Transcriptome analysis of the Macrobrachium nipponense hepatopancreas provides insights into immunoregulation under Aeromonas veronii infection

rpoS involved in immune response of Macrobrachium nipponens to Vibrio mimicus infection

Vibrio mimicus is a pathogenic bacterium that cause red body disease in Macrobrachium nipponense, leading to high mortality and financial loss. Based on previous studies, rpoS gene contribute to bacterial pathogenicity during infection, but the role of RpoS involved in the immune response of M. nipponense under V. mimicus infection remains unclear. In this study, the pathogen load and the RNA-seq of M. nipponense under wild-type and ΔrpoS strain V. mimicus infection were investigated. Over the entire infection period, the ΔrpoS strain pathogen load was always lower than that of the wild-type strain in the M. nipponense hemolymph, hepatopancreas, gill and muscle. Furthermore, the expression level of rpoS gene in the hepatopancreas was the highest at 24 hours post infection (hpi), then the samples of hepatopancreas tissue infected with the wild type and ΔrpoS strain at 24 hpi were selected for RNA-seq sequencing. The results revealed a significant change in the transcriptomes of the hepatopancreases infected with ΔrpoS strain. In contrast to the wild-type infected group, the ΔrpoS strain infected group exhibited differentially expressed genes (DEGs) enriched in 181 KEGG pathways at 24 hpi. Among these pathways, 8 immune system-related pathways were enriched, including ECM-receptor interaction, PI3K-Akt signaling pathway, Rap1 signaling pathway, Gap junction, and Focal adhesion, etc. Among these pathways, up-regulated genes related to Kazal-type serine protease inhibitors, S-antigen protein, copper zinc superoxide dismutase, tight junction protein, etc. were enriched. This study elucidates that rpoS can affect tissue bacterial load and immune-related pathways, thereby impacting the survival rate of M. nipponense under V. mimicus infection. These findings validate the potential of rpoS as a promising target for the development of a live attenuated vaccine against V. mimicus.

First report of Metschnikowia bicuspidata infection in the oriental river prawn (Macrobrachium nipponense, de Haan) in China

During breeding, some oriental river prawns (Macrobrachium nipponense, de Haan), an important aquaculture species in China, exhibit yellowish-brown body colouration, reduced appetite, and vitality. Diseased prawns revealed characteristic emulsifying disease signs, including whitened musculature, hepatopancreatic tissues, milky haemolymph, and non-coagulation. The present study investigated the causative agent of M. nipponense infection through isolation, histopathology, molecular sequencing, and infection experiments. The pathogenic strain exhibited distinctive white colonies on Bengal red medium, with microscopic examination confirming the presence of yeast cells. Histopathological analysis revealed prominent pathological alterations and yeast cell infiltration in muscles, hepatopancreas and gills. Additionally, 26S rDNA sequencing of the isolated yeast strain LNMN2022 revealed Metschnikowia bicuspidata (GenBank: OR518659) as the causative agent. This strain exhibited a 98.28% sequence homology with M. bicuspidata LNMB2021 (GenBank: OK094821) and 96.62% with M. bicuspidata LNES0119 (GenBank: OK073903). The pathogenicity test confirmed that M. bicuspidata elicited clinical signs in M. nipponense consistent with those observed in natural populations, and the median lethal concentration was determined to be 3.3 × 105  cfu/mL. This study establishes a foundation for further investigations into the host range and epidemiological characteristics of the pathogen M. bicuspidata in aquatic animals and provides an empirical basis for disease management in M. nipponense.

PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense

BACKGROUND

Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human life. Thus, more complete and accurate annotation of gene models are important for the breeding research of oriental river prawn.

RESULTS

A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform. Then, 37.99 Gb of subreads were sequenced, including 584,498 circular consensus sequences, among which 512,216 were full length non-chimeric sequences. After Illumina-based correction of long PacBio reads, 6,599 error-corrected isoforms were identified. Transcriptome structural analysis revealed 2,263 and 2,555 alternative splicing (AS) events and alternative polyadenylation (APA) sites, respectively. In total, 620 novel genes (NGs), 197 putative transcription factors (TFs), and 291 novel long non-coding RNAs (lncRNAs) were identified.

CONCLUSIONS

In summary, this study offers novel insights into the transcriptome complexity and diversity of this prawn species, and provides valuable information for understanding the genomic structure and improving the draft genome annotation of oriental river prawn.

