Molecular insights into reproduction regulation of female Oriental River prawns Macrobrachium nipponense through comparative transcriptomic analysis

Insulin-like Androgenic Gland Hormone Induced Sex Reversal and Molecular Pathways in Macrobrachium nipponense: Insights into Reproduction, Growth, and Sex Differentiation

This study investigated the potential to use double-stranded RNA insulin-like androgenic gland hormone (dsIAG) to induce sex reversal in Macrobrachium nipponense and identified the molecular mechanisms underlying crustacean reproduction and sex differentiation. The study aimed to determine whether dsIAG could induce sex reversal in PL30-male M. nipponense during a critical period. The sex-related genes were selected by performing the gonadal transcriptome analysis of normal male (dsM), normal female (dsFM), neo-female sex-reversed individuals (dsRM), and unreversed males (dsNRM). After six injections, the experiment finally resulted in a 20% production of dsRM. Histologically, dsRM ovaries developed slower than dsFM, but dsNRM spermathecae developed normally. A total of 1718, 1069, and 255 differentially expressed genes were identified through transcriptome sequencing of the gonads in three comparison groups, revealing crucial genes related to reproduction and sex differentiation, such as GnRHR, VGR, SG, and LWS. Principal Component Analysis (PCA) also distinguished dsM and dsRM very well. In addition, this study predicted that the eyestalks and the "phototransduction-fly" photoperiodic pathways of M. nipponense could play an important role in sex reversal. The enrichment of related pathways and growth traits in dsNRM were combined to establish that IAG played a significant role in reproduction, growth regulation, and metabolism. Finally, complete sex reversal may depend on specific stimuli at critical periods. Overall, this study provides valuable findings for the IAG regulation of sex differentiation, reproduction, and growth of M. nipponense in establishing a monoculture.

Dual roles of CYP302A1 in regulating ovarian maturation and molting in Macrobrachium nipponense

CYP302A1 is a member of the Halloween genes in the cytochrome P450 supergene family, which play an important regulatory role in the synthesis of 20-hydroxyecdysone (20E) in crustaceans and insects. In this study, we found that the Mn-CYP302A1sequence included typical CYP450 conserved domains. Phylogenic showed that it is closely related to crustaceans and insects. q-PCR analysis indicated that Mn-CYP302A1 was highly expressed in the ovaries and peaked before ovarian maturation. Mn-CYP302A1 expression was higher at the post-larval stage of day 15 than at other stages of embryogenesis. In situ hybridization indicated that Mn-CYP302A1 was mainly distributed in the nucleus, yolk granules, cell membrane and cytoplasm To further establish the function of CYP302A1, a 21-day RNA interference experiment was conducted. On day 16, the Gonad Somatic Index of the control group and the experimental group showed significant differences, with GSI of 11.72% in the control group and 3.21% in the experimental group. The cumulative proportion of the second entry into stage O-Ⅲ was 100% in the control group, while it was 41.67% in the experimental group on day 21. The ecdysone content was 8.91nmol/L in the control group and 6.11nmol/L in the experimental group on day 9. A significant difference in the molting proportion between the control group and the experimental group was also observed (49% in the control group and 34% in the experimental group) on day 16. Statistical results showed that the average molting cycle of the control group was 14.5 days, while that of the experimental group was 16.5 days. However, the morphological structure of ovarian tissue did not abnormal change. Therefore, the results of this study suggest that Mn-CYP302A1 can promote ovarian maturation and molting in female M. nipponense.

Mn-XRN1 Has an Inhibitory Effect on Ovarian Reproduction in Macrobrachium nipponense

XRN1 is an exoribonuclease that degrades mRNA in the cytoplasm along the 5'-3' direction. A previous study indicated that it may be involved in the reproduction of Macrobrachium nipponense. Quantitative real-time PCR was used to detect the spatiotemporal expression pattern of Mn-XRN1. At the tissue level, Mn-XRN1 was significantly expressed in the ovary. During development, Mn-XRN1 was significantly expressed at the CS stage of the embryo, on the 10th day post-larval and in the O2 stage of ovarian reproduction. The in situ hybridization results showed the location of Mn-XRN1 in the ovary. The expression of Mn-VASA was significantly increased after in vivo injection of Mn-XRN1 dsRNA. This suggests that Mn-XRN1 negatively regulates the expression of Mn-VASA. Furthermore, we counted the number of M. nipponense at various stages of ovarian reproduction on different days after RNAi. The results showed that ovarian development was significantly accelerated. In general, the results of the present study indicate that Mn-XRN1 has an inhibitory effect on the ovarian maturation of M. nipponense. The inhibitory effect might be through negative regulation of Mn-VASA.

