gene body hyper-DMGs in TYO fish were significantly enriched in terms related to RNA transcription, biosynthesis, and energy production. RNA-seq analysis of the corresponding samples indicated that most of the genes in the above terms were upregulated in TYO fish. Moreover, gene function analysis revealed that the two genes involved in energy metabolism displayed antiviral effects.

Conclusions

Collectively, these results revealed genome-wide variations in DNA methylation between grass carp of different ages. DNA methylation and gene expression variations in genes involved in immune response, biosynthesis, and energy production may contribute to age-dependent susceptibility to GCRV in grass carp. Our results provide important information for disease-resistant breeding programs for grass carp and may also benefit research on age-dependent diseases in humans.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12979-022-00285-w.

Transcriptomic Analysis of the Liver and Brain in Grass Carp (Ctenopharyngodon idella) Under Heat Stress

Temperature is a major environmental factor that influences growth, development, metabolism, and physiological performance in fish. Grass carp (Ctenopharyngodon idella) is a highly productive fish in freshwater culture. To understand the molecular mechanism of grass carp under heat stress, we used RNA-Seq to analyze the liver and brain transcriptome of 12 libraries constructed from high-temperature (36 °C) and control (28 °C) groups. We obtained 42.49 and 42.57 GB of clean data from six liver and six brain libraries, respectively, and identified 2,534 genes that were differentially expressed in liver tissue and 1622 in brain tissue (P < 0.05). According to KEGG analysis, significant differences occurred in the expression of genes involved in metabolic and immune pathways, such as the cAMP signaling pathway, apoptosis, calcium signaling pathway, lipid metabolism, and protein processing in endoplasmic reticulum and peroxisome proliferator-activated receptor signaling pathways. This study revealed that high temperature enhanced lipid metabolism, reduced fatty acid synthesis, and disrupted the immune system of grass carp. These results investigated the molecular regulation of heat stress in grass carp and provided valuable information for the healthy culture of grass carp under high temperatures.

Worldwide Population Structure of the Coffee Rust Fungus Hemileia vastatrix Is Strongly Shaped by Local Adaptation and Breeding History

The devastating disease coffee leaf rust, caused by Hemileia vastatrix, has been a major constraint to worldwide coffee production. Recently, H. vastatrix populations were shown to be structured into three divergent genetic lineages with marked host specialization (C1, C2, and C3). However, there is yet no overall understanding of the population dynamics and adaptation of the most widespread and epidemiological relevant H. vastatrix group (C3). We used restriction site-associated DNA sequencing to generate 13,804 single nucleotide polymorphisms (SNPs) across a worldwide collection of 99 H. vastatrix isolates. Phylogenetic analyses uncovered a well-supported structuring within C3, with three main subgroups (SGs; SGI, SGII, and SGIII), which seem to reflect the historical distribution, breeding, and exchange of coffee cultivars. SGI shows a ladder-like diversification pattern and occurs across all four continents sampled, SGII is mainly restricted to Africa, and SGIII is observed only in Timor, revealing a higher genetic differentiation. Outlier and association tests globally identified 112 SNPs under putative positive selection, which impacted population structure. In particular, 29 overlapping SNPs per se seemed to have an extremely strong effect on H. vastatrix population divergence. We also found exclusive and fixed alleles associated with the SGs supporting local adaptation. Functional annotation revealed that transposable elements may play a role in host adaptation. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix on cultivated coffee, showing its strong ability to adapt and the strength of the selective force imposed by coffee hosts, which should be taken into account when designing strategies for pathogen dissemination control and selective breeding.

ddRAD-Seq reveals evolutionary insights into population differentiation and the cryptic phylogeography of Hyporhamphus intermedius in Mainland China