Pathogenicity of Aeromonas veronii Causing Mass Mortality of Largemouth Bass (Micropterus salmoides) and Its Induced Host Immune Response

Aeromonas veronii is as an important opportunist pathogen of many aquatic animals, which is wildly distributed in various aquatic environments. In this study, a dominant bacterium GJL1 isolated from diseased M. salmoides was identified as A. veronii according to the morphological, physiological, and biochemical characteristics, as well as molecular identification. Detection of the virulence genes showed the isolate GJL1 carried outer membrane protein A (ompA), flagellin (flgA, flgM, flgN), aerolysin (aer), cytolytic enterotoxin (act), DNases (exu), and hemolysin (hly), and the isolate GJL1 also produced caseinase, lipase, gelatinase, and hemolysin. The virulence of strain GJL1 was confirmed by experimental infection; the median lethal dosage (LD50) of the GJL1 for largemouth bass was 3.6 × 105 CFU/mL, and histopathological analysis revealed that the isolate could cause obvious inflammatory responses in M. salmoides. Additionally, the immune-related gene expression in M. salmoides was evaluated, and the results showed that IgM, HIF-1α, Hep-1, IL-15, TGF-β1, and Cas-3 were significantly upregulated after A. veronii infection. Our results indicated that A. veronii was an etiological agent causing the mass mortality of M. salmoides, which contributes to understanding the immune response of M. salmoides against A. veronii infection.

Integrated analysis of mRNA and microRNA transcriptome related to immunity and autophagy in shrimp hemocytes infected with Spiroplasma eriocheiris

In recent years, the industry in charge of the cultivation of Macrobrachium nipponense (M.nipponense) has suffered significant economic losses due to an infectious pathogen called Spiroplasma eriocheiris (S.eriocheiris). There has therefore been a need to identify the key immune and autophagy genes that respond to M.nipponense's infection with S. eriocheiris to analyze its immune response mechanism and the regulation of related microRNAs (miRNAs). In this study, the mRNA and miRNA transcriptome of M.nipponense's hemocytes were analyzed at different stages of infection. This analysis employed the second and third-generation sequencing technologies. In the mRNA transcriptome, 1656 genes were expressed in healthy and susceptible M.nipponense. 892 of these were significantly up-regulated, while 764 were down-regulated. 118 genes with significant differences in autophagy, endocytosis, lysosome, Toll, IMD, and VEGF pathways were obtained from the transcriptome. In the miRNA transcriptome, 312 miRNAs (Conserved: 112, PN-type: 18, PC-type: 182) were sequenced. 74 were significantly up-regulated, and 57 were down-regulated. There were 25 miRNAs involved in regulating the Toll and IMD pathways, 41 in endocytosis, 30 in lysosome, and 12 in the VEGF pathway. An integrated analysis of immune-related miRNAs and mRNAs showed that miRNAs with significant differences (P < 0.05) such as ame-miR-29b-3p, dpu-miR-1and PC-3p-945_4074, had corresponding regulatory relationships with 118 important immune genes such as Relish, Dorsal, Caspase-3, and NF-κB. This study obtained the key immune and autophagy-related genes and corresponding regulatory miRNAs in M. nipponense's hemocytes in response to an infection by S.eriocheiris. The results can provide vital data that further reveals the defense mechanism of M.nipponense's immune system against S.eriocheiris. It can also help further comprehension and interpretation of M.nipponense's resistance mechanism to the invading S.eriocheiris, and provide molecular research information for the realization of host-directed therapies (HDT) for M.nipponense.

Transcriptome analysis of the spleen provides insight into the immunoregulation of Scortum barcoo under Streptococcus agalactiae infection

Jade perch (Scortum barcoo) is a freshwater fish with substantial economic value, which has been widely cultivated all over the world. However, with the intensification and expansion of farming, several bacterial and viral diseases have occurred in jade perch. To understand the immune response of jade perch against Streptococcus agalactiae (Group B Streptococcus, GBS), we performed a histopathological examination and transcriptome sequencing of jade perch spleen after artificial bacterial infection. GBS infection can cause structural changes and even necrosis of the jade perch spleen, which may affect the survival of infected individuals. A total of 144,458 unigenes were obtained through de novo assembly of spleen transcriptome. Among them, 1821 unigenes were identified as DEGs, including 1415 up-regulated and 406 down-regulated unigenes in the infection group. Moreover, the analysis of GO and KEGG revealed that many GO terms and pathways were involved in the host immune response, such as Toll-like receptor signaling pathway, Cytokine-cytokine receptor interaction, and TNF signaling pathway. In addition, according to transcriptome data and qRT-PCR analysis, the expression levels of many cytokines that participate in the inflammatory response changed a lot after GBS infection. Overall, this transcriptomic analysis provided valuable information for studying the immune response of jade perch against bacterial infection.