Function Analysis of Cholesterol 7-Desaturase in Ovarian Maturation and Molting in Macrobrachium nipponense: Providing Evidence for Reproductive Molting Progress

The Cholesterol 7-desaturase gene plays an important role in insect ecdysone synthesis, but its role in ovarian development has not been reported. In this study, characteristics and the phylogenetic relationship of Cholesterol 7-desaturase were identified by bioinformatics. qPCR showed that the Mn-CH7D gene was highly expressed in the ovary, which was much higher than that in other tissues, and the expression level of Mn-CH7D reached the highest level at the third stage of the ovarian development stage (O-III). During embryonic development, the Mn-CH7D gene expression was highest in the zoea stage. The function of the Mn-CH7D gene was explored by RNA interference. The experimental group was injected with Mn-CH7D dsRNA through the pericardial cavity of M. nipponense, while the control group was injected with the same volume of dsGFP. Statistical analysis of gonadal development and GSI calculation showed that the silencing of Mn-CH7D resulted in the suppression of gonadal development. In addition, the molting frequency of the experimental group was significantly lower than that of the control group during the second molting cycle after silencing Mn-CH7D. On the seventh day after silencing, ecdysone content in the experimental group was significantly reduced. These results demonstrated that the Mn-CH7D gene played a dual role in ovarian maturation and molting of M. nipponense.

Hepatopancreas Proteomic Analysis Reveals Key Proteins and Pathways in Regulatory of Ovary Maturation of Macrobrachium nipponense

A TMT-based (Tandem Mass Tag) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was employed to explore differentially expressed proteins (DEPs) and KEGG pathways in hepatopancreas of 5 ovary stages. In total, 17,999 peptides were detected, among which 3395 proteins were identified. Further analysis revealed 26, 24, 37, and 308 DEPs in HE-I versus HE-II, HE-II versus HE-Ⅲ, HE-Ⅲ versus HE-Ⅳ, and HE-Ⅳ versus HE-Ⅴ, respectively (HE-I, HE-II, HE-III, HE-IV, and HE-V means hepatopancreas sampled from ovary stage I to V.). Gene ontology (GO) analysis indicated that DEPs were significantly enriched in "catalytic activity", "metabolic process", and "cell" of 4 comparison groups in turn. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results showed that in hepatopancreas, as the ovaries developed to maturation, carbohydrate metabolism, lipid metabolism, amino acid metabolism, and lysosome played important roles in turn. The mRNA expression of 15 selected DEPs were consistent with proteome results by qPCR analysis. Further mRNA expression investigation results suggested 4 proteins (fatty acid-binding protein, NPC intracellular cholesterol transporter 1, Serine hydroxymethyltransferase, and Crustapin) were involved in ovary maturation. These results enhance the understanding of the regulatory role of hepatopancreas in M. nipponense ovary maturation and provide new insights for understanding the crustacean regulation mechanisms.

Eyestalk neuropeptide identification in the female red deep-sea crab, Chaceon quinquedens

Eyestalk-derived neuropeptides, primarily the crustacean hyperglycemic hormone (CHH) neuropeptide family, regulate vitellogenesis in decapod crustaceans. The red deep-sea crab, Chaceon quinquedens, a cold-water species inhabiting depths between 200 and 1800 m, has supported a small fishery, mainly harvesting adult males in the eastern US for over 40 years. This study aimed to understand the role of eyestalk-neuropeptides in vitellogenesis in C. quinquedens with an extended intermolt stage. Chromatography shows two CHH and one MIH peak in the sinus gland, with a CHH2 peak area four times larger than CHH1. The cDNA sequence of MIH and CHH of C. quinquedens is isolated from the eyestalk ganglia, and the qPCR assay shows MIH is significantly higher only at ovarian stages 3 than 4 and 5. However, MIH transcript and its neuropeptides do differ between stages 1 and 3. While CHH transcripts remain constant, its neuropeptide levels are higher at stages 3 than 1. Additionally, transcriptomic analysis of the de novo eyestalk ganglia assembly at ovarian stages 1 and 3 found 28 eyestalk neuropeptides. A GIH/VIH or GSH/VSH belonging to the CHH family is absent in the transcriptome. Transcripts per million (TPM) values of ten neuropeptides increase by 1.3 to 2.0-fold at stage 3 compared to stage 1: twofold for Bursicon α, followed by CHH, AKH/corazonin-like, Pyrokinin, CCAP, Glycoprotein B, PDH1, and IDLSRF-like peptide, and 1.3-fold of allatostatin A and short NP-F. WXXXRamide, the only downregulated neuropeptide, decreases TPM by ∼ 2-fold at stage 3, compared to stage 1. Interestingly, neuroparsin with the highest TPM values remains the same in stages 1 and 3. The mandibular organ-inhibiting hormone is not found in de novo assembly. We report that CHH, MIH, and eight other neuropeptides may play a role in vitellogenesis in this species.

MnHR4 Functions during Molting of Macrobrachium nipponense by Regulating 20E Synthesis and Mediating 20E Signaling

HR4, a member of the nuclear receptor family, has been extensively studied in insect molting and development, but reports on crustaceans are still lacking. In the current study, the MnHR4 gene was identified in Macrobrachium nipponense. To further improve the molting molecular mechanism of M. nipponense, this study investigated whether MnHR4 functions during the molting process of M. nipponense. The domain, phylogenetic relationship and 3D structure of MnHR4 were analyzed by bioinformatics. Quantitative real-time PCR (qRT-PCR) analysis showed that MnHR4 was highly expressed in the ovary. In different embryo stages, the highest mRNA expression was observed in the cleavage stage (CS). At different individual stages, the mRNA expression of MnHR4 reached its peak on the fifteenth day after hatching (L15). The in vivo injection of 20-hydroxyecdysone (20E) can effectively promote the expression of the MnHR4 gene, and the silencing of the MnHR4 gene increased the content of 20E in M. nipponense. The regulatory role of MnHR4 in 20E synthesis and 20E signaling was further investigated by RNAi. Finally, the function of the MnHR4 gene in the molting process of M. nipponense was studied by counting the molting frequency. After knocking down MnHR4, the molting frequency of M. nipponense decreased significantly. It was proved that MnHR4 plays a pivotal role in the molting process of M. nipponense.