Species differentiation and local adaptation in heterogeneous environments have attracted much attention, although little is known about the mechanisms involved. Hyporhamphus intermedius is an anadromous, brackish-water halfbeak that is widely distributed in coastal areas and hyperdiverse freshwater systems in China, making it an interesting model for research on phylogeography and local adaptation. Here, 156 individuals were sampled at eight sites from heterogeneous aquatic habitats to examine environmental and genetic contributions to phenotypic divergence. Using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in the specimens from the different watersheds, 5498 single nucleotide polymorphisms (SNPs) were found among populations, with obvious population differentiation. We find that present-day Mainland China populations are structured into distinct genetic clusters stretching from southern and northern ancestries, mirroring geography. Following a transplant event in Plateau Lakes, there were virtually no variations of genetic diversity occurred in two populations, despite the fact two main splits were unveiled in the demographic history. Additionally, dorsal, and anal fin traits varied widely between the southern group and the others, which highlighted previously unrecognized lineages. We then explore genotype-phenotype-environment associations and predict candidate loci. Subgroup ranges appeared to correspond to geographic regions with heterogeneous hydrological factors, indicating that these features are likely important drivers of diversification. Accordingly, we conclude that genetic and phenotypic polymorphism and a moderate amount of genetic differentiation occurred, which might be ascribed to population subdivision, and the impact of abiotic factors.

Genotyping-by-Sequencing Reveals the Impact of Restocking on Wild Common Carp Populations of the Southern Caspian Basin

Understanding the population structure and level of genetic diversity of wild populations is fundamental for appropriate stock management and species conservation. The common carp (Cyprinus carpio) is one of the most important bony fish throughout the Southern coastline of the Caspian Sea, but captures of this species have seen a dramatic reduction during the last decade. As a consequence, a restocking program has been put in place to maintain C. carpio populations, but its impact is not clear. In the present study, the population structure and genetic diversity of C. carpio in the Southern Caspian basin was determined using 17,828 single-nucleotide polymorphism (SNP) markers. A total of 117 individuals collected from four different locations in the southern Caspian basin and a farm were genotyped by genotyping-by-sequencing. The overall Fst obtained was 0.04, indicating a low level of differentiation between populations, and most genetic diversity was attributed to within population variation (97%). The low Fst values suggest that frequent migration events between different locations occur, and three migration events were inferred in the present study. However, each population still showed a distinct genetic profile, which allowed distinguishing the origin of the fish. This indicates that the ongoing restocking program is maintaining the differences between populations to some extent. Nonetheless, high inbreeding and low heterozygosity were detected in all populations, suggesting that additional conservation efforts are required to protect C. carpio populations in the Southern coast of the Caspian Sea.

Heterogeneity of the Tissue-specific Mucosal Microbiome of Normal Grass Carp (Ctenopharyngodon idella)

Microbiome plays key roles in the digestion, metabolism, and immunity of the grass carp (Ctenopharyngodon idella). Here, we characterized the normal microbiome of the intestinal contents (IC), skin mucus (SM), oral mucosa (OM), and gill mucosa (GM) of the grass carp, as well as the microbiome of the sidewall (SW) of the raising pool, using full-length 16S rRNA sequencing based on the PacBio platform in this specie for the first time. Twenty phyla, 38 classes, 130 families, 219 genera, and 291 species were classified. One hundred four common classified species might be core microbiota of grass carp. Proteobacteria, Bacteroides, and Cyanobacteria were the dominant phyla in the niche of grass carp. Proteobacteria and Bacteroides dominated the taxonomic composition in the SM, GM, and OM, while Proteobacteria, Planctomycetota, and Cyanobacteria preponderated in the IC and SW groups. Microbiota of IC exhibited higher alpha diversity indices. The microbial communities clustered either in SW or the niche from grass carp, significantly tighter in the SW, based on Bray-Curtis distances (P < 0.05). SM, GM, and OM were similar in microbial composition but were significantly different from IC and SW, while IC had similarity with SW due to their common Cyanobacteria (P < 0.05). Differences were also reflected by niche-specific and differentially abundant microorganisms such as Noviherbaspirillum in the SM and Rhodopseudomonas palustris, Mycobacterium fortuitum, and Acinetobacter schindleri in GM. Significantly raised gene expression was found in IC and SM associated with cell cycle control, cell division, chromosome, coenzyme transport and metabolism, replication, recombination and repair, cell motility, post-translational modification, signal transduction mechanisms, intracellular trafficking, secretion, and vesicles by PICRUSt. This work may be of great value for understanding of fish-microbial co-workshops, especially in different niche of grass carp.

