Effects of sand substrate removal on the intestinal antioxidant and metabolism in Marsupenaeus japonicus.

M. japonicus is an important specie for factory farming, and factory farming requires an environment with sand at the bottom of the pond. However, the physiological responses as well as survival in the process of factory farming without laying sand are currently unknown. In the present study, we explored the effect of sand substrate removal on the intestinal histomorphology, antioxidant enzyme activity, and metabolic profile of M. japonicus. Our results indicate a gradual increase in the mortality rate of kuruma shrimp in ponds lacking sand substrate. The intestinal mucosa exhibited necrosis and the presence of vacuoles, with their number gradually increasing over time. The intestinal villi showed significant erosion, accompanied by a decrease in intestinal superoxide dismutase (SOD) activity and catalase (CAT) activity, and consistent with an upregulation in the expression of apoptosis-related genes such as caspase-3, indicating an adaptive response to the adverse environmental conditions. Additionally, the metabolomic analysis revealed that most significantly differential metabolites were linked to amino acid and lipid metabolism. These findings enhance our understanding of the sand substrate removal on the intestinal health of kuruma shrimp, which provides a basis for the factory farming.

Effects of eyestalk ablation and seawater temperature on d-glutamate levels in the reproductive tissues of male kuruma prawn Marsupenaeus japonicus.

D-Glutamate, a novel d-amino acid found in animal tissues, exclusively exists in the male reproductive tissues of the kuruma prawn, Marsupenaeus japonicus. Herein, changes in the d-glutamate content were determined in the male reproductive tissues of M. japonicus during acclimation to breeding seawater temperatures of 18-22°C and unilateral eyestalk ablation. The d-glutamate content in the testis increased with increasing seawater temperature and with unilateral eyestalk ablation. This suggests that both stimulations induced d-glutamate synthesis in the testis. Although the d-alanine content in the testis increased after unilateral eyestalk ablation, it did not change with elevated seawater temperature. Furthermore, we determined the d-glutamate distribution in the M. japonicus spermatophore. This indicates that d-glutamate is crucial in prawn fertilization.

Molecular characterization of a short-chained pentraxin gene from kuruma shrimp Marsupenaeus japonicus hemocytes.

Pentraxins (PTXs) are a family of pattern recognition proteins (PRPs) that play a role in pathogen recognition during infection via pathogen-associated molecular patterns (PAMPs). Here, we characterized a short-chained pentraxin isolated from kuruma shrimp (Marsupenaeus japonicus) hemocytes (MjPTX). MjPTX contains the pentraxin signature HxCxS/TWxS (where x can be any amino acid), although the second conserved residue of this signature differed slightly (L instead of C). In the phylogenetic analysis, MjPTX clustered closely with predicted sequences from crustaceans (shrimp, lobster, and crayfish) displaying high sequence identities exceeding 52.67 %. In contrast, MjPTX showed minimal sequence identity when compared to functionally similar proteins in other animals, with sequence identities ranging from 20.42 % (mouse) to 28.14 % (horseshoe crab). MjPTX mRNA transcript levels increased significantly after artificial infection with Vibrio parahaemolyticus (48 h), White Spot Syndrome Virus (72 h) and Yellow Head Virus (24 and 48 h). Assays done in vitro revealed that recombinant MjPTX (rMjPTX) has an ability to agglutinate Gram-negative and Gram-positive bacteria and to bind microbial polysaccharides and bacterial suspensions in the presence of Ca2+. Taken together, our results suggest that MjPTX functions as a classical pattern recognition protein in the presence of calcium ions, that is capable of binding to specific moieties present on the surface of microorganisms and facilitating their clearance.

Characterization and function analysis of cathepsin C in Marsupenaeusjaponicus.