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.

Cathepsin D Plays a Vital Role in Macrobrachium nipponense of Ovary Maturation: Identification, Characterization, and Function Analysis

The oriental river prawn Macrobrachium nipponense is an economically important aquacultural species. However, its aquaculture is negatively impacted by the rapid sexual maturation of female M. nipponense. The fast sexual maturation produces a large number of offspring which leads to a reduction in resilience, a low survival rate, and an increased risk of hypoxia, this in turn, seriously affects the economic benefits of prawn farming. Cathepsin D is a lysosomal protease involved in the ovarian maturation of M. nipponense. In the current study, the cDNA of the gene encoding cathepsin D (Mn-CTSD) was cloned from M. nipponense. The total length was 2391 bp and consisted of an open reading frame (ORF) of 1158 bp encoding 385 amino acids. Sequence analysis confirmed the presence of conserved N-glycosylation sites and characteristic sequences of nondigestive cathepsin D. The qPCR analysis indicated that Mn-CTSD was highly expressed in all tissues tested, most significantly in the ovaries, whereas in situ hybridization showed that expression occurred mainly in oocyte nuclei. Analysis of its expression during development showed that Mn-CTSD peaked during the O-IV stage of ovarian maturation. For the RNAi interference experiment, female M. nipponense specimens in the ovary stage I were selected. Injection of Mn-CTSD double-stranded (ds)RNA into female M. nipponense decreased the expression of Mn-CTSD in the ovaries, such that the Gonad Somatic Index (GSI) of the experimental group was significantly lower than that of the control group (1.79% versus 4.57%; p < 0.05). Ovary development reached the O-III stage in 80% of the control group, compared with 0% in the experimental group. These results suggest that Mn-CTSD dsRNA inhibits ovarian maturation in M. nipponense, highlighting its important role in ovarian maturation in this species and suggesting an approach to controlling ovarian maturation during M. nipponense aquaculture.

A Novel Legumain-Like Protease in Macrobrachium nipponense: Identification, Characterization, and Function Analysis in Ovary Maturation

Legumain, also called aspartic endopeptidase (AEP), is a member of the cysteine protease family and is involved in various physiological processes. In this study, we analyzed the characteristics of a novel legumain-like (named Mn-Lel) in the female oriental river prawn, Macrobrachium nipponense, which is involved in ovary maturation. The Mn-Lel is 1,454 bp in length, including a 1,290-bp open reading frame that encodes 430 amino acids. qPCR analysis indicated that Mn-Lel is specifically highly expressed in the hepatopancreas and ovaries of female prawns. It is rarely expressed in embryogenesis, weakly expressed in early larval development stages, and then significantly increased after metamorphosis, which indicated that Mn-Lel is not a maternal gene and mainly plays a role in adults. During the different ovarian stages, Mn-Lel expression in the hepatopancreas had no obvious rules, while its expression in the ovaries had a significant peak in stage III. In situ hybridization studies revealed that Mn-Lel is localized in the oocyte of the ovary. Changes in the gonadosomatic index confirmed the inhibitory effects of Mn-Lel dsRNA on ovary maturation. These results suggest that Mn-Lel has a key role in promoting ovary maturation.

Cloning, functional and regulation analysis of a novel male reproduction-related protein gene from the oriental river prawn Macrobrachium nipponense

Gonadogenesis processes in crustaceans are complex. There, however, has been a large amount of research focused on regulation of female gonad (ovary) development in crustaceans, however, there has been little focus on the male gonad (testis). In the current study, a novel male reproduction-related protein gene (Mn-MRP) was identified from Macrobrachium nipponense. The relative abundance of Mn-MRP mRNA transcript in tissues and at different developmental stages were investigated. The relative abundance of Mn-MRP mRNA transcript was larger in the testis than other tissues, and during the testis maturation stage than at other developmental stages, suggesting Mn-MRP may have important functions in reproduction processes. The RNA interference (RNAi) was used to further investigate the Mn-MRP biological function. Silencing of the Mn-MRP gene effectively decreased the abundance of the sperm gelatinase (Mn-SG) mRNA transcript, implying the protein encoded by this gene may have functions in sperm activity during the fertilization process. Further studies with RNAi and eyestalk ablation confirmed that gonad inhibiting hormone gene (Mn-GIH) is a negative regulator of Mn-MRP, and that the insulin-like androgenic gland hormone gene (Mn-IAG) is a positive regulator. There, therefore, was cloning of the Mn-MRP gene, and investigation of its potential biological function, as well as elucidation of the positive/negative regulators in current study. The results from this study provide for a greater understanding of regulatory mechanisms of male reproduction in crustaceans.