Comparative transcriptome analysis provides novel insights into the molecular mechanism of the silver carp (Hypophthalmichthys molitrix) brain in response to hypoxia stress

The brain of fish plays an important role in regulating growth and adapting to environmental changes. However, few studies have been performed to address the changes in gene expression profiles in fish brains under hypoxic stress. In the present study, silver carp (Hypophthalmichthys molitrix) were kept under hypoxic experimental conditions by using the method of natural oxygen consumption, which resulted in a significant decrease in malondialdehyde (MDA) and glutathione (GSH) content and superoxide dismutase (SOD) activity in the brain. In addition, RNA sequencing (RNA-Seq) was performed to analyze transcriptional regulation in the brains of silver carp under normoxia (control group), hypoxia, semi-asphyxia, and asphyxia conditions. The results of KEGG enrichment pathway analysis showed that the immune system, such as antigen processing and presentation, natural killer cell-mediated cytotoxicity, was enriched in the hypoxia group; the nervous system (e.g., "glutamatergic synapse"), signal transduction (e.g., "calcium signaling pathway"; "foxo signaling pathway"), and signaling molecules and interactions (e.g., "neuroactive ligand-receptor interaction") were enriched in the semi-asphyxia group; and signaling molecules and interactions (e.g., "neuroactive ligand-receptor interaction") were enriched in the asphyxia group. These results provide novel insights into the molecular regulatory mechanism of the fish brain coping with hypoxia stress.

The Oxidative Injury of Extracellular Hemoglobin Is Associated With Reactive Oxygen Species Generation of Grass Carp (Ctenopharyngodon idella)

Intravascular hemolysis is a fundamental feature of hemorrhagic venereal infection or tissue and releases the endogenous damage-associated molecular pattern hemoglobin (Hb) into the plasma or tissues, which results in systemic inflammation, vasomotor dysfunction, thrombophilia, and proliferative vasculopathy. However, how the cytotoxic Hb affects the tissues of grass carp remains unclear. Here, we established a hemolysis model in grass carp by injecting phenylhydrazine (PHZ). The data revealed that the PHZ-induced hemolysis increased the content of Hb and activated the antioxidant system in plasma. The histopathology analysis data showed that the PHZ-induced hemolysis increased the accumulation of Hb and iron both in the head and middle kidney. The results of quantitative real-time PCR (qRT-PCR) detection suggested that the hemolysis upregulated the expressions of iron metabolism-related genes. In addition, the immunofluorescence and immunohistochemistry data revealed that the hemolysis caused an obvious deposition of collagen fiber, malondialdehyde (MDA), and 4-hydroxynonenal (4-HNE) accumulation and increased the content of oxidative-related enzymes such as β-galactosidase (β-GAL), lipid peroxide (LPO), and MDA in both the head and middle kidney. Furthermore, the PHZ-induced hemolysis significantly increased the production of reactive oxygen species (ROS), which resulted in apoptosis and modulated the expressions of cytokine-related genes. Taken together, excess of Hb released from hemolysis caused tissue oxidative damage, which may be associated with ROS and inflammation generation.