Cathepsin C is a cysteine protease widely found in invertebrates and vertebrates, and has the important physiological role participating in proteolysis in vivo and activating various functional proteases in immune/inflammatory cells in the animals. In order to study the role of cathepsin C in the disease resistance of shrimp, we cloned cathepsin C gene (MjcathC) from Marsupenaeus japonicus, analyzed its expression patterns in various tissues, performed MjcathC-knockdown, and finally challenged experimental shrimps with Vibrio alginolyticus and WSSV. The results have shown the full length of MjcathC is 1782 bp, containing an open reading frame of 1350 bp encoding 449 amino acids. Homology analysis revealed that the predicted amino acid sequence of MjcathC shared respectively 88.42 %, 87.36 % and 87.58 % similarity with Penaeus monodon, Fenneropenaeus penicillatus and Litopenaeus vannamei. The expression levels of MjcathC in various tissues of healthy M. japonicus are the highest in the liver, followed by the gills and heart, and the lowest in the stomach. The expression levels of MjcathC were significantly up-regulated in all examined tissues of shrimp challenged with WSSV or V. alginolyticus. After knockdown-MjcathC using RNAi technology in M. japonicus, the expression levels of lectin and heat shock protein 70 in MjcathC-knockdown shrimp were significantly down-regulated, and the mortality of MjcathC-knockdown shrimp challenged by WSSV and V. alginolyticus significantly increased. Knockdown of the MjcathC reduced the resistance of M. japonicus to WSSV and V. alginolyticus. The above results have indicated that cathepsin C may play an important role in the antibacterial and antiviral innate immunity of M. japonicus.

Regulation Mechanism of Dopamine Receptor 1 in Low Temperature Response of Marsupenaeus japonicus.

Dopamine receptors (DARs) are important transmembrane receptors responsible for receiving extracellular signals in the DAR-mediated signaling pathway, and are involved in a variety of physiological functions. Herein, the D1 DAR gene from Marsupenaeus japonicus (MjDAD1) was identified and characterized. The protein encoded by MjDAD1 has the typical structure and functional domains of the G-protein coupled receptor family. MjDAD1 expression was significantly upregulated in the gills and hepatopancreas after low temperature stress. Moreover, double-stranded RNA-mediated silencing of MjDAD1 significantly changed the levels of protein kinases (PKA and PKC), second messengers (cyclic AMP (cAMP), cyclic cGMP, calmodulin, and diacyl glycerol), and G-protein effectors (adenylate cyclase and phospholipase C). Furthermore, MjDAD1 silencing increased the apoptosis rate of gill and hepatopancreas cells. Thus, following binding to their specific receptors, G-protein effectors are activated by MjDAD1, leading to DAD1-cAMP/PKA pathway-mediated regulation of caspase-dependent mitochondrial apoptosis. We suggest that MjDAD1 is indispensable for the environmental adaptation of M. japonicus.

Distribution and role of d-glutamate, a novel d-amino acid identified in animals, in the reproductive tissues of male kuruma prawn Marsupenaeus japonicus.

Some aquatic invertebrates contain free d-alanine. We previously showed copious amounts of free d-glutamate, a novel d-amino acid, in the tissue of the male reproductive organs of Marsupenaeus japonicus. Herein, we clarified the distribution and potential role of d-glutamate and d-alanine in male reproductive tissues, namely the testis, vas deferens and seminal receptacle at different growth stages of M. japonicus. The percentage of d-glutamate to total glutamate was over 50% in these tissues. In particular, the content of d-glutamate was the most abundant in the vas deferens, the ratio of d-glutamate to total glutamate was approximately 80%. In contrast, d-alanine content was the lowest in the vas deferens among these tissues. d-Glutamate content was the highest when the prawn weighed 12 g, indicating that d-glutamate is actively synthesized in the younger stage. Our findings suggest that d-glutamate plays an important role in the reproductive functions of M. japonicus.

The sORF-Encoded Peptides, ATP Synthase Subunits, Facilitate WSSV Duplication in Shrimp.