RNA interference shows that Spook, the precursor gene of 20-hydroxyecdysone (20E), regulates the molting of Macrobrachium nipponense

The aim of this study was to explore the function of the Mn-Spook gene, which was found in the ovary transcriptome of the Oriental river prawn (Macrobrachium nipponense). The Spook gene, which is the precursor gene of 20-hydroxyecdysone (20E), plays an important role in the process of molting in many arthropods, but its function in M. nipponense is unclear. We cloned the full-length Mn-Spook gene from the ovary of M. nipponense and found that it had the same conserved domains as the P450 gene of the Halloween family of genes. The Mn-Spook gene was highly expressed in ovary and gill tissue during the breeding period. During ovarian development, Mn-spook gene expression was highest at the nearly-ripe stage, and it also was highly expressed in the zoea developmental stage. Cellular localization analysis showed that Mn-Spook signals accumulated in the cytoplasmic membrane and nucleus of oocytes. Finally, we used RNA interference to evaluate the function of the Mn-Spook gene. Compared with the control group, in vivo injection of Mn-Spook dsRNA effectively downregulated the expression of Mn-Spook and the content of 20E. The molting frequency of M. nipponense in the experimental group also was significantly inhibited. These results demonstrated that the Mn-Spook gene played an important role in the molting process of M. nipponense.

Transcriptome analysis of five ovarian stages reveals gonad maturation in female Macrobrachium nipponense

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07737-5.

A Review of Pedal Peptide/Orcokinin-type Neuropeptides

Neuropeptides are endogenous active substances that play important roles in a number of physiological processes and are ubiquitous in the nervous tissue in vivo. The gene encoding pedal peptide/orcokinin-type (PP/OK-type) neuropeptide is an important member of the neuropeptide gene family and is ubiquitous in invertebrates of Bilateria; orcokinin (OK) is mainly found in Arthropoda, while pedal peptide (PP) is mainly found in Mollusca. OK and PP are also present in other animals. PP/OK-type neuropeptides are a kind of multifunctional neuropeptides predominantly expressed in the nervous tissue and play important roles in the nerve regulation of movement. Moreover, OK has a number of other physiological functions. This review describes the distribution, expression, function and maturation of PP/OK-type neuropeptides to facilitate investigations of new functions and receptors of PP/OK-type neuropeptides, providing the theoretical foundation for the potential use of PP/OK-type neuropeptides in the prevention and control of agricultural and forestry pests, as an additive for skin care products and in the screening of drugs for the treatment of diabetes.

De novo assembly of the freshwater prawn Macrobrachium carcinus brain transcriptome for identification of potential targets for antibody development

Crustaceans are major constituents of aquatic ecosystems and, as such, changes in their behavior and the structure and function of their bodies can serve as indicators of alterations in their immediate environment, such as those associated with climate change and anthropogenic contamination. We have used bioinformatics and a de novo transcriptome assembly approach to identify potential targets for developing specific antibodies to serve as nervous system function markers for freshwater prawns of the Macrobrachium spp. Total RNA was extracted from brain ganglia of Macrobrachium carcinus freshwater prawns and Illumina Next Generation Sequencing was performed using an Eel Pond mRNA Seq Protocol to construct a de novo transcriptome. Sequencing yielded 97,202,662 sequences: 47,630,546 paired and 1,941,570 singletons. Assembly with Trinity resulted in 197,898 assembled contigs from which 30,576 were annotated: 9,600 by orthology, 17,197 by homology, and 3,779 by transcript families. We looked for glutamate receptors contigs, due to their main role in crustacean excitatory neurotransmission, and found 138 contigs related to ionotropic receptors, 32 related to metabotropic receptors, and 18 to unidentified receptors. After performing multiple sequence alignments within different biological organisms and antigenicity analysis, we were able to develop antibodies for prawn AMPA ionotropic glutamate receptor 1, metabotropic glutamate receptor 1 and 4, and ionotropic NMDA glutamate receptor subunit 2B, with the expectation that the availability of these antibodies will help broaden knowledge regarding the underlying structural and functional mechanisms involved in prawn behavioral responses to environmental impacts. The Macrobrachium carcinus brain transcriptome can be an important tool for examining changes in many other nervous system molecules as a function of developmental stages, or in response to particular conditions or treatments.

Function analysis and molecular characterization of cyclin A in ovary development of oriental river prawn, Macrobrachium nipponense

Macrobrachium nipponense has the characteristics of fast ovarian development cycle, which leads to the coexistence of multiple generations, the reduction of commodity specifications and the low economic benefit. Therefore, the study on the mechanism of ovarian development is of great significance to the development of industry. Cyclin A (CycA)is a key gene regulating ovarian development in vertebrates, but little information was available for its function in crustaceans. In this study, the full-length cDNA of Mn-CycA was obtained from the ovary. The full-length cDNA (2033 bp) with an open reading frame of 1368 bp, encoded a 456-amino acid protein. qRT-PCR revealed tissue-specific expression pattern of Mn-CycA, with abundant expression in the ovary. Results in different developmental stages of ovary indicated that Mn-CycA expression is positively correlated with ovarian maturation. qRT-PCR In different developmental stages, the expression of Mn-CycA mRNA gradually increased during the embryonic stage and decreased significantly on the first day of the hatching stage. At the 25th day of the metamorphosis stage, the expression level of Mn-CycAmRNA in female shrimp was 3.5 times higher than that in male shrimp, which may be related to the proliferation of oogonia and the formation of oocytes. In situ hybridization (ISH) of ovary showed Mn-CycA was examined in all stages and was mainly located in oogonia and oocytes. Compared with the control group, the obvious change of gonad somatic index (GSI) proved that injection of Mn-CycA dsRNA could delay the ovarian development cycle, which provided strong evidence for the involvement of Mn-CycA in ovarian maturation and oogenesis, and expanded a new perspective for studying the fast ovarian development cycle in M. nipponense.