Hemeprotein amplifies the innate immune receptors of Ctenopharyngodon idellus kidney cells through NF-κB- and MAPK-dependent reactive oxygen species generation

Infectious bacterial and viral diseases that cause hemolysis are considered life-threatening to grass carp (Ctenopharyngodon idellus), which is a species used in aquaculture worldwide. After heme and hemeproteins (Hb) are released as a result of hemolysis, the effect of excess Hb and heme on tissues remains to be characterized. To decipher the mechanisms, after incubation with Hb, we showed that lipopolysaccharide (LPS), Hb, and heme increased the cytotoxicity and secretion of inflammatory cytokines such as interleukin (IL)-6, chemokine (C-C motif) ligand 1 (CCL1), tumor necrosis factor (TNF)-α, IL-6, and IL-1β in vitro, which was due to stimulation of the expression of innate immune receptors, such as nucleotide-binding oligomerization domain (NOD2), toll-like receptor 2 (TLR2), TLR 4, and TLR3. The formation of reactive oxygen species (ROS) and the activation of mitogen-activated protein kinases (MAPKs) and nuclear factor (NF)-κB were important for increasing the cytokine production to induce heme, Hb, and LPS. Moreover, we confirmed that after LPS, Hb, and heme challenge, superoxide dismutase (SOD) and glutathione (GSH) synthetase (GSS) also caused remarkable destruction. However, catalase (CAT) and heme oxygenase-1 (HO-1) were strongly activated. In summary, our research findings present a framework through which heme and Hb concentrations amplify the secretions of inflammatory cytokines, which are induced by pattern recognition receptor (PRR) activation and present possible paths for immune intervention during infection with viral diseases and hemolytic bacterial.

Hemoglobin induces inflammation through NF-kB signaling pathway and causes cell oxidative damage in grass carp (Ctenopharyngodon idella)

Hemolytic disease in grass carp (C. idella) leads to hemolysis in vivo, releasing damage-related molecular patterns (DAMPs) hemoglobin (Hb; which is rapidly oxidized to Hb-Fe³⁺ and Hb-Fe⁴⁺) and generating a high level of reactive oxygen species (ROS) that cause oxidative damage. However, the effect of cell-free Hb on tissue cells of grass carp has yet to be elucidated. In this study, western blotting (WB) and immunofluorescence analysis (IFA) results showed that PHZ-induced hemolysis caused Hb and iron accumulation, increased the production of ROS and resulted in apoptosis in head kidney and middle kidney of the grass carp. Quantitative real-time PCR (qRT-PCR), WB, and IFA revealed that PHZ-induced hemolysis significantly upregulated the expression of inflammation-related genes through activation of the NF-κB signaling pathway. To further explore the effect of Hb, three forms of Hb (Hb, MetHb, and FerrylHb) were prepared. The incubation with the different forms of Hb and heme markedly upregulated the expression of cytokine genes through NF-κB signaling pathway, which was further confirmed by a specific inhibitor (caffeic acid phenethyl ester, CAPE). Flow cytometry analysis data showed that the stimulation of different forms of Hb and heme increased the production of ROS, and resulted in apoptosis. In summary, our data suggest that the excess cell-free Hb released during hemolysis modulates the inflammatory response through activation of the NF-κB signaling pathway and causes cell oxidative damage and apoptosis.

Molecular and functional characterization of MST2 in grass carp during bacterial infection

The regulation of host redox homeostasis is critically important in the immune response to pathogens. The "mammalian sterile 20-like" kinase 2 (MST2) has been shown to play a role in apoptosis, cell proliferation, and cancer; however, few studies have examined its ability to modulate redox homeostasis during innate immunity, especially in teleost fish. In this study, we cloned the MST2 gene of Ctenopharyngodon idella (CiMST2) and analyzed its tissue distribution. CiMST2 was present in most of the studied tissues, and it was most highly expressed in brain tissue. Expression patterns analysis revealed that MST2 mRNA and protein were significantly up-regulated under bacterial infection, suggesting that it is involved in the immune response. Bacterial stimulation significantly increased the level of antioxidases. To explore the interplay between CiMST2 and antioxidant regulation, we examined the effects of CiMST2 overexpression and conducted RNA interference assays in vitro. CiMST2 overexpression significantly increased the expression levels of nuclear factor E2-related factor 2 (Nrf2) and other antioxidases and vice versa, revealing that CiMST2 regulated host redox homeostasis via Nrf2-antioxidant responsive element (ARE) signaling. Overall, our findings provide a new perspective on the role of MST2 in innate immunity in teleosts as well as insights that will aid the prevention and control of disease in the grass carp farming industry.