Short open reading frames (sORFs) are a newly identified family of genes, and the functions of most sORF genes and their encoded peptides (SEPs) are still unknown. In this study, two ATP synthase subunits were identified in kuruma shrimp (Marsupenaeus japonicus) as SEPs, namely MjATP5I and MjATP5L. They were widely distributed in all of the tested tissues of shrimp and upregulated in hemocytes and intestines in response to WSSV challenge. The injection of recombinant proteins (rMjATP5I and rMjATP5L) increased the expression of Ie1 and Vp28, while the knockdown of MjATP5I and MjATP5L decreased the expression of Ie1 and Vp28. All of the results suggest that MjATP5I and MjATP5L were beneficial for WSSV replication. Further exploration found that MjATP5I and MjATP5L RNAi significantly improved the shrimp survival rates, reduced ATP production, and upregulated the expression of antimicrobial peptide genes post viral challenge, and the two ATPase subunits and Relish negatively regulated each other. These results reveal that MjATP5I and MjATP5L facilitated WSSV duplication by regulating the production of ATP contents and the expression of antimicrobial peptide genes in shrimp.

Integrated analysis of intestinal microbiota and metabolomic reveals that decapod iridescent virus 1 (DIV1) infection induces secondary bacterial infection and metabolic reprogramming in Marsupenaeus japonicus.

In recent years, with global warming and increasing marine pollution, some novel marine viruses have become widespread in the aquaculture industry, causing huge losses to the aquaculture industry. Decapod iridescent virus 1 (DIV1) is one of the newly discovered marine viruses that has been reported to be detected in a variety of farmed crustacean and wild populations. Several previous studies have found that DIV1 can induce Warburg effect-related gene expression. In this study, the effects of DIV1 infection on intestinal health of shrimp were further explored from the aspects of histological, enzymatic activities, microorganisms and metabolites using Marsupenaeus japonicus as the object of study. The results showed that obvious injury in the intestinal mucosa was observed after DIV1 infection, the oxidative and antioxidant capacity of the shrimp intestine was unbalanced, the activity of lysozyme was decreased, and the activities of digestive enzymes were disordered, and secondary bacterial infection was caused. Furthermore, the increased abundance of harmful bacteria, such as Photobacterium and Vibrio, may synergized with DIV1 to promote the Warburg effect and induce metabolic reprogramming, thereby providing material and energy for DIV1 replication. This study is the first to report the changes of intestinal microbiota and metabolites of M. japonicus under DIV1 infection, demonstrating that DIV1 can induce secondary bacterial infection and metabolic reprogramming. Several bacteria and metabolites highly associated with DIV1 infection were screened, which may be leveraged for diagnosis of pathogenic infections or incorporated as exogenous metabolites to enhance immune response.

Lysyl Oxidase-like Protein Recognizes Viral Envelope Proteins and Bacterial Polysaccharides against Pathogen Infection via Induction of Expression of Antimicrobial Peptides.

Lysyl oxidases (LOXs) are copper-dependent monoamine oxidases, and they play critical roles in extracellular matrix (ECM) remodeling. The LOX and LOX-like (LOXL) proteins also have a variety of biological functions, such as development and growth regulation, tumor suppression, and cellular senescence. However, the functions of LOXLs containing repeated scavenger receptor cysteine-rich (SRCR) domains in immunity are rarely reported. In this study, we characterized the antiviral and antibacterial functions of a lysyl oxidase-like (LOXL) protein containing tandem SRCR domains in Marsupenaeus japonicus. The mRNA level of LoxL was significantly upregulated in the hemocytes and intestines of shrimp challenged using white spot syndrome virus (WSSV) or bacteria. After the knockdown of LoxL via RNA interference, WSSV replication and bacterial loads were apparently increased, and the survival rate of the shrimp decreased significantly, suggesting that LOXL functions against pathogen infection in shrimp. Mechanistically, LOXL interacted with the envelope proteins of WSSV or with lipopolysaccharide and peptidoglycan from bacteria in shrimp challenged using WSSV or bacteria, and it promoted the expression of a battery of antimicrobial peptides (AMPs) via the induction of Dorsal nuclear translocation against viral and bacterial infection. Moreover, LOXL expression was also positively regulated by Dorsal in the shrimp challenged by pathogens. These results indicate that, by acting as a pattern recognition receptor, LOXL plays vital roles in antiviral and antibacterial innate immunity by enhancing the expression of AMPs in shrimp.

Immunostimulation of shrimp through oral administration of silkworm pupae expressing VP15 against WSSV.

White spot syndrome virus (WSSV) is one of the most concerning pathogens in penaeid shrimp and can cause severe loss in shrimp aquaculture worldwide. Among the WSSV structural proteins, VP15, a DNA-binding protein located in the WSSV nucleocapsid, is an antiviral protein candidate to protect kuruma shrimp (Marsupenaeus japonicus) from WSSV infection. We identified that the truncated VP15, VP15(26-57), is responsible for the protective effect against the WSSV. This study attempts to develop an immunizing agent against WSSV using silkworm pupa as a delivery vector through oral administration. The VP15, VP15(26-57), and SR11 peptide derived from VP15(26-57) were expressed in silkworm pupae. Oral administration of feed mixed with the powdered pupae that expressed VP15-derived constructs enhanced the survivability of kuruma shrimp with an overall relative percent survival (RPS) higher than 70%. There is no death for the group receiving pupa/VP15(26-57), and the RPS is 100%. In addition, we also investigated the relative mRNA expression levels of immune-related genes by qPCR at different time points. Our results indicate that the oral administration of pupa/VP15-derived products could provide a high protective effect against WSSV and be a practical approach for controlling WSSV in aquaculture.

Phenotypic and genomic characterization of pathogenic Providencia rettgeri from kuruma shrimp Marsupenaeus japonicus.

Providencia rettgeri has been recognized as a zoonotic pathogen of humans and aquaculture animals and has become a global public health concern. However, scarce information is available on the characterization of pathogenic P. rettgeri from kuruma shrimp Marsupenaeus japonicus. In the present study, a P. rettgeri isolate (KM4) was confirmed as a causative agent of red leg disease in cultured M. japonicus, which showed a median lethal dose (LD50 ) value of 5.01 × 105 CFU·ml-1 and had multiple resistances to aminoglycosides, sulfonamides, and tetracycline antimicrobials used in aquaculture. In addition, the whole genome of isolate KM4 was sequenced and found to consist of a single circular chromosome of 4,378,712 bp and a circular plasmid of 171,394 bp. The genome sequence analysis further revealed the presence of potential virulence and antibiotic resistance genes in isolate KM4, which probably rendered this isolate particularly virulent. To our knowledge, this is the first study to characterize P. rettgeri pathogens from kuruma shrimp infected with red leg disease. The findings of this study can provide novel insights into the presence and distribution of pathogenicity-associated genes in shrimp-pathogenic P. rettgeri.

Antibacterial activity of an anti-lipopolysaccharide factor (MjALF-D) identified from kuruma prawn (Marsupenaeus japonicus).

Antimicrobial peptides (AMPs) play important roles in host innate immune systems. Anti-lipopolysaccharide factor (ALF), which is a primary AMP in crustaceans, is active against bacteria, fungi and some viruses. MjALF-D, an anionic peptide, is a group D ALF isolated from Marsupenaeus japonicus. In the present study, a series of experiments were performed to study its antibacterial spectrum and further explore its antibacterial and bacterial binding activities. Liquid growth inhibition data demonstrated that recombinant MjALF-D (rMjALF-D) possessed strong antibacterial activity against the gram-positive bacterium Micrococcus luteus and the gram-negative bacterium Photobacterium damselae, with a minimum inhibitory concentration (MIC) or minimum bactericidal concentration (MBC) lower than 1.25 µM. The kinetic analysis showed that the antibacterial activity of rMjALF-D was dose- and time-dependent. Additionally, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations the potential bactericidal process. rMjALF-D treatment resulted in a large number of unidentified filamentous structures wrapped around the bacteria, and during the incubation, the cell surface became obviously rough and disrupted. rMjALF-D showed distinct binding ability after direct incubation with M. luteus and P. damselae but no binding ability to Escherichia coli, which was weakly inhibited by rMjALF-D. These data suggest that MjALF-D displays modest antibacterial activity and may provide more insights into the function and role of ALF in shrimp immunity.

Peroxiredoxin 4 Interacts With Domeless and Participates in Antibacterial Immune Response Through the JAK/STAT Pathway.

The JAK/STAT pathway plays an important role in the development and immune responses of animals. In vertebrates, families of cytokines or growth factors act as activators of the JAK/STAT pathway; however, the activators for the JAK/STAT signaling pathway in arthropods are largely unknown. Herein we report a new ligand, peroxiredoxin 4 (Prx4), for the Domeless in the JAK/STAT pathway of shrimp Marsupenaeus japonicus. Prx4 was induced to secrete into the extracellular surroundings upon Vibrio challenge, which then facilitated the anti-Vibrio activity of shrimp by activating the phosphorylation and nuclear translocation of STAT and the expression of STAT-responsive antimicrobial peptides. Blocking the expression of Prx4 in vivo abrogated the activation of the JAK/STAT pathway by Vibrio infection, while injection of Prx4 protein activated the pathway. The interaction between Prx4 and Domeless was proved by immuno-precipitation and protein pull-down assays. Moreover, two cysteine residues in Prx4 that are critical for the interaction and Prx4's anti-Vibrio role were identified, and the binding site in Domeless for Prx4 was proved to be the cytokine-binding homology module fragment. Taken together, our study revealed a new function for Prx4 enzyme and established a new enzyme-type ligand for the activation of the JAK/STAT pathway in an aquatic arthropod.

Infection with white spot syndrome virus affects the microbiota in the stomachs and intestines of kuruma shrimp.

Maintaining eubiosis of the gastrointestinal (GI) microbiota is essential for animal health. White spot syndrome virus (WSSV) is the most lethal viral pathogen because it causes extremely high mortality in shrimp farming. However, it remains poorly understood how WSSV infection affects the microbiota in different regions of the GI tract of shrimp. In the present study, we established an experimental model of kuruma shrimp (Marsupenaeus japonicus) infection with WSSV and then investigated the effects of WSSV infection on the microbiota in the cardiac stomach, pyloric stomach, and intestines using metataxonomics. We identified 34 phyla and 576 genera of bacteria collectively. At the phylum level, Proteobacteria and Firmicutes were the most abundant in all the three GI segments. The WSSV infection decreased microbial diversity to a different extent in the stomachs and in a time-dependent manner. The infection with WSSV affected the microbiota composition in the two stomachs, but not the intestines. Firmicutes increased significantly, while Actinobacteria, Bacteroidetes, and Cyanobacteria decreased in the two stomachs of the WSSV-infected shrimp. At the genus level, Trichococcus and Vibrio increased, but Bradyrhizobium and Roseburia decreased in the cardiac stomach of the WSSV-infected shrimp. Trichococcus and Photobacterium increased in the pyloric stomach. Although Vibrio showed a slight downward trend, Aliivibrio (formerly Vibrio) increased in the pyloric stomach. Thiothrix, Fusibacter, and Shewanella decreased in the pyloric stomach, but no significant differences in these genera were detected in the cardiac stomach. Analysis of the predicted functions of the GI microbiota indicated that the WSSV infection resulted in losses of some microbiota functions. The new information from this study may help better understand the bacteria-virus interaction in the GI tract of shrimp and other crustacean species, and inform pathogen prevention/control and sustainable aquaculture production.

Hypoxia stress affects the physiological responses, apoptosis and innate immunity of Kuruma shrimp, Marsupenaeus japonicus.

For commercial aquatic animals, hypoxia phenomenon often occurs in live transport and aquaculture. In previous studies, much interest has been focused on antioxidant enzyme activities and could not present the complexities. The multifaceted responses, especially considering physiological indexes, histological structure, cell apoptosis, and immune pathways, are still unknown. In this study, we investigated the comprehensive hypoxic responses of Marsupenaeus japonicus. The results showed that the physiological indexes showed time-dependent changes upon hypoxia stress. Hypoxia stress led to significant tissue damage and cell apoptosis in the gill and hepatopancreas. Compared with the control group, the apoptosis index (AI) of the 12 h hypoxic treatment increased significantly (p < 0.05) in the gills and hepatopancreas. Comparative transcriptome analysis identified 900 and 1400 differentially expressed genes (DEGs) in the gill and hepatopancreas, respectively. Several DEGs were related to the lysosome, glycolysis/gluconeogenesis, citrate cycle, and apoptosis, and seven of them were validated using quantitative real-time PCR. This study provided valuable clues to understanding the mechanisms underlying the hypoxic responses of M. japonicus.

Probiotic Effects of a Marine Purple Non-Sulfur Bacterium, Rhodovulum sulfidophilum KKMI01, on Kuruma Shrimp (Marsupenaeus japonicus).

Purple non-sulfur bacteria (PNSB) are used as probiotics in shrimp aquaculture; however, no studies have examined the probiotic effects of PNSB in shrimp at the gene expression level. In this study, we examined the effects of a marine PNSB, Rhodovulum sulfidophilum KKMI01, on the gene expression of kuruma shrimp (Marsupenaeus japonicus). Short-term (3 days) effects of R. sulfidophilum KKMI01 on the gene expression in shrimp were examined using small-scale laboratory aquaria experiments, while long-term (145 days) effects of R. sulfidophilum KKMI01 on the growth performance and gene expression were examined using 200-ton outdoor aquaria experiments. Gene expression levels were examined using qRT-PCR. Results of the short-term experiments showed the upregulation of several molting-related genes, including cuticle proteins, calcification proteins, and cuticle pigment protein, suggesting that PNSB stimulated the growth of shrimp. The upregulation of several immune genes, such as prophenoloxidase, antimicrobial peptides, and superoxide dismutase, was also observed. In the 145-day outdoor experiments, the average body weight at harvest time, survival rate, and feed conversion ratio were significantly improved in PNSB-treated shrimp, and upregulation of molting and immune-related genes were also observed. When PNSB cells were added to the rearing water, the effective dosage of PNSB was as low as 103 cfu/mL, which was more than a million times dilution of the original PNSB culture (2-3 × 109 cfu/mL), indicating that R. sulfidophilum KKMI01 provides a feasible and cost-effective application as a probiotic candidate in shrimp aquaculture.

Cloning, expression and function analysis of trehalose-6-phosphate synthase gene from Marsupenaeus japonicu.

Trehalose is an important disaccharide that plays an important role in extreme environmental conditions. Trehalose-6-phosphate synthase (TPS) gene is the key gene for trehalose synthesis in Marsupenaeus japonicus. In this study, a TPS gene was isolated and characterized from M. japonicus. The full-length cDNA of TPS gene of M. japonicus (MjTPS) was 3308 bp, encoding 844 amino acids. The protein of the deduced MjTPS contained a glycol_transf_20 domain and a trehalose_PPase domain. The mRNA expression level of MjTPS was the highest in hepatopancreas. The further analysis found that MjTPS gene expression was up-regulated in a short time under low-salinity and high-nitrite stress, indicating that MjTPS gene had certain resistance to low-salinity and high-nitrite stress. Compared with the control group, both the expression of MjTPS and the trehalose content significantly decreased from 3 h to 24 h after MjTPS gene interference,. After RNAi, the mortality of M. japonicus increased, the expression level of MjTPS and the synthesis of downstream products decreased under low-salinity and high-nitrite stress, and what's more, the expression of immune genes PMO25, ERP, CD, HSP90, HSP70, HSP60, HMC and CLEC2 were significantly changed, implying that MjTPS might be participated in the immune response of M. japonicus. In addition, MjTPS gene silencing could affect the expression of CHI1 and CHS, suggesting that MjTPS might be involved in molting behavior of M. japonicus. These results provide new information for further studying the function of trehalose-6-phosphate synthase in shrimp.