Transcriptomic analysis reveals the immune changes associated with reproduction in the clam Meretrix petechialis

Substantial mortality and economic losses in marine mollusk culture has drawn considerable attention in recent years. The changes in immune status and environmental stress are thought to be the main causes of shellfish summer mortality. The reproduction and immune defense are both physiologically demanding processes, therefore, the immune status of mollusk is likely to be affected by reproduction during breeding. In present study, we performed transcriptome and gene expression analyses in the clam Meretrix petechialis pre-/post-spawning. DEGs enrichment analysis revealed important immune signaling pathways and key genes changed after spawning. Further analysis showed females up-regulated genes involved in apoptosis, TLR signal pathway and heat shock, whereas males down-regulated complement-related genes after spawning. Additionally, both genders of clams up-regulated its immune response level to against Vibrio infection after spawning revealed by the changes of four immune-related DEGs. The up-regulation of two marker genes at the transcription and protein levels further confirmed that pathogen reinforced the expression differences of immune-related genes between the two groups. Our study provides a new insight into the understanding of molecular mechanisms underlying reproduction influenced immune differences in M. petechialis.

MnFtz-f1 Is Required for Molting and Ovulation of the Oriental River Prawn Macrobrachium nipponense

Molting and ovulation are the basic processes responsible for the growth and reproduction of Macrobrachium nipponense; however, the molecular mechanisms of molting and ovulation in M. nipponense are poorly understood. The present study aimed to use MnFtz-f1 as the starting point to study the molting and ovulation phenomena in M. nipponense at the molecular level. The full-length MnFtz-f1 cDNA sequence was 2,198 base pairs (bp) in length with an open reading frame of 1,899 bp encoding 632 amino acids. Quantitative real-time PCR analysis showed that MnFtz-f1 was highly expressed in the ovary at the cleavage stage and on the fifth day after hatching. In vivo administration of 20-hydroxyecdysone (20E) showed that 20E effectively inhibited the expression of the MnFtz-f1 gene, and the silencing of the MnFtz-f1 gene reduced the content of 20E in the ovary. In situ hybridization (ISH) analysis revealed the localization of MnFtz-f1 in the ovary. Silencing of MnFtz-f1 by RNA interference (RNAi) resulted in significant inhibition of the expression of the vitellogenin (Vg), Spook, and Phantom genes, thus confirming that MnFtz-f1 had a mutual regulatory relationship with Vg, Spook, and Phantom. After RNAi, the molting frequency and ovulation number of M. nipponense decreased significantly, which demonstrated that MnFtz-f1 played a pivotal role in the process of molting and ovulation.

Three neuroparsin genes from oriental river prawn, Macrobrachium nipponense, involved in ovary maturation

In this study, we identified three neuroparsin (NP) genes in Macrobrachium nipponense: Mn-NP1, Mn-NP2, and Mn-NP3, encoding 99, 100, and 101 amino acid proteins, respectively. Multiple sequence alignments showed that these genes contained 12 cysteine residues, of which 11 were at conserved positions. The total sequence identity between the genes was 47.5%, and they showed a high degree of sequence identity (> 54% similarity) with other crustacean genes. Phylogenetic tree analysis showed that Mn-NPs were clustered at different branches, indicating that Mn-NPs may have different functions. Tissue distribution data revealed that the three genes were present in males and females during the breeding and nonbreeding season, but their expression patterns differed. Mn-NP1 was highly expressed in the breeding season, in the male testis, and highly expressed in the nonbreeding season, in the female ovary. Mn-NP3 exhibited biased female expression in the breeding and nonbreeding season, with dominant expression in the ovary. All Mn-NPs were detected during embryo development, but with different expression patterns. These data indicated that Mn-NP1 may function during embryonic development, and that Mn-NP2 may be expressed during early embryo cell division, and late larval development. Mn-NP3 expression patterns reflected maternal inheritance, and may be associated with ovarian maturation. These expression data suggested that Mn-NP1 and Mn-NP2 are negatively correlated with ovarian development, with inhibition roles during this development. Mn-NP3 may be involved in vitellogenesis.