Expression and functional analysis of the BCL2-Associated agonist of cell death (BAD) gene in grass carp (Ctenopharyngodon idella) during bacterial infection

The BCL2-associated agonist of cell death protein is a key participant in apoptosis dependent on mitochondria and in disease progression that involves the regulation of cell death, such as tumorigenesis, diabetes, sepsis shock, and epilepsy. Nevertheless, the mechanisms underlying the immune responses to teleost BAD bacterial infection and mitochondrial-dependent apoptosis remains unclear. In order to elucidate the mechanisms involved, in this study, a Ctenopharyngodon idella (grass carp) BAD gene named GcBAD1 was firstly cloned and characterized. The results indicated that the ORF (open reading frame) of GcBAD1 was 438 bp in length, encoding a 145-amino acid putative protein of 16.66 kDa. This deduced amino acid sequence has a better identity than another teleost species according to a phylogenetic analysis, and contains a Bcl2-BAD-1 domain. In healthy grass carp fish, the mRNA transcripts of GcBAD1 were widely present in the studied tissues, which could be ranked as follows; spleen > brain > middle-kidney > head-kidney > liver > gills > intestines > heart and muscle. In addition, during infection by Aeromonas hydrophila and Staphylococcus aureus, the mRNA transcription and protein levels expression of GcBAD1 in the head-kidney, spleen, and liver tissues of the fish were significantly up-regulated. Moreover, when the C. idellus kidney cell line (CIK) cells were incubated with Lipopolysaccharide (LPS) and lipoteichoic acid (LTA), the GcBAD1 expression transcripts were also significantly up-regulated. Additionally, overexpression of GcBAD1 in CIK cells was able to activate apoptosis-related genes, including those encoding p53, Cytochrome C (CytoC), caspase-3, and caspase-9. Besides, in the TUNEL assays, when pEGFP-BAD1 was over-expressed, the number of red signals associated with apoptosis were significantly increased in the CIK cells infected with LPS or LTA at 12 h. This study demonstrates that GcBAD1 has a significant role in the mitochondrial apoptosis pathway of grass carp's innate immunity. Our findings provide new insight into the potential mechanisms of teleost antibacterial immunity.

Psychological Construction and Cultivation of New Entrepreneurs Using Industrial Cluster Theory and Multidimensional Structure Model

This study aims to analyze the influencing factors and training plans of cultivating new entrepreneurs in the new era based on industrial cluster theory. First, the status of the research on the correlation between psychological characteristics and entrepreneurial performance of new entrepreneurs is reviewed. Second, 200 new entrepreneurs in the Xi’an City of Shaanxi Province are randomly selected as the research objects. An empirical model of the correlation between entrepreneurial psychological characteristics and entrepreneurial performance is innovatively proposed. Finally, the questionnaire data are analyzed by correlation analysis and SPSS 26.0 (Chicago) statistical analysis. The results show that most of the entrepreneurs are between 30 and 50 years old, with a larger number of mens, and most graduate from junior colleges. The gender and education level of the new entrepreneurs have a little impact on their entrepreneurial performance (P > 0.05), whereas their age has a significant impact on their entrepreneurial performance (P < 0.05). Moreover, there is a significant correlation between the psychological characteristics of the entrepreneur and the two dimensions of entrepreneurial performance (development and profitability) (P < 0.05). This shows that the key to cultivating new entrepreneurs is to develop their age and psychological characteristics, which can enhance the entrepreneurial ability of new entrepreneurs and provide a basis for cultivating multidimensional entrepreneurial talents in new enterprises.

