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The eyestalk of crustaceans, such as Macrobrachium nipponense , contains many neurosecretory hormones affecting the process of reproduction, molting, metabolism of glucose, and other functions. In this study, important metabolic pathways and candidate genes involved in male sexual development were selected from M. nipponense . The methodology involved performing long-read and next generation transcriptome sequencing of genes from the androgenic gland after eyestalk ablation. qPCR analysis revealed that the mRNA expression of Mn-IAG was significantly increased after ablation of both the single-side (SS) and double-side (DS) eyestalk, compared with the control group (CG). The long-read transcriptome generated 49,840 non-redundant transcripts. A total of 1319, 2092 and 4351 differentially expressed genes (DEGs) were identified between CG versus SS, SS versus DS and CG versus DS, respectively. These data indicated that ablation of the double-sided eyestalk played stronger regulatory roles than the single-side ablation on male sexual development in M. nipponense . This was consistent with the qPCR analysis. Cell Cycle, Cellular Senescence, Oxidative Phosphorylation, Glycolysis/Gluconeogenesis and Steroid Hormone Biosynthesis were the primary enriched metabolic pathways in all three comparisons, and the important genes from these metabolic pathways were also selected. qPCR permitted secondary confirmation of ten DEGs identified through RNA-seq. RNAi-mediated silencing analyses of Hydroxysteroid dehydrogenase like 1 ( HSDL1 ) revealed that HSDL1 has a positive regulatory effect on testes development. This study provides valuable insight into male sexual development in M . nipponense , including metabolic pathways and genes, paving the way for advanced studies on male sexual development in this species and in other crustaceans.

Macrobrachium nipponense is a commercially important freshwater species of prawn that is widely distributed across Asian countries. In order to investigate the molecular mechanisms of growth in M. nipponense , and to provide a foundation for molecular breeding, we used genome-wide association analysis (GWAS) and transcriptomic analysis to screen polymorphisms and genes related to growth traits. We recorded the growth traits of 100 adult M. nipponense at the same growth stage, and each individual genotype was evaluated by whole genome resequencing. GWAS of growth traits detected 12 growth-related single-nucleotide polymorphisms (SNPs) and eight growth-related genes from 49 chromosomes. Of the 100 individuals, we sampled muscle tissue from a total of 18 female and male M. nipponense exhibiting large differences in growth rate for RNA-seq. Transcriptome analysis revealed a total of 27,996 unigenes; of these, 33 and 60 differentially expressed genes were identified from males and females, respectively. Of these, 12 genes associated with energy metabolism and cytoskeletal pathways were identified as growth-related genes. Notably, genes from the actin family and the ubiquitin C-terminal hydrolase 2 ( UCH2 ) gene were identified by both GWAS and transcriptomic analysis. Two growth-related SNPs, S40_12327385 and S40_12327391, were found to be mapped to the ACTB gene. The ACTA1 gene, also from the actin family, was up-regulated in fast-growing males and females, while the ACT57B was down-regulated. In addition, the growth associated SNP S7_35313774 was located in the UCH2 gene; transcriptomics analysis revealed that the UCH2 gene was up-regulated in female individuals exhibiting high growth rates. Overall, our results provided a set of markers and candidate genes related to the growth of M. nipponense . These findings could facilitate the breeding management of this species and help us to further understand the genetic mechanisms of growth in crustaceans.

Background Macrobrachium nipponense is an economically important species of freshwater shrimp in China. Unlike other marine shrimps, the ovaries in adult female M. nipponense can mature rapidly and periodically during the reproductive period, but the resulting high stocking densities and environmental deterioration can negatively impact the harvest yield and economic benefits. To better understand ovary development in female M. nipponense , we performed systematic transcriptome sequencing of five different stages of ovarian maturation. Results We obtained 255,966 Gb of high quality transcriptome data from 15 samples. Of the 105,082 unigenes that were selected, 30,878 were successfully annotated. From these unigenes, we identified 17 differentially expressed genes and identified three distinct gene expression patterns related to different biological processes. We found that cathepins, legumains, and cystatin were enriched in the lysosome pathway, and they are related to vitellogenin hydrolysis. Additionally, we found that myosin heavy chain 67 participated in oocyte excretion. Conclusions We provide the first detailed transcriptome data relating to the ovarian maturation cycle in M. nipponense . Our results provide important reference information about the genomics, molecular biology, physiology, and population genetics of M. nipponense and other crustaceans. It is conducive to further solve the problem of M. nipponense rapid ovarian maturation from the aspects of energy supply and cell division.