Comparative metabolomics analysis of ovarian developmental stages in Macrobrachium nipponense

Rapid sexual maturity of female Macrobrachium nipponense is a severe problem for the aquaculture industry. To date, there have been only transcriptome studies investigating ovarian development, and studies using other tools, such as metabolomics are lacking. Metabolomics reveals changes in the level of metabolites in tissues in relation to current physiological characteristics, and can yield valuable insight into the growth and development of organisms. In this study, we systematically analyzed 15 samples from five different ovarian developmental stages in M. nipponense to learn more about how metabolites change over reproduction. Gas chromatography/time-of-flight mass spectroscopy revealed an array of different compounds and 83-162 pathways depending on the stage. Furthermore, 89 metabolites and 14 pathways were significantly different across stages. It is hypothesized that N-acetyl-N-formyl-5-methoxykynurenamine, ascorbate, fructose-2,6-bisphosphate, cortexolone and other metabolites that significantly differed by stage are regulated by hormones and are closely related to ovarian development. However, for other metabolites that changed with development, such as cytidine and xanthine, an association with ovarian development has yet to be revealed. Quantitative polymerase chain reaction was used to correlate gene changes to metabolites in the pathway for biosynthesis of plant secondary metabolites. We found that the TCA cycle rate may be the cause of female miniaturization during the reproductive period, and that the control of fatty acid content via aquaculture nutrition may be an exogenous tool for regulatory control of maturation. This study provides a systematic and comprehensive metabolomics analysis of ovarian development in M. nipponense and lays a foundation for addressing the problem of rapid sexual maturity.

Molecular insights into ovary degeneration induced by environmental factors in female oriental river prawns Macrobrachium nipponense

The oriental river prawn, Macrobrachium nipponense, is an important breeding species in China. The ovary development of this prawn is regulated by the genetic factors and external environmental factors and has obvious seasonal regularity. However, the molecular mechanism of regulating ovary degradation in M. nipponense remains unclear. To address this issue, we performed transcriptome sequencing and gene expression analyses of eyestalks, cerebral ganglia (CG) and thoracic ganglia (TG) of female M. nipponense between the full ovary stage and degenerate ovary stage. Differentially expressed genes enrichment analysis results identified several important pathways such as "phototransduction-fly," "circadian rhythm-fly" and "steroid hormone biosynthesis secretion." In the period of ovarian degeneration, the expressions of Tim, Per2 and red pigment concentration hormone (RPCH) were significantly decreased in the eyestalk, CG and TG. And expression of 7 genes in the steroid synthesis pathway, including steryl-sulfatase, cytochrome P450 family 1 subfamily A polypeptide 1, estradiol 17β-dehydrogenase 2, glucuronosyltransferase, 3-oxo-5-alpha-steroid 4-dehydrogenase 1, estradiol 17-dehydrogenase 1 and estrone sulfotransferase was significantly decreased in the CG. Food and light signals affect the expression of clock genes and thereby decrease the expression of RPCH and the estradiol synthesis-related genes in the nervous system, which may be the main cause of ovarian degeneration in M. nipponense. The results will contribute to a better understanding of the molecular mechanisms of ovarian development regulation in crustaceans.

Integrated analysis of differentially expressed microRNAs and mRNAs to screen miRNAs and genes related to reproduction in Macrobrachium nipponense

Female Macrobrachium nipponense has the characteristic of short sexual maturity during the breeding season, which can increase breeding risk and lead to prevalent female individual miniaturization. In this study, we characterized micro (mi)RNA-seq data of the eyestalk (E) and cerebral ganglia (B) of female M. nipponense during breeding and non-breeding seasons. A total of 393 and 189 differentially expressed miRNAs (DE miRNAs) were identified in BSE vs. NBSE and BSB vs. NBSB, respectively. The most abundant up- and down-regulated DE miRNAs were miR-124, miR-14, and miR-7. Enrichment analysis showed that DE miRNA target genes were mainly involved in 'metabolic process' and 'binding', and were associated with 'neurohormonal regulation' and 'photoreceptor activity' signaling pathways. Integrated analysis of miRNA-mRNA expression showed that the most abundant DE miRNAs were miR-14 and miR-278 in BSE vs. NBSE and BSB vs. NBSB, respectively. Four pairs of DE miRNAs and their corresponding target annotated genes were selected from the DE miRNA-mRNA interaction network (bmo-miR-316-5p/opsin protein, ame-miR-125/skeletal muscle actin 8, dmo-miR-278/sugar transporter, and tca-miR-3885-5p/5-HT1 receptor). Gene expression analysis of these four pairs in different ovary development stages showed their potential regulatory roles in ovary maturation.

Molecular cloning, expression pattern analysis, and in situ hybridization of a Transformer-2 gene in the oriental freshwater prawn, Macrobrachium nipponense (de Haan, 1849)

In this study, we isolated a full-length cDNA sequence from Macrobrachium nipponense and investigated its gene function. We named the gene Mntra-2a because of high similarities and close evolutionary divergence with arthropod tra-2. The full-length cDNA of Mntra-2a was 1293 bp, consisting of a 212 bp 5' UTR, a 268 bp 3' UTR, and an ORF of 813 bp encoding 270 amino acids. It contained an RNA recognition motif and a linker region. Real-time PCR analysis showed that Mntra-2a was highly expressed in the gonads of both males and females. Further in situ hybridization analysis showed that Mntra-2a was mainly located in oocytes and spermatocytes. During embryogenesis, Mntra-2a expression was higher in the cleavage and nauplius stages. During the ovarian reproductive cycle, Mntra-2a expression reached a peak at OvaryV and decreased to the lowest level at OvaryIV. These results indicated that Mntra-2a probably played important roles in embryonic development and early gonad development in M. nipponense. Our results provide basic information for further functional studies of tra-2 in M. nipponense.

Neural Ganglia Transcriptome and Peptidome Associated with Sexual Maturation in Female Pacific Abalone (Haliotis discus hannai)

Genetic information of reproduction and growth is essential for sustainable molluscan fisheries and aquaculture management. However, there is limited knowledge regarding the reproductive activity of the commercially important Pacific abalone Haliotisdiscushannai. We performed de novo transcriptome sequencing of the ganglia in sexually immature and mature female Pacific abalone to better understand the sexual maturation process and the underlying molecular mechanisms. Of the ~305 million high-quality clean reads, 76,684 transcripts were de novo-assembled with an average length of 741 bp, 28.54% of which were annotated and classified according to Gene Ontology terms. There were 256 differentially expressed genes between the immature and mature abalone. Tandem mass spectrometry analysis, as compared to the predicted-peptide database of abalone ganglia transcriptome unigenes, identified 42 neuropeptide precursors, including 29 validated by peptidomic analyses. Label-free quantification revealed differential occurrences of 18 neuropeptide families between immature and mature abalone, including achatin, FMRFamide, crustacean cardioactive peptide, and pedal peptide A and B that were significantly more frequent at the mature stage. These results represent the first significant contribution to both maturation-related transcriptomic and peptidomic resources of the Pacific abalone ganglia and provide insight into the roles of various neuropeptides in reproductive regulation in marine gastropods.

Characterization of G-protein coupled receptors from the blackback land crab Gecarcinus lateralis Y organ transcriptome over the molt cycle

BACKGROUND

G-protein coupled receptors (GPCRs) are ancient, ubiquitous, constitute the largest family of transducing cell surface proteins, and are integral to cell communication via an array of ligands/neuropeptides. Molt inhibiting hormone (MIH) is a key neuropeptide that controls growth and reproduction in crustaceans by regulating the molt cycle. It inhibits ecdysone biosynthesis by a pair of endocrine glands (Y-organs; YOs) through binding a yet uncharacterized GPCR, which triggers a signalling cascade, leading to inhibition of the ecdysis sequence. When MIH release stops, ecdysone is synthesized and released to the hemolymph. A peak in ecdysone titer is followed by a molting event. A transcriptome of the blackback land crab Gecarcinus lateralis YOs across molt was utilized in this study to curate the list of GPCRs and their expression in order to better assess which GPCRs are involved in the molt process.

RESULTS

Ninety-nine G. lateralis putative GPCRs were obtained by screening the YO transcriptome against the Pfam database. Phylogenetic analysis classified 49 as class A (Rhodopsin-like receptor), 35 as class B (Secretin receptor), and 9 as class C (metabotropic glutamate). Further phylogenetic analysis of class A GPCRs identified neuropeptide GPCRs, including those for Allatostatin A, Allatostatin B, Bursicon, CCHamide, FMRFamide, Proctolin, Corazonin, Relaxin, and the biogenic amine Serotonin. Three GPCRs clustered with recently identified putative CHH receptors (CHHRs), and differential expression over the molt cycle suggests that they are associated with ecdysteroidogenesis regulation. Two putative Corazonin receptors showed much higher expression in the YOs compared with all other GPCRs, suggesting an important role in molt regulation.

CONCLUSIONS

Molting requires an orchestrated regulation of YO ecdysteroid synthesis by multiple neuropeptides. In this study, we curated a comprehensive list of GPCRs expressed in the YO and followed their expression across the molt cycle. Three putative CHH receptors were identified and could include an MIH receptor whose activation negatively regulates molting. Orthologs of receptors that were found to be involved in molt regulation in insects were also identified, including LGR3 and Corazonin receptor, the latter of which was expressed at much higher level than all other receptors, suggesting a key role in YO regulation.

Transcriptome analysis of the brain of the Chinese mitten crab, Eriocheir sinensis, for neuropeptide abundance profiles during ovarian development

Neuropeptides, important messenger molecules, regulate various physiological processes, such as growth, development, and reproduction. In the present study, cDNA libraries from brains of E. sinensis were constructed and sequenced using the Illumina technique for transcript analysis and neuropeptides discovery. There were 233,887 transcripts assembled for 194,286 unigenes. According to the annotations of NCBI non-redundant protein (NR) database, 2487 (11.31%) unigenes were annotated successfully. In total, 1273 transcripts were assigned to the "signal transduction mechanisms" category using KOG analysis. The results of KEGG indicate signal transduction and translation pathways were the dominant and enriched signal pathways. Additionally, results indicated C2H2 was the main transcription factor (TF) family. Analysis of the assembled transcripts indicated there were 22 neuropeptide transcripts, such as allatostatin, crustacean female sex hormone, crustacean hyperglycemic hormone, diuretic hormone 31, and eclosion hormone. The detection of these neuropeptides provide for a basic understanding for future study of functions in development, reproduction, and sexual maturation in crustaceans.