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of F_ST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (F_IS =  − 0.092) and low total fixation index (F_IT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

Multi-Omics Sequencing Provides Insights Into Age-Dependent Susceptibility of Grass Carp (Ctenopharyngodon idellus) to Reovirus

Grass carp (Ctenopharyngodon idellus) is an important aquaculture species in China that is affected by serious diseases, especially hemorrhagic disease caused by grass carp reovirus (GCRV). Grass carp have previously shown age-dependent susceptibility to GCRV, however, the mechanism by which this occurs remains poorly understood. Therefore, we performed transcriptome and metabolome sequencing on five-month-old (FMO) and three-year-old (TYO) grass carp to identify the potential mechanism. Viral challenge experiments showed that FMO fish were susceptible, whereas TYO fish were resistant to GCRV. RNA-seq showed that the genes involved in immune response, antigen presentation, and phagocytosis were significantly upregulated in TYO fish before the GCRV infection and at the early stage of infection. Metabolome sequencing showed that most metabolites were upregulated in TYO fish and downregulated in FMO fish after virus infection. Intragroup analysis showed that arachidonic acid metabolism was the most significantly upregulated pathway in TYO fish, whereas choline metabolism in cancer and glycerophospholispid metabolism were significantly downregulated in FMO fish after virus infection. Intergroup comparison revealed that metabolites from carbohydrate, amino acid, glycerophospholipid, and nucleotide metabolism were upregulated in TYO fish when compared with FMO fish. Moreover, the significantly differentially expressed metabolites showed antiviral effects both in vivo and in vitro. Based on these results, we concluded that the immune system and host biosynthesis and metabolism, can explain the age-dependent viral susceptibility in grass carp.

RNA-Seq Transcriptome Analysis of the Liver and Brain of the Black Carp (Mylopharyngodon piceus) During Fasting

The black carp (Mylopharyngodon piceus) is an important carnivorous freshwater-cultured species. To understand the molecular basis underlying the response of black carp to fasting, we used RNA-Seq to analyze the liver and brain transcriptome of fasting fish. Annotation to the NCBI database identified 66,609 unigenes, of which 22,841 were classified into the Gene Ontology database and 15,925 were identified in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Comparative analysis of the expression profile between fasting and normal feeding fish revealed 13,737 differentially expressed genes (P < 0.05), of which 12,480 were found in liver tissue and 1257 were found in brain tissue. The KEGG pathway analysis showed significant differences in expression of genes involved in metabolic and immune pathways, such as the insulin signaling pathway, PI3K-Akt signaling pathway, cAMP signaling pathway, FoxO signaling pathway, AMPK signaling pathway, endocytosis, and apoptosis. Quantitative real-time PCR analysis confirmed that expression of the genes encoding the factors involved in those pathways differed between fasting and feeding fish. These results provide valuable information about the molecular response mechanism of black carp under fasting conditions.

The immune function of heme oxygenase-1 from grass carp (Ctenopharyngodon idellus) in response to bacterial infection

Heme oxygenase (HO)-1, a rate-limiting enzyme in heme catabolism, results in the formation of equivalent amounts of biliverdin (BV), carbon monoxide (CO) and ferrous iron (Fe²⁺). Previous studies have revealed that HO-1 plays an important role in immune responses. However, the mechanism underlying the immune responses against bacterial infection of teleost HO-1 remains enigmatic. To decipher the mechanisms, we have cloned and characterized the HO-1 gene of grass carp (designated as GcHO-1) in this research. The results showed that the open reading frame (ORF) of GcHO-1 was 819 bp, which encoded a putative protein of 272 amino acids. The deduced amino acid sequence phylogenetically shared the highest identity with other teleosts, and contained two domains of heme-oxygenase and a single-pass transmembrane domain. The mRNA expressions of GcHO-1 in healthy grass carp have widely existed in examined tissues in the following order of spleen > head-kidney > middle head-kidney > intestines > liver > gills > heart > muscle > brain. Besides, the mRNA and protein transcription of GcHO-1 were both significantly up-regulated in the liver and head-kidney tissues after Staphylococcus aureus and Aeromonas hydrophila infection. In addition, overexpression of GcHO-1 in kidney cell line (CIK) cells of grass carp could reduce the expression of inflammatory cytokines (IL-1β, IL-8, TNFα, CCL1 and IL-6). Herein, we demonstrate that GcHO-1 plays an anti-inflammatory role in innate immunity. Our results shed new light on the mechanisms underlying the antibacterial immunity of teleost.