Nitric Oxide Synthase Regulates Gut Microbiota Homeostasis by ERK-NF-κB Pathway in Shrimp.

The gut microbiota is a complex group of microorganisms that is not only closely related to intestinal immunity but also affects the whole immune system of the body. Antimicrobial peptides and reactive oxygen species participate in the regulation of gut microbiota homeostasis in invertebrates. However, it is unclear whether nitric oxide, as a key mediator of immunity that plays important roles in antipathogen activity and immune regulation, participates in the regulation of gut microbiota homeostasis. In this study, we identified a nitric oxide synthase responsible for NO production in the shrimp Marsupenaeus japonicus. The expression of Nos and the NO concentration in the gastrointestinal tract were increased significantly in shrimp orally infected with Vibrio anguillarum. After RNA interference of Nos or treatment with an inhibitor of NOS, L-NMMA, NO production decreased and the gut bacterial load increased significantly in shrimp. Treatment with the NO donor, sodium nitroprusside, increased the NO level and reduced the bacterial load significantly in the shrimp gastrointestinal tract. Mechanistically, V. anguillarum infection increased NO level via upregulation of NOS and induced phosphorylation of ERK. The activated ERK phosphorylated the NF-κB-like transcription factor, dorsal, and caused nuclear translocation of dorsal to increase expression of antimicrobial peptides (AMPs) responsible for bacterial clearance. In summary, as a signaling molecule, NOS-produced NO regulates intestinal microbiota homeostasis by promoting AMP expression against infected pathogens via the ERK-dorsal pathway in shrimp.

Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus.

BACKGROUND: Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. RESULTS: Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. CONCLUSIONS: This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.

The Molecular Mechanism of Hemocyte Immune Response in Marsupenaeus japonicus Infected With Decapod Iridescent Virus 1.

As a new type of shrimp lethal virus, decapod iridescent virus 1 (DIV1) has caused huge economic losses to shrimp farmers in China. Up to now, DIV1 has been detected in a variety of shrimps, but there is no report in Marsupenaeus japonicus. In the current study, we calculated the LC50 to evaluate the toxicity of DIV1 to M. japonicus and determined through nested PCR that M. japonicus can be the host of DIV1. Through enzyme activity study, it was found that DIV1 can inhibit the activities of superoxide dismutase, catalase, lysozyme, and phenoloxidase, which could be a way for DIV1 to achieve immune evasion. In a comprehensive study on the transcriptomic changes of M. japonicus in response to DIV1 infection, a total of 52,287 unigenes were de novo assembled, and 20,342 SSR markers associated with these unigenes were obtained. Through a comparative transcriptomic analysis, 6,900 differentially expressed genes were identified, including 3,882 upregulated genes and 3,018 downregulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that some GO terms related to virus invasion, replication, and host antiviral infection were promoted under DIV1 infection, such as carbohydrate binding, chitin binding, chitin metabolic process, and DNA replication initiation, and some KEGG pathways related to immune response were significantly influenced by DIV1 infection, including Toll and IMD signaling pathway, JAK-STAT signaling pathway, IL-17 signaling pathway, C-type lectin receptor signaling pathway, complement and coagulation cascades, antigen processing and presentation, necroptosis, apoptosis, NOD-like receptor signaling pathway, apoptosis-multiple species, and TNF signaling pathway. Further analysis showed that STAT, Dorsal, Relish, heat shock protein 70 (HSP70), C-type lectins, and caspase play an important role in DIV1 infection. This is the first detailed study of DIV1 infection in M. japonicus, which initially reveals the molecular mechanism of DIV1 infection in M. japonicus by using the transcriptome analysis of hemocytes combined with enzyme activity study.