Transcriptomic analysis of zebrafish (Danio rerio) embryos to assess integrated biotoxicity of Xitiaoxi River waters

Assessing the toxicity posed by mixtures of unknown chemicals to aquatic organisms is challenging. In this study, water samples from six cross-sections along the Xitiaoxi River Basin (XRB) were monthly or bimonthly collected in 2014. The year-period physiochemical parameters as well as one-month-water sample based acute biotoxicity tests showed that the river water quality of the year was generally in a good status. High performance liquid chromatography (HPLC) screening based on one-month-water samples suggested that the organic pollutants might be non-to-moderately-polar chemicals in very low concentrations. One-month-water sample based RNA-seq was performed to measure the mRNA differential expression profile of zebrafish larvae to furtherly explore the potential bioeffect and the spatial water quality change of the river. Result indicated that the number of deferentially expressed genes (DEGs) tended to increase along the downstream direction of the river. Gene ontology (GO) enrichment analysis implied that the key pollutants might mainly be the function disruptors of biological processes. Principle components analysis (PCA) combining with transcripts and one-month-water sample based physiochemical parameters indicated that the pollution might be similar at TP, DP and CTB sites while pollution homology existed on some extent between YBQ and JW sites. Although the water quality of the river had a complex time-space alternation during the year, and the one-month-data based RNA-seq could not reflex the whole year-water quality of a watershed, the gene expression profile via RNA-seq provided an alternative way for assessing integrated biotoxicity of surface water, and it was relatively fit for early-warning of water quality of a watershed with unobservable acute toxicity. However, the identification of detail toxicants and the links between DEGs and pollution level as well as physiological-biochemical toxicity needed further investigation.

Comparative transcriptional analysis and RNA interference reveal immunoregulatory pathways involved in growth of the oriental river prawn Macrobrachium nipponense

A source of premium animal protein, crustaceans are widely distributed and cultivated around the world. Short-term or long-term starvation events occur frequently owing to natural environment changes or manual management strategies in the life cycle of crustaceans. The result induced by starvation is that somatic growth of crustaceans will be retarded, while the immune mechanism is activated in this process. The aim of this study was to investigate whether the immune regulatory pathways are involved in the growth of crustaceans. Twelve muscle tissue transcriptomes of the oriental river prawn Macrobrachium nipponense were sequenced across four fasting stages lasting 0, 7, 14 and 21 d. The results showed that three immune-related pathways were involved in the growth of M. nipponense by regulating actin expression inducing the chemokine signaling pathway, the leukocyte transendothelial migration pathway and the FcR-mediated phagocytosis pathway. Furthermore, we employed RNA interference (RNAi) to further verify the effects that genes involved in the pathways had on regulating growth of M. nipponense. Comparative transcriptional analysis and RNA interference reveal that VASP and WAVE positively regulated the expression of actin; however, WASP negatively regulated the expression of actin. This is the first report that the immune regulatory pathways play key roles in the growth of crustaceans. Our results will not only provide an entirely new understanding of the immune mechanism of crustaceans from a unique angle but also further enrich and develop the theory of growth and developmental biology in crustaceans.

Validation and Evaluation of Reference Genes for Quantitative Real-Time PCR in Macrobrachium Nipponense

Quantitative real-time PCR (qPCR) is widely used in molecular biology, although the accuracy of the quantitative results is determined by the stability of the reference genes used. Recent studies have investigated suitable reference genes for some crustaceans under various conditions, but studies in Macrobrachium nipponense are currently lacking. In this study, we selected the following seven genes from among 35 commonly used housekeeping genes as candidate qPCR reference genes for temporal and spatial expression: EIF (eukaryotic translation initiation factor 5A), 18S (18S ribosomal RNA), EF-1α (elongation factor-1α), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), TUB (α-tubulin), β-act (β-actin), and RPL18 (Ribosomal protein L18). The stability of each reference gene was evaluated by GeNorm, NormFinder, BestKeeper, and comparative ∆C _t methods, and was comprehensively ranked using RefFinder. RPL18 was shown to be the most suitable reference gene for adult M. nipponense tissues, while EIF was the most stable in different ovarian and embryo stages and in white spot syndrome virus infection, and β-act was the most stable reference gene under hypoxia stress. The reliability of the rankings was confirmed by RNA interference experiments. To the best of our knowledge, this represents the first systematic analysis of reference genes for qPCR experiments in M. nipponense, and the results will provide invaluable information for future research in closely related 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 and characterization of opsin gene and its role in ovarian maturation in the oriental river prawn Macrobrachium nipponense

Opsins are photoreceptors with important roles in reproductive regulation in birds and fishes. In the present study, we identified an opsin gene from the eyes of the oriental river prawn Macrobrachium nipponense using expressed sequence tag analysis and rapid amplification of cDNA ends. The full-length transcript contained 1382 base pairs, encoding 375 amino acids. It was classified into the long-wavelength opsin group by phylogenetic analysis, and designated Mn-LW. Mn-LW expression demonstrated significant seasonal variation in somatic tissues from both male and female prawns, with the highest expression in the eyes, and expression also shown in the ovary. The expression profiles of Mn-LW in eyes and ovary were positively related to ovarian development. In situ hybridization showed that Mn-LW was present in retinular cells in the eye and oocytes in the ovary. Injection of Mn-LW dsRNA in vivo effectively down-regulated Mn-LW expression levels compared with control levels. Mn-LW dsRNA injection also significantly reduced vitellogenin (Vg) expression, indicating a close relationship between Mn-LW and Vg in ovarian development. These results suggest that Mn-LW may play an important role in Vg synthesis and accumulation during ovarian maturation in M. nipponense.