Fish complement C4 gene evolution and gene/protein regulatory network analyses and simulated stereo conformation of C4-MASP-2 protein complex

Complement C4 is a central protein by acting as pivotal molecule in the activation of the complement system. More than a decade ago, C4 gene duplication had been found in several species including fish, revealing the evolutionary origin of C4 gene. However, the evolutionary pattern and systematic function of C4 are still limited. In this study, C4 D and H types in different species groups were completely diverged. The codon usage of C4 H type in higher vertebrates were much closer to their own genome environment, in contrast to lower vertebrates, suggesting that the evolution may provide the dynamic for homogeneous codon usage between specific gene and genome. Multiple C4 sequence alignment showed that the sequences were conserved among different species. However, sequence similarity was obviously different between species C4 D and H type. Negative selection pressure was found on C4 gene evolution and it may be one of the possible reasons for the sequence broad similarity and conservation among interspecies. Proteins from C4 protein-protein interaction (PPI) network were enriched in more hematopoiesis, infections, diseases and immune-related pathways in human than zebrafish. The result suggested that the functional complexities of C4 isotypes are distinct in species from different evolutionary positions. The simulated C4 protein structures between human and grass carp shared structural similarity and the stereo structures of grass carp C4-MASP-2 protein complexes were further simulated according to a study of human. These results suggested that the interaction between C4 and MASP-2 proteins may also exist in grass carp. Our results can provide an insight for the evolutionary process of C4 and better understanding to the potential mechanism of interaction between C4 and MASP-2 in fish species.

Bacillus subtilis H2 modulates immune response, fat metabolism and bacterial flora in the gut of grass carp (Ctenopharyngodon idellus)

Functional ingredients such as Bacillus subtilis are used in aquaculture to improve fish condition, modulate microbiota and promote a healthy intestinal system. However, the underlying mechanisms of grass carp treated with B. subtilis are not fully characterized. This study investigated the gut microbes of grass carp after treated with B. subtilis H2 (10⁶ CFU/mL) and Aeromonas hydrophila (10⁶ CFU/mL). The intestinal flora was found that the dominant bacterial phyla identified in all samples were Proteobacteria, Actinobacteria, Fusobacteria, Bacteroidetes and Acidobacteria. Compared with the control group, the relative abundance of Proteobacteria and Bacteroidetes in B. subtilis group were significantly increased. In addition, the relative abundances of Aeromonas and Shewanella in A. hydrophila group were more than the control group. For the intestinal transcriptomic profiling of the grass carp treated with B. subtilis H2, 824 different expressed genes (DEGs) between the B. subtilis H2 treated and non-treated groups were detected, including 365 up-regulated and 459 down-regulated genes. Six DEGs were randomly selected for further validation by quantitative real-time RT-PCR (qRT-PCR) and the results were consistent with the RNA-seq data. Additionally, eight immunomodulatory genes (IL-4, IL-11, IFN-α, CSF, FOSB, MAPK12b, IGHV3-11 and IGHV3-21) were significantly up-regulated after treated with B. subtilis H2. Furthermore, almost all the lipid metabolism-associated genes were significantly up-regulated after treated with B. subtilis H2 according to the lipid metabolism pathways. Eleven lipid metabolism-associated genes were selected by qRT-PCR, which showed that the expressions of almost all the selected genes were increased, especially Apob-48, ABCG8 and DGAT. Taken together, our results support that B. subtilis could modulate the immune response, fat metabolism and bacterial assembly in the gut of grass carp.

Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region

The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise F_ST estimates high genetic divergence between wild and domesticated broodstock populations. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture.