A transcriptome study on Macrobrachium rosenbergii hepatopancreas experimentally challenged with white spot syndrome virus (WSSV)

Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management of Litopenaeus stylirostris

The Pacific blue shrimp (Litopenaeus stylirostris) is a premium product in the international seafood market. However, intensified farming has increased disease incidence and reduced genetic diversity. In this study, we developed a transcriptome database for L. stylirostris and mined microsatellite markers to analyze their genetic diversity. Using the Illumina HiSeq 4000 platform, we identified 53,263 unigenes from muscle, hepatopancreas, the intestine, and lymphoid tissues. Microsatellite analysis identified 36,415 markers from 18,657 unigenes, predominantly dinucleotide repeats. Functional annotation highlighted key disease resistance pathways and enriched categories. The screening and PCR testing of 42 transcriptome-based and 58 literature-based markers identified 40 with successful amplification. The genotyping of 200 broodstock samples revealed that Na, Ho, He, PIC, and FIS values were 3, 0.54 ± 0.05, 0.43 ± 0.09, 0.41 ± 0.22, and 0.17 ± 0.27, respectively, indicating moderate genetic variability and significant inbreeding. Four universal microsatellite markers (CL1472.Contig13, CL517.Contig2, Unigene5692, and Unigene7147) were identified for precise diversity analysis in Pacific blue, Pacific white (Litopenaeus vannamei), and black tiger shrimps (Penaeus monodon). The transcriptome database supports the development of markers and functional gene analysis for selective breeding programs. Our findings underscore the need for an appropriate genetic management system to mitigate inbreeding depression, reduce disease susceptibility, and preserve genetic diversity in farmed shrimp populations.

Transcriptomic profiling and characterization of microRNAs in Macrobrachium rosenbergii potentially involved in immune response to Enterobacter cloacae infection

Enterobacter cloacae is a member of the Enterobacter family, which could prevent Macrobrachium rosenbergii from growing and cause mass mortality. However, no research has focused on microRNA immunity in M. rosenbergii infected with E. cloacae. To clarify the immune response mechanisms, transcriptomic analysis was performed on the miRNAs of M. rosenbergii infected with E. cloacae YZ3 strain. Following quality screening, 10,616,712 clean reads were obtained from the control group and 12,726,421 from the infected group. Among 899 known miRNAs, 446 differentially expressed miRNAs (DEMs) were identified. Meanwhile, 59 novel miRNAs were predicted, along with 39 DEMs. Target genes of DEMs have been predicted in order to gain a deeper understanding of the immune-related functions. GO and KEGG pathway analysis revealed the biological functions and signaling pathways of target genes. The results indicated that E. cloacae significantly affected the NOD-like receptor, RIG-I-like receptor and Toll-like receptor pathways. Ten DEMs were randomly selected, and their expression level was verified by Quantitative Real-time PCR technology. Overall, this study highlights the influential role of miRNAs in the innate immune system of M. rosenbergii, which has important implications for developing new strategies to prevent and treat related diseases in the future.

Ajpacifastin-like is involved in the immune response of Apostichopus japonicus challenged by Vibrio splendidus

Pacifastin proteins are previously found to regulate the phenoloxidase system in invertebrates and arthropods. In this study, the immune response that was regulated by Ajpacifastin-like in the sea cucumber Apostichopus japonicus was determined. RNA interference was used to knock down the expression of the Ajpacifastin-like gene in A. japonicus, followed by challenge with Vibrio splendidus, and the colony count showed that the survival of V. splendidus in the si-Ajpacifastin group increased 4.64-fold compared to that of the control group. The purified recombinant Ajpacifastin-like showed an inhibitory effect on the extracellular protease activity of the supernatant collected from the V. splendidus culture. Consequently, a comparative transcriptome analysis of the coelomocytes from the control group and the si-Ajpacifastin group was performed to explore the global regulatory effect of the Ajpacifastin-like. A total of 1486 differentially expressed genes (DEGs) were identified, including 745 upregulated genes and 741 downregulated genes. GO enrichment showed that the DEGs were mainly enriched in translation, cytosolic ribosomal subunit and structural constituent of ribosome. KEGG analysis showed that the DEGs were significantly enriched in the retinoic acid-inducible gene I (RIG-I)-like receptor signaling pathway, antigen processing and presentation, toll-like receptor signaling pathway, mitogen-activated protein kinase signaling pathway, nuclear factor-kappa B signaling pathway and other immune-related pathways. Furthermore, real-time reverse transcriptase PCR was used to determine the RNA levels of six DEGs, i.e., cathepsinB, CYLD, caspase8, TRAF6, hsp90 and FADD, to verify the RNA-seq results. Overall, our results specified the immune response and pathways of A. japonicus in which Ajpacifastin-like was involved in.

Transcriptome analysis of Macrobrachium rosenbergii hemocytes in response to Staphylococcus aureus infection

The aquaculture industry has suffered significant financial losses as a result of disease outbreaks. In particular, disease outbreaks have become a major problem that can seriously affect the sustainable development of the Macrobrachium rosenbergii aquaculture industry. It is crucial to determine the defense mechanism of the host after pathogenic invasion in order to provide effective defense measures after disease outbreaks. Shrimp, like other invertebrates, primarily depend on their innate immune systems to defend against pathogens, and recognize and resist pathogens through humoral and cellular immune responses. In this investigation, we used RNA-seq technology to investigate the transcriptome of hemocytes from M. rosenbergii induced by Staphylococcus aureus. Our main targets were immune pathways and genes related to innate immunity. RNA-seq identified 209,069 and 204,775 unigenes in the control and experimental groups, respectively. In addition, we identified 547 and 1734 differentially expressed genes (DEGs) following S. aureus challenge after 6 and 12 h (h), respectively. GO and KEGG enrichment analysis revealed that the DEGs were significantly enriched in several biological signalling pathways, including NOD-like receptor, PI3K-Akt, Toll and Imd, IL-17, TGF-beta, RIG-I-like receptor, cAMP, apoptosis, and C-type lectin receptor. Sixteen DEGs were chosen at random for qPCR verification; these results concurred with those from sequencing. Our findings revealed that immune-related genes play an important role in antibacterial activities and have specific functions for gram-positive bacteria. These results provide more data for the prevention of M. rosenbergii diseases and offer a basis for the better prevention of diseases.

Transcriptome analysis of Macrobrachium rosenbergii hemocytes reveals in-depth insights into the immune response to Vibrio parahaemolyticus infection

Macrobrachium rosenbergii as one of the common freshwater prawn species in Southeast Asia, which breeding industry is seriously threatened by vibriosis and causes high mortality. In this study, the RNA-seq was employed for assessing the M. rosenbergii hemocytes transcriptomes following Vibrio parahaemolyticus challenge. After challenge for 6 h (h), there were overall 1849 DEGs or differentially expressed genes, including 1542 up-regulated and 307 down-regulated genes, and there was a total of 1048 DEGs, including 510 up-regulated genes and 538 down-regulated genes, after challenge for 12 h. Mitogen-activated protein kinase (MAPK) immune-related pathways, Toll, immune deficiency (IMD), and Janus kinase (JAK)/signal transducer and activator of transcription (STAT) were among the immune pathways where a lot of the DEGs were connected. The expression patterns of 18 chosen immune-related genes were examined utilizing qRT-PCR or quantitative real-time polymerase chain reaction, which revealed that the V. parahaemolyticus infection activated the M. rosenbergii's immune response. Permutational multivariate analysis of variance (PERMANOVA) showed that V. parahaemolyticus infection modulated immune regulation and apoptosis pathways. The gathered information provided new insight into M. rosenbergii's immunity and suggested a novel approach to fight against bacterial infection.

Transcriptome analysis of hepatopancreas in penaeus monodon under acute low pH stress

The decrease of seawater pH can affect the metabolism, acid-base balance, immune response and immunoprotease activity of aquatic animals, leading to aquatic animal stress, impairing the immune system of aquatic animals and weakening disease resistance, etc. In this study, we performed high-throughput sequencing analysis of the hepatopancreas transcriptome library of low pH stress penaeus monodon, and after sequencing quality control, a total of 43488612-56271828 Clean Reads were obtained, and GO annotation and KEGG pathway enrichment analysis were performed on the obtained Clean Reads, and a total of 395 DEGs were identified. we mined 10 differentially expressed and found that they were significantly enriched in the Metabolic pathways (ko01100), Biosynthesis of secondary metabolites (ko01110), Nitrogen metabolism (ko00910) pathways, such as PIGA, DGAT1, DGAT2, UBE2E on Metabolic pathways; UGT, GLT1, TIM genes on Biosynthesis of secondary metabolites; CA, CA2, CA4 genes on Nitrogen metabolism, are involved in lipid metabolism, induction of oxidative stress and inflammation in the muscular body of spot prawns. These genes play an important role in lipid metabolism, induction of oxidative stress and inflammatory response in the muscle of the shrimp. In summary, these genes provide valuable reference information for future breeding of low pH-tolerant shrimp.

LncRNA-mRNA integrated profiling analysis in response to white spot syndrome virus in hepatopancreas in Penaeus japonicus

Penaeus japonicas is an important shrimp species, which is exposed to stressors including a variety of epidemic diseases. To date, little is known about the mechanisms involved in the response to white spot syndrome virus (WSSV) mediated by long non-coding RNAs (lncRNAs). A total of 6544 putative lncRNAs were identified in the hepatopancreas in P. japonicas, which provides a useful lncRNA reference resource for use in future studies. In addition, a total of 444 differentially expressed mRNAs and 457 differentially expressed lncRNAs were identified at 6, 12, and 24 h after WSSV infection in the hepatopancreas of P. japonicas. Functional enrichment analysis showed that the differentially expressed mRNAs were enriched in terms related to immune response and viral infectivity such as defense response, aminopeptidase activity, whereas the differentially expressed lncRNA partner genes were enriched in ubiquitin-dependent protein catabolic process, lipoprotein metabolic process, and antigen processing and presentation. Moreover, several lncRNAs were induced by WSSV infection, indicating these lncRNAs might participate in regulating many immune processes referring to their partner genes. Co-expression analysis of the lncRNAs and their partner genes identified some high lncRNA-mRNA correlations. These results suggest that WSSV stimulates the immune response in the hepatopancreas potentially through an important coding and non-coding gene network, thereby providing valuable information regarding non-coding responses to WSSV in Penaeus species.

Acute toxic effects of diclofenac exposure on freshwater crayfish (Procambarus clarkii): Insights from hepatopancreatic pathology, molecular regulation and intestinal microbiota

In this study, we exposed adult male crayfish (Procambarus clarkii) to different concentrations of diclofenac (DCF) for 96 h. In the meantime, we investigated the alternations of hepatopancreatic pathology, molecular regulation and intestinal microbiota of P. clarkii exposed to DCF. The results demonstrated DCF led to histological changes including epithelium vacuolization and tubule lumen dilatation in the hepatopancreas. Transcriptome sequencing analysis showed that 642 and 586 genes were differentially expressed in the hepatopancreas of P. clarkii exposed to 1 and 10 mg/L DCF, respectively. DCF could affect the functions of antioxidation, immunity and metabolism of hepatopancreas by inducing the abnormal expressions of immune- and redox-related genes. GO enrichment results demonstrated that 10 mg/L DCF exposure could modulate the processes of molting, amino sugar metabolism, protein hydrolysis and intracellular protein translocation of P. clarkii. Additionally, the abundances of bacterial families including Shewanellaceae, Bacteroidaceae, Vibrionaceae, Erysipelotrichaceae, Aeromonadaceae, Moraxellaceae, etc. in the intestine were significantly changed after DCF exposure, and the disruption of intestinal flora might further cause abnormal intestinal metabolism in P. clarkii. This study provides novel mechanistic insights into the toxic effects of anti-inflammatory drugs on aquatic crustaceans.

Effects of air exposure stress on crustaceans: Histopathological changes, antioxidant and immunity of the red swamp crayfish Procambarus clarkii

Air exposure stress may result in oxidative damage and ultimately disease or death in crustaceans. Using the Procambarus clarkia, one of the main commercial aquaculture species in China, as a study model, the molecular mechanism including histopathological changes, antioxidant capacity and immunity response under the air exposure stress were firstly evaluated. Results showed that the surfaces of gill were wrinkled while the morphologies of the nuclei and mitochondria in the hepatopancreas were altered after 48 h of air exposure stress, and the damage of mitochondria was more serious after additional bacterial infection. Moreover, the activity of antioxidant enzymes increased at first and then decreased along with increasement of air exposure time. The concentration of malondialdehyde (MDA) in hepatopancreas was significantly increased under the air exposure stress, while the bacterial infection further aggravated such oxidative damage. The transcriptome analysis exhibited that the stress- and immunity-related genes in hepatopancreas altered when response to the air exposure stress. This study could help uncover the mechanisms of aerial exposure stress responses in Procambarus clarkii.

Combined dynamic transcriptomics and metabolomics analyses revealed the effects of trans-vp28 gene Synechocystis sp. PCC6803 on the hepatopancreas of Litopenaeus vannamei

Litopenaeus vannamei is the most important shrimp species throughout the world. However, diseases are increasing with the development of the industry, so enhancing the immunity of shrimp is of great significance. In this study, 1800 shrimp were divided into two groups randomly: the control group (N, feed with brine shrimp flake) and the experimental group (M, feed with mutant of Synechocystis sp. cells) (300 shrimp/group/replication) and each trial was conducted in triplicates. After immunization, sixty shrimp (with three replicates of twenty) were collected at 0 h in group N and 24, 72, and 144 h in group M, respectively, and the hepatopancreas were isolated for transcriptomic and metabolomic analysis. Transcriptome data revealed that compared with group N, genes related to antimicrobial peptides, cytoskeleton remodeling, detoxification, apoptosis, blood coagulation, immune defense, and antioxidant systems were differentially expressed in group M. In addition, combined transcriptomic and metabolomic analysis revealed that some immune-related differential genes or differential metabolites were consistently expressed in both omics. All the above results indicated that trans-vp28 gene Synechocystis sp. PCC6803 could improve the immunity of L. vannamei. This is the first report of the integration of dynamic transcriptomics combined with metabolomics to study the effect of trans-vp28 gene Synechocystis sp. PCC6803 in the hepatopancreas of L. vannamei and provided important information about the defense and immune mechanisms used by invertebrates against pathogens.

Investigation on Natural Infection of Covert Mortality Nodavirus in Farmed Giant Freshwater Prawn (Macrobrachium rosenbergii)

Simple Summary

Covert mortality nodavirus (CMNV) is a newly discovered aquatic animal virus in recent years. Here, we detected CMNV positive in farmed giant freshwater prawn (Macrobrachium rosenbergii) from Jiangsu, China by TaqMan RT-qPCR. Meanwhile, in situ hybridization and histological analysis indicated that the intestine, gill, hepatopancreas and ovary of giant freshwater prawn were the target organs of CMNV. In addition, a large number of CMNV-like particles were observed in the hepatopancreas and gill tissues under transmission electron microscopy. Overall, our study confirms that giant freshwater prawn is a susceptible host of CMNV, further expands the known host range of CMNV, and provided a new direction for further investigation and exploration of multiple pathogenic factors of giant freshwater prawn disease.

Abstract

Covert mortality nodavirus (CMNV), from the Nodaviridae family, is characterized by its unique cross-species transmission and wide epidemic distribution features. In this study, Macrobrachium rosenbergii was proved to be infected naturally by CMNV, which further expand the known host range of CMNV. Here, 61.9% (70/113) of the M. rosenbergii samples collected from Jiangsu Province were CMNV positive in the TaqMan RT-qPCR assay, which indicated the high prevalence of CMNV in M. rosenbergii. Meanwhile, the sequences of CMNV RdRp gene cloned from M. rosenbergii were highly identical to that of the original CMNV isolate from Penaeus vannamei. In situ hybridization (ISH) and histology analysis indicated that the intestine, gill, hepatopancreas and ovary were the targeted organs of CMNV infection in M. rosenbergii, and obvious histopathological damage including vacuolation and karyopyknosis were occurred in the above organs. Notably, the presence of CMNV in gonad alerted its potential risk of vertical transmission in M. rosenbergii. Additionally, numerous CMNV-like particles could be observed in tissues of hepatopancreas and gill under transmission electron microscopy. Collectively, our results call for concern of the potential negative impact of the spread and prevalence of CMNV in M. rosenbergii on its aquaculture, as well as providing a renewed orientation for further investigation and exploration of the diverse pathogenic factors causing M. rosenbergii diseases.

Transcriptome analysis of differentially expressed genes in the red swamp crayfish Procambarus clarkii challenged with Aeromonas hydrophila

As an important economic species in China, aquaculture of the crayfish Procambarus clarkii has suffered huge losses due to infection by pathogenic bacteria, mainly by Aeromonas hydrophila, which leads to high mortality and huge economic loss. To better understand the immune response of crayfish against bacterial infection, we compared and analyzed transcriptome data of hepatopancreatic tissue from P. clarkii that were either challenged with A. hydrophila or treated with PBS. After assembly and annotation of the data, 32,041 unigenes with an average length of 1512 base pairs were identified. Compared to control group, Differential gene expression (DEG) analysis revealed 608 DEGs were obtained, of which 274 unigenes were upregulated and 334 were downregulated in the A. hydrophila group. Furthermore, the expression levels of eight selected immune-related DEGs were validated by qRT-PCR, substantiating the reliability of RNA-seq results. This study not only provides effective data support for immune defense strategies of P. clarkii in response to bacterial infections, but also provides new information about the P. clarkii immune system and defense mechanisms, and a valuable basis for further studies to elucidate the molecular immune mechanisms of this species.

Differential STAT gene expressions of Penaeus monodon and Macrobrachium rosenbergii in response to white spot syndrome virus (WSSV) and bacterial infections: Additional insight into genetic variations and transcriptomic highlights

Diseases have remained the major issue for shrimp aquaculture industry for decades by which different shrimp species demonstrated alternative disease resistance or tolerance. However, there had been insufficient studies on the underlying host mechanisms of such phenomenon. Hence, in this study, the main objective involves gaining a deeper understanding into the functional importance of shrimp STAT gene from the aspects of expression, sequence, structure, and associated genes. STAT gene was selected primarily because of its vital signalling roles in stress, endocrine, and immune response. The differential gene expressions of Macrobrachium rosenbergii STAT (MrST) and Penaeus monodon STAT (PmST) under White Spot Syndrome Virus (WSSV) and Vibrio parahaemolyticus/VpAHPND infections were identified through qPCR analysis. Notably, during both pathogenic infections, MrST demonstrated significant gene expression down-regulations (during either early or later post-infection time points) whereas PmST showed only significant gene expression up-regulations. Important sequence conservation or divergence was highlighted through STAT sequence comparison especially amino acid alterations at 614 aa [K (Lysine) to E (Glutamic Acid)] and 629 aa [F (Phenylalanine) to V (Valine)] from PmST (AY327491.1) to PmST (disease tolerant strain). There were significant differences observed between in silico characterized structures of MrST and PmST proteins. Important functional differentially expressed genes (DEGs) in the aspects of stress, endocrine, immune, signalling, and structural were uncovered through comparative transcriptomic analysis. The DEGs associated with STAT functioning were identified including inositol 1,4,5-trisphosphate receptor, hsp90, caspase, ATP binding cassette transmembrane transporter, C-type Lectin, HMGB, ALF1, ALF3, superoxide dismutase, glutathione peroxidase, catalase, and TBK1. The main findings of this study are STAT differential gene expression patterns, sequence divergence, structural differences, and associated functional DEGs. These findings can be further utilized for shrimp health or host response diagnostic studies. STAT gene can also be proposed as a suitable candidate for future studies of shrimp innate immune enhancement.

Transcriptome analysis of hepatopancreas from different living states oriental river prawn (Macrobrachium nipponense) in response to hypoxia

As an important economical freshwater prawn, Macrobrachium nipponense has difficulty with adapting to hypoxia. In this study, comparative transcriptome analysis was used for the first time to explore the differences between different living states of Macrobrachium nipponense under hypoxia. A total of 94.22 Gb clean reads were obtained and assembled into 54,688 unigenes. A total of 224, 266, and 750 differently expressed genes were found in the comparison of the control and death groups, the control and moribund groups, and the control and survived groups, respectively. Three signal pathways closely related to hypoxia were found by enriching of the signal pathways in three comparison groups. In addition, much attention was focused on the differential genes in these pathways. Oxidative stress related genes, such as 70 kDa heat shock protein, phosphoenolpyruvate carboxykinase and cyclooxygenase were differentially expressed in different comparisons. After comparing with previous studies, cyclooxygenase was found to be an important hypoxia-related gene that is fully involved in the hypoxic response. Interestingly, two new genes with no Nr annotation were found in this manuscript. This manuscript will enrich our understanding of oxidative stress response to hypoxia and provide a theoretical basis for the subsequent solution of apoptosis caused by hypoxia.

Hepatopancreatic transcriptome analysis and humoral immune factor assays in red claw crayfish (Cherax quadricarinatus) provide insight into innate immunomodulation under Vibrio parahaemolyticus infection

Red claw crayfish (Cherax quadricarinatus) is an economically and nutritionally important specie. We aimed to assess the immunostimulatory response to C. quadricarinatus infection with Vibrio parahaemolyticus. After determining the LD50, we infected C. quadricarinatus and examined the differential expression profiles of hepatopancreas transcriptional genes, and observed the temporal changes of hepatopancreas pathological sections and serum immunoenzymatic activities at different time points to reveal the infection mechanism of V. parahaemolyticus and the immune detoxification mechanism of the organism. The results showed that V. parahaemolyticus infection with C. quadricarinatus caused hepatopancreas injury and the immune enzyme activity of the organism changed with time delay. Transcriptome analysis of 47,338 single genes obtained by RNA sequencing and de nove transcriptome assembly identified a total of 3678 differentially expressed genes (P < 0.05) in the expression profiles of susceptible and normal animals for comparative analysis, and 2516 differentially expressed genes (P < 0.05) in the expression profiles of asymptomatic (infection-resistant) and normal animals. GO and KEGG and analyses revealed immune-related pathways under V. parahaemolyticus infection, including Vibrio cholerae infection, phagosome, lysozyme, oxidative phosphorylation, antigen processing and presentation, apoptosis, and Toll-like receptor signaling, as well as significant differences in the expression patterns of related immune genes at different times (P < 0.05). These new experimental results reveal the molecular response of the hepatopancreas to V. parahaemolyticus infection and the corresponding adaptive mechanisms, thus further revealing the pathogenesis due to bacterial infection in the aquatic environment, and providing a reference for further understanding of microbial-host interactions in aquatic systems.

iTRAQ-based quantitative proteomic analysis of differentially expressed proteins in the hepatopancreas of Litopenaeus vannamei after WSSV infection

White spot syndrome virus (WSSV) is the most destructive virus among invertebrates. In this study, we analyzed the immune response after WSSV infection in Pacific white shrimp Litopenaeus vannamei using isobaric tags for relative and absolute quantitation (iTRAQ). We identified 325 differentially expressed proteins (DEPs) in the hepatopancreas of L. vannamei. Among them, 212 were up-regulated proteins, and several of them might be related to immunity (e.g. arginine kinase and peroxiredoxin). Of the 113 down-regulated proteins, some were related to immunity (e.g. cathepsin C and cathepsin L) and others to the antioxidant defense process (e.g. glutathione peroxidase and catalase). One down-regulated DEP (C7M84_014268) and 3 up-regulated DEPs (C7M84_003456, C7M84_020702, and C7M84_007135) were randomly selected and analyzed using parallel reaction monitoring. This study is an important step for a comprehensive understanding of the immune relationship between L. vannamei and WSSV and provides valuable information for the prevention of viral diseases in the crustacean aquaculture industry.

Silencing of prophenoloxidase (proPO) gene in freshwater prawn, Macrobrachium rosenbergii, makes them susceptible to white spot syndrome virus (WSSV)

Prophenoloxidase (proPO) is very important to protect the invertebrates from microbial infections. Our previous studies revealed that proPO was up-regulated in WSSV-injected Macrobrachium rosenbergii and is responsible for protecting M. rosenbergii from WSSV. In order to prove this mechanism, an attempt was made in the present study to silence the proPO gene in freshwater prawn by injection of dsRNA-proPO followed by WSSV challenge. Two partial fragments of proPO with the size of 251 and 331 bp were used to synthesize dsRNA using LITMUS38i vector and E. coli. The bacterially synthesized dsRNA-proPO was used to silence proPO gene to determine its involvement in developing resistance in prawn against WSSV. In proPO gene-silenced prawn, 100% mortality was observed after WSSV challenge whereas no mortality was observed in prawn injected with WSSV alone. The WSSV infection in gene-silenced prawn was confirmed by PCR, and its propagation was quantified by ELISA and real-time PCR at different time intervals. Real-time PCR assay revealed a significant reduction in the expression of proPO gene in WSSV-challenged proPO-silenced prawn when compared to normal prawn. Level of proPO was reduced significantly in the haemolymph of proPO-silenced prawn when compared to prawn injected with PBS.

MicroRNA transcriptome analysis of oriental river prawn Macrobrachium nipponense in responding to starvation stress

Food deprivation or fasting is an important environmental factor, and a regular occurrence in both natural aquatic habitats and artificial ponds. However, the potential immunoregulatory mechanisms underlying starvation stress in crustaceans remain unclear. MicroRNAs (miRNAs) are a new class of non-coding RNAs that can regulate various biological processes, such as stress and immune responses. In the present work, miRNAs related to starvation stress responses and immune properties were identified and characterised in oriental river prawn Macrobrachium nipponense using high-throughput sequencing and bioinformatics analyses. Twelve small RNA libraries from hepatopancreas tissue were sequenced across four fasting stages lasting 0, 7, 14 or 21 days. In total, 550 miRNAs were identified including 198 putative novel miRNAs and 352 conserved miRNAs belonging to 57 families. Moreover, compared with expression levels at 0 days, 27, 27 and 43 miRNAs were differentially expressed (DE-miRNAs) at 7, 14 and 21 days, respectively. Among these, four DE-miRNAs (ame-miR-190-5p, dme-miR-307a-3p, hme-miR-2788-3p and novel_68) were co-expressed at all three timepoints. Furthermore, 661 target genes regulated by these DE-miRNAs were identified, and associated functional annotations were derived by GO enrichment and KEGG pathway analyses, which showed that most DE-miRNAs were mainly participated in metabolic processes and immune responses. Furthermore, 26 host DE-miRNAs potentially participated in interactions with white spot syndrome virus (WSSV) were identified by predicting and analysing target genes from WSSV. The further WSSV challenge under starvation stress showed that dme-miR-307a-3p played a part in the antiviral responses against WSSV. Our results demonstrate that dme-miR-307a-3p may play vital regulatory roles in responding to starvation stress and WSSV infection. The findings contribute new insight into the molecular mechanisms associated with immune responses to environmental stress in crustaceans.

Structure, gene expression, and putative functions of crustacean heat shock proteins in innate immunity

Heat shock proteins (HSPs) are molecular chaperones with critical roles in the maintenance of cellular proteostasis. HSPs, which regulate protein folding and refolding, assembly, translocation, and degradation, are induced in response to physiological and environmental stressors. In recent years, HSPs have been recognized for their potential role in immunity; in particular, these proteins elicit a variety of immune responses to infection and modulate inflammation. This review focuses on delineating the structural and functional roles of crustacean HSPs in the innate immune response. Members of crustacean HSPs include high molecular weight HSPs (HSP90, HSP70, and HSP60) and small molecular weight HSPs (HSP21 and HSP10). The sequences and structures of these HSPs are highly conserved across various crustacean species, indicating strong evolutionary links among this group of organisms. The expression of HSP-encoding genes across different crustacean species is significantly upregulated upon exposure to a wide range of pathogens, emphasizing the important role of HSPs in the immune response. Functional studies of crustacean HSPs, particularly HSP70s, have demonstrated their involvement in the activation of several immune pathways, including those mediating anti-bacterial resistance and combating viral infections, upon heat exposure. The immunomodulatory role of HSPs indicates their potential use as an immunostimulant to enhance shrimp health for control of disease in aquaculture.

Innate immune function of serine/threonine-protein kinase from Macrobrachium rosenbergii in response to host-pathogen interactions

The occurrences of multiple drug-resistant strains have been relentlessly increasing in recent years. The aquaculture industry has encountered major disease outbreaks and crucially affected by this situation. The usage of non-specific chemicals and antibiotics expedites the stimulation of resistant strains. Triggering the natural defense mechanism would provide an effective and safest way of protecting the host system. Hence, we have investigated the innate immune function of serine/threonine-protein kinase (STPK) in Macrobrachium rosenbergii (Mr). The in-silico protein analysis resulted in the identification of cationic antimicrobial peptide, MrSL-19, with interesting properties from STPK of M. rosenbergii. Antimicrobial assay, FACS and SEM analysis demonstrated that the peptide potentially inhibits Staphylococcus aureus by interacting with its membrane. The toxic study on MrSL-19 demonstrated that the peptide is not toxic against HEK293 cells as well as human erythrocytes. This investigation showed the significant innate immune property of an efficient cationic antimicrobial peptide, MrSL-19 of STPK from M. rosenbergii.

Molecular characterization of prohibitins and their differential responses to WSSV infection in hemocyte subpopulations of Fenneropenaeus chinensis

In our previous work, prohibitin1 (PHB1) was identified to be only expressed in granulocytes of Fenneropenaeus chinensis. In order to elucidate the potential immunological properties of prohibitins in hemocyte subpopulations, in this paper, the full-length cDNAs of PHB1 and PHB2 were firstly cloned from F. chinensis using rapid amplification of cDNA ends approach, and they were designated FcPHB1 and FcPHB2, respectively. Based on the sequence analysis and multiple sequence alignment, FcPHB1 and FcPHB2 were members of SPFH protein family. By quantitative real-time RT-PCR, the higher mRNA transcription levels of FcPHB1 and FcPHB2 were detected in intestine and hemocytes of F. chinensis, and these two genes in hemocytes were significantly up-regulated upon WSSV infection. The FcPHB1 and FcPHB2 were recombinantly expressed in Escherichia coli BL21 (DE3), and employed as immunogens to produce the polyclonal antibodies (PAbs) in rabbits. Indirect immunofluorescence assay (IFA) revealed that the FcPHB1 and FcPHB2 were located both in the cytoplasm and nuclei of hemocytes, which could also be specifically recognized by the PAbs against FcPHB1 or FcPHB2 in Western blot. Interestingly, it was found that FcPHB1 and FcPHB2 were only expressed in the granulocytes of heathy shrimp and highly expressed in the WSSV-infected granulocytes, however only weak expressions of FcPHB1 and FcPHB2 were observed in the hyalinocytes of WSSV-infected shrimp. Meanwhile, silencing of FcPHB1 and FcPHB2 genes were performed by small interfering RNA, and the results showed that the WSSV copies in hemocytes were increased by knockdown of either FcPHB1 or FcPHB2, and the cumulative mortalities of shrimp in the silenced groups were also markedly increased. These results demonstrated that FcPHB1 and FcPHB2 played important roles in anti-WSSV infection, and their differential expression characteristics in hemocyte subpopulations provided a further understanding of the immune functions of granulocytes and hyalinocytes.

iTRAQ-based proteomic analysis of the hepatopancreas from Litopenaeus vannamei after trans-vp28 gene Synechocystis sp. PCC6803 immunization

Litopenaeus vannamei (Pacific white shrimp) is one of the most commercially important varieties of shrimp cultivated in the world. Shrimp farming is a high-risk, capital-intensive industry that is susceptible to periodic outbreaks of diseases caused by viral and bacterial pathogens. Thus, there is a need to develop economically viable methods of disease control. The hepatopancreas of crustaceans are known to have an important role in their innate immune response. In this study, we have explored the immune response of the hepatopancreas from L. vannamei fed with trans-vp28 gene Synechocystis sp. PCC6803 using iTRAQ-based proteomics. A total of 214 differentially expressed proteins (DEPs) were identified, of which 143 were up-regulated and 71 were down-regulated. These proteins have diverse roles in the cell cytoskeleton and cell phagocytosis, antioxidant defense process and the response of immune related proteins. Among these proteins, the immunity associated with the functional annotation of L. vannamei was further analysed. In addition, 4 DEPs (act1, N/A, H and C7M84_013542) were analysed using parallel reaction monitoring (PRM). This is the first report of proteomics in the hepatopancreas of L. vannamei immunized with trans-vp28 gene Synechocystis sp. PCC6803.

Transcriptome analysis and immune-related genes expression reveals the immune responses of Macrobrachium rosenbergii infected by Enterobacter cloacae

Macrobrachium rosenbergii is an important cultural species in China and other Southeast Asian countries. However, Enterobacter cloacae infection has caused a great economic loss in M. rosenbergii culture industry. The immune responses of M. rosenbergii to the E. cloacae infection is not fully characterized. To investigate the immune response of M. rosenbergii against E. cloacae, we performed transcriptome analysis of the M. rosenbergii hepatopancreas with and without E. cloacae infection using RNA-seq. After assembly and annotation, 29,731 high quality unigenes were obtained from RNA-seq data. Differential expression analysis revealed the existence of 2498 significantly differently expressed genes (DEGs) at 12 h post infection, with 1365 up-regulated and 1133 down-regulated genes. Among these DEGs, some well-known immune-related genes were up-regulated significantly, including C-type lectin 1, lectin 3, anti-lipopolysaccharide factor 2, Cu/Zn superoxide dismutase and heat shock protein 70. GO analysis demonstrated 24 biological process subcategories, 14 cellular component subcategories, and 12 molecular function subcategories that were enriched among these DEGs, and some DEGs were clustered into immune related subcategories such as immune system process, response to stimulus, biological adhesion, and antioxidant activity. These DEGs were enriched into 216 KEGG pathways including a core set of immune correlated pathways notably in phagosome and lysosome. In addition, 5 up-regulated and 5 down-regulated immune-related DEGs were selected for further validation by quantitative real-time PCR and the results showed consistence with the RNA-seq data. Additionally, the expression level of six selected immune-related genes (ALF2, CLEC1, LEC3, hemocyanin1, HSP70 and SOD) based on the transcriptomic data were monitored at different point of time in hepatopancreas, gill, hemolymph and intestine. Results revealed these immune-related genes were significantly up-regulated in different tissues from 6 to 24 h after E. cloacae infection. Overall, these results provided valuable information for further studying the immune response of M. rosenbergii against E. cloacae infection.

A comparative synthesis of transcriptomic analyses reveals major differences between WSSV-susceptible Litopenaeus vannamei and WSSV-refractory Macrobrachium rosenbergii

Since the 1990s White Spot Syndrome Virus (WSSV) has severely affected shrimp aquaculture worldwide causing a global pandemic of White Spot Disease (WSD) in penaeid culture. However, not all decapod species that can be infected by WSSV show the same susceptibility to the virus, thus raising interesting questions regarding the potential genetic traits that might confer resistance to WSSV. In order to shed light into the genetic markers of WSSV resistance, we employed a dual approach: i) we initially analysed the transcriptomes derived from the hepatopancreas of two species, the susceptible white shrimp Litopenaeus vannamei and the refractory fresh water prawn Macrobrachium rosenbergii, both infected with WSSV. We found a large number of differentially expressed genes (DEGs) belonging to the immune system (mostly anti-microbial peptides and haemolymph clotting components) that were generally up-regulated in M. rosenbergii and down-regulated in L. vannamei. Further, in both species we identified many up-regulated DEGs that were related to metabolism (suggesting a metabolic shift during the infection) and, interestingly, in L. vannamei only, we found several DEGs that were related to moult and suggested an inhibition of the moult cycle in this species following WSSV infection. ii) we then identified a limited number of genetic markers putatively linked with WSD tolerance by employing an ecological genomics approach in which we compared published reports with our own RNA-seq datasets for different decapod species infected with WSSV. Using this second comparative approach, we found nine candidate genes which are consistently down-regulated in susceptible species and up-regulated in refractory species and which have a role in immune response. Together our data offer novel insights into gene expression differences that can be found in susceptible and refractory decapod species infected with WSSV and provide a valuable resource towards our understanding of the potential genetic basis of tolerance to WSSV.

Transcriptomics of Cherax quadricarinatus hepatopancreas during infection with Decapod iridescent virus 1 (DIV1)

Cherax quadricarinatus is a large-sized, highly fecund, and fast-growing species of freshwater crayfish, and has become one of the world's most intensely studied crustaceans. Decapod iridescent virus 1 (DIV1), a newly described species in the family Iridoviridae, is known to infect various crustaceans, including C. quadricarinatus, and may pose a new threat in the shrimp-farming industry. The present study performed de novo transcriptome sequencing of C. quadricarinatus hepatopancreas during DIV1 infection. A total of 114,784 transcripts and 56,418 genes were obtained; 1070 genes were upregulated and 775 genes were downregulated when compared with the uninfected samples (controls). Three pattern recognition receptor genes (fibrinogen-related protein, C-type lectin, and beta-1,3-glucan-binding protein) were upregulated during DIV1 infection. Among the top-30 upregulated unigenes, 9 unigenes were identified as vitellogenin (Vg) genes, and the top-3 upregulated unigenes were identified as involved in Vg lipid transport, lipid localization, and lipid transporter activity, which were all significantly over-representative GO terms in the GO enrichment analysis of total and upregulated differentially expressed genes (DEGs). Many genes associated with Jak-STAT signaling pathway, Endocytosis, Phagosome, MAPK signaling pathway, Apoptosis and Lysosome were positively modified after DIV1 infection. The predicted protein-protein interaction (PPI) analysis showed NF1 and TUBA, CRM1 and TUBB were involved in protein interactions. This research showed that DIV1 infection has a significant impact on the transcriptome profile of C. quadricarinatus hepatopancreas, and the results enhance our understanding of virus-host interactions. Furthermore, the high number of transcripts generated in the present study will provide information for identifying novel genes in the absence of a full C. quadricarinatus genome sequence.

Comparative transcriptome analysis of the gills of Procambarus clarkii provides novel insights into the immune-related mechanism of copper stress tolerance

The red-swamp crayfish (Procambarus clarkii) is the most important economic shrimp species in China, and is an important model crustacean organism in many fields of research. In crustaceans, gills interface directly with the ambient environment and thus play a vital role in the toxicology. In the context of increasing environmental heavy metal pollution, the relationship between copper (Cu²⁺) stress and the immune response of P. clarkii has recently received considerable attention. However, impact of Cu²⁺ on the crayfish immune system is still not fully understood. In this study, we used Illumina sequencing technology to perform a transcriptome analysis of the gills of P. clarkii after 24 h of Cu²⁺ treatment. A total of 37,226,812 unigenes were assembled, and 1943 unigenes were significantly differentially expressed between the control and Cu²⁺ treatment groups. Functional categorization of differentially expressed genes (DEGs) revealed that genes related to antioxidant activity, detoxication, metabolic processes, biosynthetic processes, and immune system processes were differentially regulated during Cu²⁺ stress. In addition, DEGs in the immune system were classified as being related to the MAPK signaling pathway, purine metabolism, Toll and Imd signaling pathway, PI3K-Akt signaling pathway and Hippo signaling pathway. Five genes (CuZnSOD, CAT, IDH1, PHYH and DECR2) were significantly up-regulated in the peroxisome pathway, which plays an important role in reacting to oxidative stress. Importantly, qRT-PCR validation of the results for seven genes chosen at random (NDK, ATP6L, ATP5C1, RPS14, RPL22e, CTSF and HSP90A) confirmed the Illumina sequencing results. This study provides a valuable starting point for further studies to elucidate the molecular basis of the immune system's response to Cu²⁺ stress in crayfish.

Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation

Background

Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on how M. rosenbergii post-larvae launches an immune response to an infection with MrNV is not currently available. We therefore compared the whole transcriptomic sequence of M. rosenbergii post-larvae before and after MrNV infection.

Results

Transcriptome for M. rosenbergii post-larvae demonstrated high completeness (BUSCO Complete: 83.4%, fragmentation: 13%, missing:3.3%, duplication:16.2%; highest ExN50 value: 94%). The assembled transcriptome consists of 96,362 unigenes with N₅₀ of 1308 bp. The assembled transcriptome was successfully annotated against the NCBI non-redundant arthropod database (33.75%), UniProt database (26.73%), Gene Ontology (GO) (18.98%), Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (EggNOG) (20.88%), and Kyoto Encyclopedia of Genes and Genome pathway (KEGG) (20.46%). GO annotations included immune system process, signaling, response to stimulus, and antioxidant activity. Differential abundance analysis using EdgeR showed 2413 significantly up-regulated genes and 3125 significantly down-regulated genes during the infection of MrNV.

Conclusions

This study reported a highly complete transcriptome from the post-larvae stage of giant river prawn, M. rosenbergii. Differential abundant transcripts during MrNV infection were identified and validated by qPCR, many of these differentially abundant transcripts as key players in antiviral immunity. These include known members of the innate immune response with the largest expression change occurring in the M. rosenbergii post-larvae after MrNV infection such as antiviral protein, C-type lectin, prophenol oxidase, caspase, ADP ribosylation factors, and dicer.

Gill transcriptome alterations in Macrobrachium rosenbergii under copper exposure

Copper is one of common contaminants in estuaries and coastal zones, which may cause physiological dysfunction in aquatic organisms. However, molecular response triggered by Cu have remained largely unknown in freshwater prawn Macrobrachium rosenbergii. In the present study, we performed transcriptomic analysis to characterize molecular mechanisms of copper immunotoxicity in gills from M. rosenbergii. A large number of potential simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) loci in the transcriptome were identified. 19,417 and 8989 differentially expressed genes (DEGs) were obtained at 3 h and 48 h after exposure, respectively. Most of these DEGs were down-regulated implying that gene expressions were largely inhibited by Cu, which might lead to impairments of biological functions. Functional enrichment analysis of these DEGs revealed that immune, detoxification and apoptosis were the differentially regulated processes by Cu stress. 12 DGEs involved in immune response and heavy metal detoxification were discovered and validated by qRT-PCR. The results indicated that the M. rosenbergii might counteract the toxicity of Cu at the transcriptomic level by increasing expressions of immune- and heavy metal detoxification-related genes, and these selected genes could be used as molecular indicators for Cu stress. Our study firstly reported the stress response at transcriptional level in M. rosenbergii during Cu exposure. The genes and pathways identified here not only give us new insight into molecular mechanisms underlying Cu toxicity effects in prawn, but facilitate biomarker identification and stress-resistant breeding studies.

Temporal changes in transcriptome profile provide insights of White Spot Syndrome Virus infection in Litopenaeus vannamei

Shrimp aquaculture is severely affected by WSSV. Despite an increasing effort to understand host/virus interaction by characterizing changes in gene expression (GE) following WSSV infection, the majority of published studies have focussed on a single time-point, providing limited insight on the development of host-pathogen interaction over the infection cycle. Using RNA-seq, we contrasted GE in gills of Litopenaeus vannamei at 1.5, 18 and 56 hours-post-infection (hpi), between WSSV-challenged and control shrimps. Time course analysis revealed 5097 differentially expressed genes: 63 DEGs were viral genes and their expression in WSSV group either peaked at 18 hpi (and decreased at 56 hpi) or increased linearly up to 56 hpi, suggesting a different role played by these genes during the course of infection. The remaining DEGs showed that WSSV altered the expression of metabolic, immune, apoptotic and cytoskeletal genes and was able to inhibit NF-κB and JAK/STAT pathways. Interestingly, GE changes were not consistent through the course of infection but were dynamic with time, suggesting the complexity of host-pathogen interaction. These data offer novel insights into the cellular functions that are affected during the course of infection and ultimately provide a valuable resource towards our understanding of the host-pathogen dynamics and its variation with time.

The Single-molecule long-read sequencing of Scylla paramamosain

Scylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) and 131561 simple sequence repeats (SSRs) were identified. Meanwhile, the isoforms of many genes were also identified in this study. Our study provides a rich set of full-length cDNA sequences for S. paramamosain, which will greatly facilitate S. paramamosain research.

Description of a Natural Infection with Decapod Iridescent Virus 1 in Farmed Giant Freshwater Prawn, Macrobrachium rosenbergii

Macrobrachium rosenbergii is a valuable freshwater prawn in Asian aquaculture. In recent years, a new symptom that was generally called "white head" has caused high mortality in M. rosenbergii farms in China. Samples of M. rosenbergii, M. nipponense, Procambarus clarkii, M. superbum, Penaeus vannamei, and Cladocera from a farm suffering from white head in Jiangsu Province were collected and analyzed in this study. Pathogen detection showed that all samples were positive for Decapod iridescent virus 1 (DIV1). Histopathological examination revealed dark eosinophilic inclusions and pyknosis in hematopoietic tissue, hepatopancreas, and gills of M. rosenbergii and M. nipponense. Blue signals of in situ digoxigenin-labeled loop-mediated isothermal amplification appeared in hematopoietic tissue, hemocytes, hepatopancreatic sinus, and antennal gland. Transmission electron microscopy of ultrathin sections showed a large number of DIV1 particles with a mean diameter about 157.9 nm. The virogenic stromata and budding virions were observed in hematopoietic cells. Quantitative detection with TaqMan probe based real-time PCR of different tissues in naturally infected M. rosenbergii showed that hematopoietic tissue contained the highest DIV1 load with a relative abundance of 25.4 ± 16.9%. Hepatopancreas and muscle contained the lowest DIV1 loads with relative abundances of 2.44 ± 1.24% and 2.44 ± 2.16%, respectively. The above results verified that DIV1 is the pathogen causing white head in M. rosenbergii. M. nipponense and Pr. clarkii are also species susceptible to DIV1.

Comparative transcriptomic analysis of Marsupenaeus japonicus hepatopancreas in response to Vibrio parahaemolyticus and white spot syndrome virus

Vibrio parahaemolyticus and white spot syndrome virus (WSSV) are pathogens that cause epidemics in kuruma shrimp (Marsupenaeus japonicus) during aquaculture, resulting in severe economic losses to local farmers. To characterise the mechanisms of the molecular responses to V. parahaemolyticus and WSSV infection in M. japonicus, the transcriptome of hepatopancreas was sequenced using next-generation sequencing after infection. A total of 29,180 unigenes were assembled, with an average length of 1,151 bp (N50 = 1,951 bp). After BLASTX searching against the Nr database (E-value cut-off = 10^-5), 15,176 assembled unigenes remained, with 3,039 and 1,803 differentially expressed transcripts identified in the V. parahaemolyticus- and WSSV-infected groups, respectively. Of these, 1466 transcripts were up-regulated and 1573 were down-regulated in V. parahaemolyticus-infected shrimps, and 970 transcripts were up-regulated and 833 were down-regulated in the WSSV-infected shrimps. Additionally, 761 transcripts were differentially expressed in both V. parahaemolyticus- and WSSV-infected shrimps. Several known immune-related genes including caspase 4, integrin, crustin, ubiquitin-conjugating enzyme E2, C-type lectin, and α₂-macroglobulin were among the differentially expressed transcripts. These results provide valuable information for characterising the immune mechanisms of the shrimp responses of to V. parahaemolyticus andWSSV infection.

WSV181 inhibits JAK/STAT signaling and promotes viral replication in Drosophila

The Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway plays a critical role in host defense against viral infections. Here, we report the use of the Drosophila model system to investigate the modulation of the JAK/STAT pathway by the white spot syndrome virus (WSSV) protein WSV181. WSV181 overexpression in transgenic flies resulted in the downregulation of STAT92E and STAT92E-targeted genes. This result indicates that WSV181 can suppress JAK/STAT signaling by controlling STAT92E expression. An infection experiment was carried out on transgenic Drosophila infected with Drosophila C virus and on Litopenaeus vannamei injected with recombinant WSV181 and WSSV. The increased viral load and suppressed transcript levels of JAK/STAT pathway components indicate that WSV181 can promote viral proliferation by inhibiting the JAK/STAT pathway. This study provided evidence for the role of WSV181 in viral replication and revealed a new mechanism through which WSSV evades host immunity to maintain persistent infection.

Changes of microRNAs expression profiles from red swamp crayfish (Procambarus clarkia) hemolymph exosomes in response to WSSV infection

MicroRNAs (miRNAs) as short noncoding RNAs play important regulatory roles in diverse biological processes by degrading the target mRNAs, and could be delivered by exosomes. WSSV is a highly pathogenic and prevalent virus, and has brought high mortality of P. clarkia. Till present, no studies focus on the miRNAs changes in exosomes during WSSV infection. To understand the different virulence of WSSV on miRNAs expression in P. clarkia hemolymph exosome, the deep sequencing was performed to compare the small RNA libraries from the hemolymph exosome of P. clarkia individuals with or without WSSV infections. From the TEM observations, NTA and Western Blot analysis, the extracted exosomes were well identified with classic characteristics. The 209 conserved miRNAs and 250 novel miRNAs were identified from the small RNA libraries. In response to WSSV infection, there were about 98 miRNAs significantly up-regulated and 59 miRNAs significantly down-regulated. The target genes prediction, GO and KEGG enrichment analysis revealed that some target genes of P. clarkia miRNAs were grouped mainly into the categories of biological regulation, immune system process, signal pathway and other more functions. This is the first report of comprehensive identification of P. clarkia hemolymph exosome miRNAs being differentially regulated in response to WSSV infection. These results will help to understand the hemolymph exosome miRNAs response to different virulence WSSV infection.

Comparative transcriptome analysis of red swamp crayfish (Procambarus clarkia) hepatopancreas in response to WSSV and Aeromonas hydrophila infection

To better study the immune system of shrimp and understand the similarities and differences between the host's immune defense against viral and bacterial infections, this study used a comparative transcriptomics method to systematically analyze the hepatopancreas of the crayfish Procambarus clarkia in response to WSSV and A. hydrophila infection. After assembly, there was an average of 24,404,837 clean reads were obtained after filtering out low-quality reads. Unigenes were annotated by comparing against nr, Swiss-Prot\KEGG\COG\KOG\GO and Pfam databases, and 17,954 unigenes were annotated in at least one database. 2600 and 2073 differentially expressed genes (DEGs) in the hepatopancreas in response to WSSV and A. hydrophila infections were identified respectively. The GO and KEGG enrichment analyses of DEGs were conducted to further explore their functions. The pathways like PI3K-Akt signaling pathway, mTOR signaling pathway, Jak-STAT signaling pathway, NF-κB signaling pathway, VEGF signaling pathway, Ras signaling pathway, were the most prominent for immunity-related DEGs in C-/W-Groups, while Endocytosis, Lysozyme, Focal adhesion, Phagosome, Peroxisome, MAPK signaling pathway were observed in C-/A-Groups. Furthermore, the expression levels of nine selected immune-related DEGs were validated by qRT-PCR, substantiating the reliability of RNA-Seq results. This study not only provides effective data support to reveal the different immune defense strategies by P. clarkia to cope with bacterial and WSSV infections, but also to provide new information about the immune system and defense mechanisms of shrimp.

Single-molecule long-read sequencing facilitates shrimp transcriptome research

Although shrimp are of great economic importance, few full-length shrimp transcriptomes are available. Here, we used Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology to generate transcripts from the Pacific white shrimp (Litopenaeus vannamei). We obtained 322,600 full-length non-chimeric reads, from which we generated 51,367 high-quality unique full-length transcripts. We corrected errors in the SMRT sequences by comparison with Illumina-produced short reads. We successfully annotated 81.72% of all unique SMRT transcripts against the NCBI non-redundant database, 58.63% against Swiss-Prot, 45.38% against Gene Ontology, 32.57% against Clusters of Orthologous Groups of proteins (COG), and 47.83% against Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Across all transcripts, we identified 3,958 long non-coding RNAs (lncRNAs) and 80,650 simple sequence repeats (SSRs). Our study provides a rich set of full-length cDNA sequences for L. vannamei, which will greatly facilitate shrimp transcriptome research.

Novel fibrinogen-related protein with single FReD contributes to the innate immunity of Macrobrachium rosenbergii

Fibrinogen-related proteins (FREPs) are widely found in vertebrates and invertebrates, and they play crucial roles in innate immunity. Here, a new FREP named as MrFREP was identified from giant freshwater prawn (Macrobrachium rosenbergii). The full-length cDNA of MrFREP measures 1649 bp in length and consists of a 1086 bp open reading frame encoding a polypeptide composed of 361 amino acids. The MrFREP sequence has a signal peptide with 20 amino acids and a fibrinogen-related domain (FReD) with 223 amino acids. Phylogenetic analysis showed that MrFREP was grouped with FREPs from Marsupenaeus japonicus and Litopenaeus vannamei. BLASTp results showed that it had 43% identity with a FREP from M. japonicus. The expression of MrFREP was higher in gills, intestine, and hepatopancreas than in hemocytes, heart, stomach, and muscles. The expression levels of MrFREP in gills and intestine were obviously upregulated after they were exposed to Vibrio parahaemolyticus or White spot syndrome virus infection. Recombinant MrFReD protein (rMrFReD) could bind to Gram-positive and Gram-negative bacteria and agglutinate the tested bacteria in the presence of calcium. rMrFReD demonstrated lipopolysaccharide and peptidoglycan binding activities. rMrFReD could accelerate the clearance of V. parahaemolyticus in vivo. These results suggested that MrFREP could function as a pattern recognition receptor contributing to the innate immunity of M. rosenbergii.

Transcriptome analysis of Macrobrachium rosenbergii intestines under the white spot syndrome virus and poly (I:C) challenges

Intestine is a primary site of the white spot syndrome virus (WSSV) infection in most crustaceans. To date, little is known about its role in the anti-viral immune response in the freshwater prawn Macrobrachium rosenbergii. In this study, next-generation sequencing was employed to investigate the M. rosenbergii intestine transcriptomes following WSSV or poly I:C challenges. A total of 41.06 M, 39.58 M and 47.00 M clean reads were generated and assembled into 65,340, 71,241 and 70,614 transcripts from the negative control group (NG), WSSV challenge group (WG) and poly I:C treatment group (PG) respectively. Based on homology searches, functional annotation with 7 databases (NR, NT, GO, COG, KEGG, Swissprot and Interpro) for 88,412 transcripts was performed. After WSSV or poly (I:C) challenge, the numbers of up-regulated differentially expressed genes (DEGs) were greater than the down-regulated DEGs. Gene Ontology (GO) classification of the DEGs also distributed similarly, with the same top 10 annotations and were all assigned to the signaling pathways, including spliceosome, Rap1 signaling pathway, proteoglycans, PI3K-Akt signaling pathway, ECM receptor interaction. Results could contribute to a better understanding of the intestinal immune response to viral pathogens.

Molecular cloning and expression analysis of a prawn (Macrobrachium rosenbergii) juvenile hormone esterase-like carboxylesterase following immune challenge

Methyl farnesoate (MF), the crustacean juvenile hormone (JH), plays critical roles in various physiological processes in crustaceans. The titer of MF is precisely regulated by specific carboxylesterase. Here, we report for the first time that the cloning and expression analysis of a JH esterase-like carboxylesterase from the prawn Macrobrachium rosenbergii (named as MrCXE). MrCXE contained a 1935-bp open reading frame (ORF) conceptually translated into a 644-amino acids protein. MrCXE protein shared the highest identity (36%) with JH esterase-like carboxylesterase from the swimming crab, Portunus trituberculatus and exhibited the typical motifs of JH esterase-like carboxylesterases. MrCXE was most abundantly expressed in hepatopancreas, the major tissue for MF metabolism. MrCXE was expressed at a low level in gut and was not detected in other tissues. Additionally, MrCXE expression was upregulated in hepatopancreas by eyestalk ablation to increase MF level. Furthermore, the mRNA level of MrCXE was significantly increased in the hepatopancreas when challenged by the bacterial pathogens Aeromonas hydrophila and Vibrio parahaemolyticus. To our knowledge, this is the first report that the JH esterase-like carboxylesterase is involved in the innate immune response of the crustaceans.

A transcriptome study on Macrobrachium nipponense hepatopancreas experimentally challenged with white spot syndrome virus (WSSV)

White spot syndrome virus (WSSV) is one of the most devastating pathogens of cultured shrimp, responsible for massive loss of its commercial products worldwide. The oriental river prawn Macrobrachium nipponense is an economically important species that is widely farmed in China and adult prawns can be infected by WSSV. However, the molecular mechanisms of the host pathogen interaction remain unknown. There is an urgent need to learn the host pathogen interaction between M. nipponense and WSSV which will be able to offer a solution in controlling the spread of WSSV. Next Generation Sequencing (NGS) was used in this study to determin the transcriptome differences by the comparison of control and WSSV-challenged moribund samples, control and WSSV-challenged survived samples of hepatopancreas in M. nipponense. A total of 64,049 predicted unigenes were obtained and classified into 63 functional groups. Approximately, 4,311 differential expression genes were identified with 3,308 genes were up-regulated when comparing the survived samples with the control. In the comparison of moribund samples with control, 1,960 differential expression genes were identified with 764 genes were up-regulated. In the contrast of two comparison libraries, 300 mutual DEGs with 95 up-regulated genes and 205 down-regulated genes. All the DEGs were performed GO and KEGG analysis, overall a total of 85 immune-related genes were obtained and these gene were groups into 13 functions and 4 KEGG pathways, such as protease inhibitors, heat shock proteins, oxidative stress, pathogen recognition immune receptors, PI3K/AKT/mTOR pathway, MAPK signaling pathway and Ubiquitin Proteasome Pathway. Ten genes that valuable in immune responses against WSSV were selected from those DEGs to furture discuss the response of host to WSSV. Results from this study contribute to a better understanding of the immune response of M. nipponense to WSSV, provide information for identifying novel genes in the absence of genome of M. nipponense. Furthermore, large number of transcripts obtained from this study could provide a strong basis for future genomic research on M. nipponense.

Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses

Litopenaeus vannamei is one of the most important shrimp species for worldwide aquaculture. Despite this, little genomic information is available for this penaeid and other closely related taxonomic crustaceans. Consequently, genes, proteins and their respective polymorphisms are poorly known for these species. In this work, we used the RNA sequencing technology (RNA-seq) in L. vannamei shrimp evaluated for growth performance, and exposed to the White Spot Syndrome Virus (WSSV), in order to investigate the presence of Single Nucleotide Polymorphisms (SNPs) within genes related to innate immunity and growth, both features of great interest for aquaculture activity. We analyzed individuals with higher and lower growth rates; and infected (unhealthy) and non-infected (healthy), after exposure to WSSV. Approximately 7,000 SNPs were detected in the samples evaluated for growth, being 3,186 and 3,978 exclusive for individuals with higher and lower growth rates, respectively. In the animals exposed to WSSV we found about 16,300 unique SNPs, in which 9,338 were specific to non-infected shrimp, and 7,008 were exclusive to individuals infected with WSSV and symptomatic. In total, we describe 4,312 unigenes containing SNPs. About 60% of these unigenes returned GO blastX hits for Biological Process, Molecular Function and Cellular Component ontologies. We identified 512 KEGG unique KOs distributed among 275 pathways, elucidating the majority of metabolism roles related to high protein metabolism, growth and immunity. These polymorphisms are all located in coding regions, and certainly can be applied in further studies involving phenotype expression of complex traits, such as growth and immunity. Overall, the set of variants raised herein enriches the genomic databases available for shrimp, given that SNPs originated from nextgen are still rare for this relevant crustacean group, despite their huge potential of use in genomic selection approaches.

Dystrophin gene expression and intracellular calcium changes in the giant freshwater prawn, Macrobrachium rosenbergii, in response to white spot symptom disease infection

Background

Dystrophin, an essential protein functional in the maintenance of muscle structural integrity is known to be responsible for muscle deterioration during white spot syndrome virus (WSSV) infection among prawn species. Previous studies have shown the upregulation of dystrophin protein in Macrobrachium rosenbergii (the giant freshwater prawn) upon white spot syndrome virus (WSSV) infection. The literature has also suggested the important role of calcium ion alterations in causing such muscle diseases. Thus, the interest of this study lies within the linkage between dystrophin functioning, intracellular calcium and white spot syndrome virus (WSSV) infection condition.

Methods

In this study, the dystrophin gene from M. rosenbergii (MrDys) was first characterised followed by the characterization of dystrophin gene from a closely related shrimp species, Penaeus monodon (PmDys). Dystrophin sequences from different phyla were then used for evolutionary comparison through BLAST analysis, conserved domain analysis and phylogenetic analysis. The changes in mRNA expression levels of dystrophin and the alteration of intracellular calcium concentrations in WSSV infected muscle cells were then studied.

Results

A 1246 base pair long dystrophin sequence was identified in the giant freshwater prawn, Macrobrachium rosenbergii (MrDys) followed by 1082 base pair long dystrophin sequence in P. monodon (PmDys). Four conserved domains were identified from the thirteen dystrophin sequences compared which were classified into 5 different phyla. From the phylogenetic analysis, aside from PmDys, the characterised MrDys was shown to be most similar to the invertebrate phylum of Nematoda. In addition, an initial down-regulation of dystrophin gene expression followed by eventual up-regulation, together with an increase in intracellular calcium concentration [Ca²⁺]_i were shown upon WSSV experimental infection.

Discussion

Both the functionality of the dystrophin protein and the intracellular calcium concentration were affected by WSSV infection which resulted in progressive muscle degeneration. An increased understanding of the role of dystrophin-calcium in MrDys and the interactions between these two components is necessary to prevent or reduce occurrences of muscle degeneration caused by WSSV infection, thereby reducing economic losses in the prawn farming industry from such disease.

Identification of novel EST-SSR markers by transcriptome sequencing in ridgetail white prawn Exopalaemon carinicauda

The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of 14273 SSR loci were identified from 130,082 assembled transcripts, with 6590 pairs of PCR primers designed. A total of 12,155 sequences containing SSR were predicted; and 2764 (22.74%) transcripts had significant matches to the NCBI non redundant protein (Nr) database. 11,563 transcripts were assigned into gene ontology (GO) categories. A set of 200 primers selected randomly were synthesized, of which 152 (76.0%) were successfully amplified. Further test with 60 pairs of polymorphic SSR primers to evaluate the genetic diversity of 30 wild populations and 43 loci were polymorphic, which had a polymorphic information content between 0.204 and 0.911. The results enriched genomic resources of E. carinicauda and provided powerful information for future conservation and breeding researches.

Myeloid leukemia factor functions in anti-WSSV immune reaction of kuruma shrimp, Marsupenaeus japonicus

Myeloid leukemia factor (MLF) plays an important role in development, cell cycle, myeloid differentiation, and regulates the RUNX transcription factors. However, the function of MLF in immunity is still unclear. In this study, an MLF was identified and characterized in kuruma shrimp Marsupenaeus japonicus, and named as MjMLF. The full-length cDNA of MjMLF contained 1111 nucleotides, which had an opening reading frame of 816 bp encoding a protein of 272 amino acids with an MLF1-interacting protein domain. MjMLF could be ubiquitously detected in different tissues of shrimp at the transcriptional level. The expression pattern analysis showed that MjMLF could be upregulated in shrimp hemocytes and hepatopancreas after white spot syndrome virus challenge. The RNA interference and protein injection assay showed that MjMLF could inhibit WSSV replication in vivo. Flow cytometry assay showed that MjMLF could induce hemocytes apoptosis which functioned in the shrimp antiviral reaction. All the results suggested that MjMLF played an important role in the antiviral immune reaction of kuruma shrimp. The research indicated that MjMLF might function as a novel regulator to inhibit WSSV replication in shrimp.

Experimental inoculation of oriental river prawn Macrobrachium nipponense with white spot syndrome virus (WSSV)

The oriental river prawn Macrobrachium nipponense is an economically important species that is widely farmed in China. White spot syndrome virus (WSSV) is one of the most devastating pathogens of the cultured shrimp Litopenaeus vannamei, responsible for massive loss of its commercial products worldwide. We investigated the infectivity and pathogenicity of WSSV in adult M. nipponense using standardized conditions for L. vannamei. The median lethal dose of WSSV in adult M. nipponense was 103.84±0.06 copies g-1, which was about 1000-fold higher than in L. vannamei (100.59±0.22 copies g-1). WSSV was detected by 2-step PCR in the gills, hepatopancreas, muscle, stomach, heart, gut, nerve, integument, pereopod, eyestalk, testis, and ovary of experimentally infected dead M. nipponense. Lesions were observed histologically following WSSV injection, showing basophilic intranuclear inclusion bodies in the hepatopancreas and subsequently in the gills. The clearance of WSSV was observed in hepatopancreas and gills at 48 and 96 h post-inoculation, respectively. No histological lesions were detected in muscle from 0-96 h post-injection. The results show that the oriental river prawn M. nipponense can be infected by WSSV and the infections are self limiting over time; therefore, M. nipponense may serve as a useful model for studying resistance to WSSV.

Transcriptome, antioxidant enzyme activity and histopathology analysis of hepatopancreas from the white shrimp Litopenaeus vannamei fed with aflatoxin B1(AFB1)

Aflatoxin produced by Aspergillus flavus or Aspergillus parasiticus fungi during grain and feed processing and storage. Aflatoxins cause severe health problems reducing the yield and profitability of shrimp cultures. We sought to understand the interaction between shrimp immunity and aflatoxin B1 (AFB1), analyzing transcriptome expression, antioxidant enzyme activity, and histological features of the hepatopancreas of shrimp fed with AFB1. From over 4 million high-quality reads, de novo unigene assembly produced 103,644 fully annotated genes. A total of 1024 genes were differentially expressed in shrimp fed with AFB1, being involved in functions, such as peroxidase metabolism, signal transduction, transcriptional control, apoptosis, proteolysis, endocytosis, and cell adhesion and cell junction. Upon AFB1 challenge, there were severe histological alterations in shrimp hepatopancreas. AFB1 challenge increased the activity of several antioxidant enzymes. Our data contribute to improve the current understanding of host-AFB1 interaction, providing an abundant source for identification of novel genes.

Transcriptome analysis reveals temperature-regulated antiviral response in turbot Scophthalmus maximus

Megalocytivirus is a severe pathogen to turbot (Scophthalmus maximus), a popular aquaculture species in many countries. In this study, we investigated the effect of temperature on the antiviral response of turbot at transcriptome level. We found that when turbot were infected with megalocytivirus RBIV-C1 at low temperatures (14 °C, 16 °C, and 18 °C), viral replication was undetectable or moderate and no fish mortality occurred; in contrast, when turbot were infected with RBIV-C1 at high temperatures (20 °C, 22 °C, and 24 °C), viral replication was robust and 100% host mortality was observed. During the course of viral infection, downward temperature shift curbed viral replication and augmented host survival, whereas upward temperature shift promoted viral replication and reduced host survival. Comparative transcriptome analyses were conducted to examine the whole-genome transcription of turbot infected with RBIV-C1 at 16 °C and 22 °C for 4 days (samples S16-4d and S22-4d, respectively) and 8 days (samples S16-8d and S22-8d, respectively). The results showed that compared to S22-4d and S22-8d, 1600 and 5927 upregulated unigenes of various functional categories were identified in S16-4d and S16-8d, respectively. Of these genes, 22 were immune-related, most of which were detected in S16-8d and exhibited more genetic subtypes in S16-8d than in S16-4d. In addition, upregulated genes associated with cell junctions and cell membrane were also identified. These results indicate that temperature had a profound effect on the global transcription of turbot, which consequently affects the immune as well as physical resistance of the fish against viral infection.

Transcriptome profiling of the Macrobrachium rosenbergii lymphoid organ under the white spot syndrome virus challenge

Macrobrachium rosenbergii is a crustacean with economic importance, and adult prawns are generally thought to be tolerant to white spot syndrome virus (WSSV) infection. Although certain genes are known to respond to WSSV infection and lymphoid tissue is an important immune organ, the response of lymphoid organ to WSSV infection is unclear. Next-generation sequencing was employed in this study to determine the transcriptome differences between WSSV infection and mock lymphoid organs. A total of 44,606,694 and 40,384,856 clean reads were generated and assembled into 73,658 and 72,374 unigenes from the control sample and the WSSV infection sample, respectively. Based on homology searches, KEGG, GO, and COG analysis, 21,323 unigenes were annotated. Among them, 4951 differential expression genes were identified and categorized into 244 metabolic pathways. Coagulation cascades, and pattern recognition receptor signaling pathways were used as examples to discuss the response of host to WSSV infection. We also identified 12,308 simple sequence repeats, which can be further used as functional markers. Results contribute to a better understanding of the immune response of prawn lymphoid organ to WSSV and provide information for identifying novel genes in the absence of the prawn genome.