Hepatopancreas transcriptome analyses provide new insights into the molecular regulatory mechanism of fast ovary maturation in Macrobrachium nipponense

Background

Macrobrachium nipponense is an economically and ecologically important freshwater prawn that is widely farmed in China. In contrast to other species of marine shrimp, M. nipponense has a short sexual maturity period, resulting in not only high stocking densities, but also a reduced survival rate and increased risk of hypoxia. Therefore, there is an urgent need to study the molecular mechanisms underlying fast ovary maturation in this species.

Results

Comparative transcriptome analysis was performed using hepatopancreatic tissue from female M. nipponense across five ovarian maturation stages to explore differentially expressed genes and pathways involved in ovarian maturation. In total, 118.01 Gb of data were generated from 15 transcriptomes. Approximately 90.46% of clean reads were mapped from the M. nipponense reference genome. A comprehensive comparative analysis between successive ovarian maturation stages generated 230–5814 differentially expressed genes. Gene Ontology (GO) enrichment was highly concentrated in the “biological process” category in all four comparison groups, and mainly focused on energy synthesis and accumulation, energy decomposition and transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results showed that, among 20 significantly enriched KEGG pathways, nine were involved in the synthesis, degradation, and metabolism of carbohydrates, lipids, and other nutrient intermediates, suggesting that the hepatopancreas has an important role in energy supply during ovarian maturation. Furthermore, the “Insect hormone biosynthesis” pathway was found to have a dominant role in the development of the ovary from immaturity to maturity, supporting the hypothesis that ecdysteroid- and juvenile hormone-signaling pathways have an important role in hepatopancreas regulation of ovarian maturation.

Conclusion

Taken together, this study sheds light on the role of the hepatopancreas in the molecular regulation of ovary maturation in M. nipponense. The present study provided new insights for understanding the mechanisms of reproductive regulation in crustaceans.

A C-type lectin containing two carbohydrate recognition domains participates in the antibacterial response by regulating the JNK pathway and promoting phagocytosis

C-type lectins (CTLs) are important immune-related molecules in crustaceans. However, the immunologic mechanism by which CTLs eliminate invading pathogens is still unclear. In this study, we studied the antimicrobial mechanism of a CTL containing two carbohydrate recognition domains (DClec). After Aeromonas hydrophila challenge, several antimicrobial peptides (ALF1, ALF4, ALF5 and lys-i2) were upregulated. The transcript levels of ALF1, ALF4 and ALF5 were downregulated after A. hydrophila challenge in groups with DClec interference or inhibition compared with the control group. Similar results were obtained after c-Jun N-terminal kinase (JNK) interference. This finding indicates that DClec might regulate the JNK signalling pathway and subsequently adjust antimicrobial peptide (AMP) expression. Additionally, we found that DClec was secreted into the hemolymph. Recombinant protein DClec (rDClec) agglutinated gram-positive or gram-negative bacteria. Both rDClec and the native DClec in hemolymph bound to different bacteria. In this process, Ca²⁺ promoted the rDClec bacterial binding ability. After DClec interference, the phagocytosis ability of hemocytes was lower than that of the control group. Therefore, DClec can facilitate bacterial elimination by promoting AMPs expression and hemocyte phagocytosis.

The pathogenic characterization of Citrobacter freundii and its activation on immune related genes in Macrobrachium nipponense

Out breaks of mass mortalities occurred in Macrobrachium nipponense farms in Jintan county, Jiangsu Province. The bacterial isolates from M. nipponense exhibited the same phenotypic traits and biochemical characteristics, and were identified as Citrobacter freundii according to biochemical characteristics and molecular identification. The infection test revealed that the strain YG2 was pathogenic to M. nipponense, and the half lethal dose (LD₅₀) was 3.35 × 10⁵ CFU/mL at 7 d post-infection. Detection of virulence genes indicated that YG2 was positive for cfa, ureG, ureF, ureE, ureD, viaB, ompX, and LDH. Furthermore, the results of extracellular enzyme analysis revealed that the strain can produce protease, amylase, lecithin, urease, and hemolysin. Antibiotic resistance results showed that the isolate was resistant to ampicillin, cefazolin, cephalothin, cefoxitin, aboren, doxycycline, neomycin, penicillin, erythromycin, and vancomycin. The expression level of MyD88, α2M, CDSP, and Relish were detected in hepatopancreas, hemolymph, gills and intestine tissues by quantitive real-time PCR (qRT-PCR), and clear transcriptional activation of these genes were observed in M. nipponense after C. freundii infection. These results revealed pathogenicity of C. freundii and its activation of host immune response, which will provide a scientific reference for the breeding and disease prevention in M. nipponense culture.

Comparison of lipid metabolism between broodstock and hybrid offspring in the hepatopancreas of juvenile shrimp (Macrobrachium nipponense): Response to chronic ammonia stress

Ammonia nitrogen is a major pollutant that causes great physiological harm to crustaceans in culture. In this study, we conducted a 28 day chronic ammonia nitrogen stress experiment with broodstock populations (Dianshan, DS) and hybrid offspring populations (DS ♀ × CD (Changjiang ♂ × Dongting ♀), SCD) exposed to 0, 1 and 10 mg/L of ammonia concentrations. A 28 day feeding trial and chronic ammonia nitrogen stress were used to investigate the effects on the growth performance, histological structure and lipid metabolism of juvenile shrimp, Macrobrachium nipponense. Our results indicated that survival rates in the SCD groups were significantly higher than those in the DS groups, whereas weight and length gain rates were not significantly different between the groups (p > 0.05). Histological structure results showed that the number of vacuoles in the DS group was significantly higher than that in the SCD group and hepatopancreas cell structures were disrupted in the ammonia treatment groups. The results of oil red staining showed that the number of lipid droplets increased significantly with the increase in ammonia concentration. As the ammonia concentration increased, fatty acid contents, lipid enzyme activities and lipid metabolism-related gene expression all tended to rise. In conclusion, ammonia nitrogen exposure caused damage to the hepatopancreas structure of juvenile shrimp and disturbed the lipid metabolism of the hepatopancreas. In addition, the SCD population had stronger stress resistance than the DS population when subjected to the same concentration of ammonia nitrogen stress.

Identification of four Spätzle genes (MnSpz1, MnSpz2, MnSpz2-isoform, and MnSpz3) and their roles in the innate immunity of Macrobrachium nipponense

Spätzle, an extracellular ligand of the Toll receptor, is involved in the innate immunity of crustaceans. In this study, four Spätzle genes were cloned from Macrobrachium nipponense and designed as MnSpz1, MnSpz2, MnSpz2-isoform, and MnSpz3. The coding region of the four Spätzle genes all contained one intron and two exons, and they were predicted to be produced by gene duplication based on sequence similarities and phylogenetic tree. The predicted MnSpz1, MnSpz2, and MnSpz3 proteins all contained a signal peptide and a Spätzle domain. No signal peptide but a Spätzle domain existed in MnSpz2-isoform because of frameshift mutation caused by 50 bp nucleotide deletion compared with MnSpz2. Quantitative real-time polymerase chain reaction (RT-qPCR) analysis showed that MnSpz1, MnSpz2, and MnSpz3 were expressed in all the detected tissues of M. nipponense, and MnSpz2 was found to be the major isoform in the heart, gills, stomach, and intestine. After stimulation by Vibrio parahaemolyticus, Staphylococcus aureus, or White spot syndrome virus (WSSV), the expression levels of MnSpz1, MnSpz2, and MnSpz3 changed. Given the high similarities among MnSpz1-3, RNA interference (RNAi) using dsRNA of MnSpz1 inhibited the expression of the three Spätzle genes (MnSpz1, MnSpz2 and MnSpz3). Silencing of MnSpz1-3 down-regulated the expression levels of nine antimicrobial peptide (AMP) genes in M. nipponense. After Knockdown of MnSpzs, the number of V. parahaemolyticus, S. aureus and WSSV copies in M. nipponense increased significantly in vivo. Our results suggest that Spätzles are involved in the innate immunity of M. nipponense. The expansion of MnSpz genes through gene duplication is beneficial to enhance the innate immune defense ability of M. nipponense.

Histopathology, antioxidant responses, transcriptome and gene expression analysis in triangle sail mussel Hyriopsis cumingii after bacterial infection

Bacterial disease outbreaks in filter feeder bivalve Hyriopsis cumingii as water contamination become more frequent in the water ecosystem, especially in intensive aquaculture habitats. To characterize host-pathogen interactions between H. cumingii and bacterial infection, we investigated the effects of Stenotrophomonas maltophilia HOP3 and Aeromonas veronii GL1 on the antioxidant response, tissue invasion and transcriptome expression of H. cumingii by infectivity trials. We showed that bacterial infections resulted in tubular necrosis of the hepatopancreas and induced the acute immune response in H. cumingii. The transcriptomic study identified a total of 5957 differentially expressed genes (DEGs) after A. veronii challenge. These DEGs were implicated in 302 KEGG pathways, notably in Apoptosis, Phagosome and Lysosome. The results showed that the relative expressions of all six immune-related DEGs were effectively stimulated with A. veronii, accompanied by tissue differences. Overall, these findings will contribute to an analysis of the immune response of H. cumingii to bacterial infection at the transcriptomic level and its genomic resource for research.