The median lethal concentration value of alkalinity tolerance for Macrobrachium nipponense over 96 h is only 14.42 mmol/L with a safety value of 4.71 mmol/L, which is insufficient to perform the aquaculture program in a water environment with high alkalinity. Thus, the present study aims to explore the effects of alkalinity exposure on the gills of M. nipponense through identifying the changes in antioxidant enzymes, morphology, and gene expressions after 1 day, 4 days, and 7 days of exposure under an alkalinity of 10 mmol/L. The activities of MDA, GSH-PX, CAT, T-AOC, and Ca2+Mg2+-ATPase are significantly stimulated by 62.6%, 6.57%, 32.1%, 33.3%, and 14.9%, compared to those from Day 0 (control group), indicating that these antioxidant enzymes play essential roles in the protection of prawns from the damage of reactive oxygen species caused by alkalinity exposure. In addition, alkalinity exposure results in an increase in the hemolymph vessels, affecting the normal respiratory function of the gills. Transcriptome profiling analysis reveals that short-term alkali exposure (4 days) does not result in significant changes in gene expression in the present study. Furthermore, metabolic pathways, biosynthesis of amino acids, amino sugar and nucleotide sugar metabolism, lysosomes, glycolysis/gluconeogenesis, and phagosomes represent the main enriched metabolic pathways of differentially expressed genes (DEGs) between Day 4 and Day 7. Biosynthesis of amino acids, lysosomes, and phagosomes are immune-related metabolic pathways, while amino sugar and nucleotide sugar metabolism and glycolysis/gluconeogenesis are energy metabolism-related metabolic pathways, indicating that the processes of immune response and energy metabolism play essential roles in the response to alkalinity exposure in M. nipponense. Thus, the DEGs from these metabolic pathways are considered as candidate genes involved in the regulation of alkaline acclimation in M. nipponense. The present study provides valuable evidence for analysis of the adaptive mechanism when exposed to alkalinity, contributing to the survival rate and aquaculture of this species under water environments with high alkalinity.

Sex differentiation in crustaceans is a complex process influenced by various factors, including the androgenic gland and sex-related genes. This study characterized the role of the Mn-DHCR24 gene in the oriental river prawn ( Macrobrachium nipponense ). We used bioinformatics to analyze sequence features and phylogenetic relationships of a single Mn-DHCR24 gene. The expression patterns of Mn-DHCR24 across different tissues and developmental stages were determined by real-time PCR, and its localization in testis was determined by in situ hybridization. RNA interference was used to knock down Mn-DHCR24 expression, followed by examining changes in sex ratio and gonadal development at the PL10 stage. Additionally, an enzyme-linked immunosorbent assay measured 17α-methyltestosterone levels, and tissue sections were used to characterize gonadal development. The results indicated that Mn-DHCR24 was high expression in testis, which was critical for sperm maturation and gonadal differentiation. RNAi experiments showed the role of Mn-DHCR24 during reproductive regulation rather than as a master gene for sex differentiation. This study further showed that Mn-DHCR24 regulated sex and hormone-related genes, influencing steroid biosynthesis pathways. Together, these findings provided valuable insights into the genetic and hormonal mechanisms of gonadal differentiation in M. nipponense , and supported the development of monosex culture technology.

Macrobrachium nipponense is an important commercial freshwater species in China. However, the ability of alkali tolerance of M. nipponense is insufficient to culture in the major saline-alkali water source in China. Thus, it is urgently needed to perform the genetic improvement of alkali tolerance in this species. In the present study, we aimed to analyse the effects of alkali treatment on gills in this species after 96 h alkalinity exposure under the alkali concentrations of 0 mmol/L, 4 mmol/L, 8 mmol/L, and 12 mmol/L through performing the histological observations, measurement of antioxidant enzymes, metabolic profiling analysis, and transcriptome profiling analysis. The results of the present study revealed that alkali treatment stimulated the contents of malondialdehyde, glutathione, glutathione peroxidase in gills, indicating these antioxidant enzymes plays essential roles in the protection of body from the damage, caused by the alkali treatment. In addition, high concentration of alkali treatment (> 8 mmol/L) resulted in the damage of gill membrane and haemolymph vessel, affecting the normal respiratory function of gill. Metabolic profiling analysis revealed that Metabolic pathways, Biosynthesis of secondary metabolites, Biosynthesis of plant secondary metabolites, Microbial metabolism in diverse environments, Biosynthesis of amino acids were identified as the main enriched metabolic pathways of differentially expressed metabolites, which are consistent with the previous publications, treated by the various environmental factors. Transcriptome profiling analyses revealed that the alkali concentration of 12 mmol/L has more regulatory effects on the changes of gene expression than the other alkali concentrations. KEGG analysis revealed that Phagosome, Lysosome, Glycolysis/Gluconeogenesis, Purine Metabolism, Amino sugar and nucleotide sugar metabolism, and Endocytosis were identified as the main enriched metabolic pathways in the present study, predicting these metabolic pathways may be involved in the adaption of alkali treatment in M. nipponense . Phagosome, Lysosome, Purine Metabolism, and Endocytosis are immune-related metabolic pathways, while Glycolysis/Gluconeogenesis, and Amino sugar and nucleotide sugar metabolism are energy metabolism-related metabolic pathways. Quantitative PCR analyses of differentially expressed genes (DEGs) verified the accuracy of the RNA-Seq. Alkali treatment significantly stimulated the expressions of DEGs from the metabolic pathways of Phagosome and Lysosome, suggesting Phagosome and Lysosome play essential roles in the regulation of alkali tolerance in this species, as well as the genes from these metabolic pathways. The present study identified the effects of alkali treatment on gills, providing valuable evidences for the genetic improvement of alkali tolerance in M. nipponense .

China possesses vast saline-alkaline water resources, necessitating their utilization. Macrobrachium nipponense , an economically important freshwater shrimp with notable salinity tolerance, is a candidate for saline aquaculture. This study determined the 96-h LC 50 of salinity for the genetically improved \" Taihu No. 3 \" strain juveniles across a gradient (0–30 parts per thousand) and investigated associated stress responses. Morphological, physiological, and molecular responses were analyzed via antioxidant enzyme activity (glutathione peroxidase (GPx), glutathione reductase (GR), catalase (CAT), superoxide dismutase (SOD), malondialdehyde (MDA)) and immune gene expression in hepatopancreas and gills. Results showed the 96-h LC 50 was 11.841 ppt, significantly lower than wild populations, suggesting enhanced energy allocation towards growth over osmoregulation in \" Taihu No. 3 \". Acute and chronic stress significantly elevated GPx, GR, CAT, SOD activities and MDA levels ( P  < 0.05), indicating their critical role in mitigating oxidative damage and maintaining homeostasis. Salinity ≥ 10 ppt induced structural damage, including hepatopancreatic basement membrane disruption and gill alterations (enlarged interlamellar spaces, epithelial swelling). Chronic exposure significantly upregulated immune genes ( CAT , Mn-SOD , Cu/Zn-SOD ) in both tissues ( P  < 0.05), demonstrating their involvement in saline acclimation. These findings define measurable salinity tolerance limits and elucidate key immune response mechanisms in \" Taihu No. 3 \", providing a scientific basis for its cultivation in saline-alkaline aquaculture.

Macrobrachium nipponense represents a commercial decapod species that predominantly inhabits freshwater ecosystems or environments with low salinity. However, the species exhibits normal survival and reproductive capacity in natural aquatic habitats with salinity levels up to 10 parts per thousand (ppt). The present study aimed to elucidate the molecular mechanisms underlying salinity acclimation in M. nipponense by investigating alterations in oxidative stress, morphological adaptations, and hepatopancreatic gene expression profiles following exposure to a salinity level of 10 ppt. The present study demonstrates that glutathione peroxidase and Na+/K+-ATPase play critical roles in mitigating oxidative stress induced by elevated salinity in M. nipponense. Furthermore, histological analysis revealed distinct pathological alterations in the hepatopancreas of M. nipponense following 7-day salinity exposure, including basement-membrane disruption, luminal expansion, vacuolization, and a marked reduction in storage cells. Transcriptomic profiling of M. nipponense hepatopancreas suggested coordinated activation of both immune (lysosome and protein processing in endoplasmic reticulum pathways) and energy (pyruvate metabolism, glycolysis/gluconeogenesis, and citrate cycle) metabolic processes during salinity acclimation in M. nipponense. Quantitative real-time PCR validation confirmed the reliability of RNA-seq data. This study provides molecular insights into the salinity adaptation mechanisms in M. nipponense, offering potential applications for improving cultivation practices in brackish water environments.

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.

This study conducted a bioinformatic analysis of two Hyaluronidase-like isoforms (Mn-HyaL1 and Mn-HyaL2) in Macrobrachium nipponense and investigated their phylogenetic relationships. The open reading frames of Mn-HyaL1 and Mn-HyaL2 were 1101 bp (encoding 366 amino acids) and 1164 bp (encoding 387 amino acids), respectively. Both isoforms exhibited similar conserved domains, with an amino acid sequence similarity of 60.21%. Quantitative PCR analysis revealed that the expression levels of Mn-HyaL1 and Mn-HyaL2 increased during the mid-to-late phase of each developmental stage, were higher during the reproductive season than in the non-reproductive season, and were more abundant in the hepatopancreas than in other tissues. RNA interference experiments targeting both genes simultaneously demonstrated that knockdown of Mn-HyaL2 significantly accelerated ovarian development in M. nipponense, indicating that Mn-HyaL genes function as negative regulators of ovarian maturation. A comparative analysis of multiple genes revealed the following descending order of potency in promoting ovarian development in M. nipponense: Mn-Cholesterol 7-desaturase > Mn-Cathepsin L1. The order of potency in inhibiting ovarian development in M. nipponense, from strongest to weakest, was determined to be Mn-Gonad-inhibiting hormone > Mn-HyaL2.