Hemolymph transcriptome analysis of Chinese mitten crab (Eriocheir sinensis) with intact, left cheliped autotomy and bilateral eyestalk ablation

A myogenic regulatory factor is required for myogenesis during limb regeneration in the Chinese mitten crab

Myogenic regulatory factors (MRFs) are a group of transcription factors that regulate the activity of skeletal muscle cells during embryonic development and postnatal myogenesis in various vertebrate species. However, the role of MRFs in limb regeneration remains poorly understood in crustaceans. In this study, we identified a full-length cDNA encoding a myogenic regulatory factor from Eriocheir sinensis (EsMRF) and evaluated its mRNA expression profile during muscle development, growth, and regeneration. The expression of EsMRF was found to correlate with the onset of muscle formation during development and with the regeneration process following limb autotomy. To elucidate the function of MRF during limb regeneration in E. sinensis, we assessed regenerative efficiency using RNA interference (RNAi) targeting EsMRF. Our findings revealed that the blockade of MRF delayed limb regeneration by disrupting the proliferation and myogenesis of blastema cells at the basal growth stage. Furthermore, luciferase assays results demonstrated that EsMRF can transcriptionally activate target myogenic genes, either through direct binding to their promoters or by interacting with co-regulators such as EsHEB or EsMEF2. This study identifies a novel MRF in E. sinensis and elucidates its function during limb regeneration, thereby contributing to our understanding of muscle growth and regeneration mechanisms in crustaceans.

Identifying the genes involved in the egg-carrying ovigerous hair development of the female blue crab Callinectes sapidus: transcriptomic and genomic expression analyses

BACKGROUND

Crustacean female sex hormone (CFSH) controls gradually developing adult female-specific morphological features essential for mating and brood care. Specifically, ovigerous hairs are developed during the prepuberty molt cycle of the blue crab Callinectes sapidus that are essential for carrying the eggs until they finish development. Reduced CFSH transcripts by CFSH-dsRNA injections result in fewer and shorter ovigerous hairs than the control. This study aimed to identify the specific genes responsible for ovigerous hair formation using transcriptomic, genomic and expression analyses of the ovigerous setae at three stages: prepuberty at early (OE) and late premolt (OL), and adult (AO) stages.

RESULTS

The de novo Trinity assembly on filtered sequence reads produced 96,684 Trinity genes and 124,128 transcripts with an N50 of 1,615 bp. About 27.3% of the assembled Trinity genes are annotated to the public protein sequence databases (i.e., NR, Swiss-Prot, COG, KEGG, and GO databases). The OE vs. OL, OL vs. AO, and OE vs. AO comparisons resulted in 6,547, 7,793, and 7,481 differentially expressed genes, respectively, at a log2-fold difference. Specifically, the genes involved in the Wnt signaling and cell cycle pathways are positively associated with ovigerous hair development. Moreover, the transcripts of ten cuticle protein genes containing chitin-binding domains are most significantly changed by transcriptomic analysis and RT-qPCR assays, which shows a molt-stage specific, down-up-down mode across the OE-OL-AO stages. Furthermore, the expression of the cuticle genes with the chitin-binding domain, Rebers and Riddiford domain (RR)-1 appears at early premolt, followed by RR-2 at late premolt stage. Mapping these 10 cuticle protein sequences to the C. sapidus genome reveals that two scaffolds with a 549.5Kb region and 35 with a 1.19 Mb region harbor 21 RR1 and 20 RR2 cuticle protein genes, respectively. With these findings, a putative mode of CFSH action in decapod crustaceans is proposed.

CONCLUSIONS

The present study describes a first step in understanding the mechanism underlying ovigerous hair formation in C. sapidus at the molecular level. Overall, demonstrating the first transcriptome analysis of crustacean ovigerous setae, our results may facilitate future studies into the decapod female reproduction belonging to the suborder Pleocyemata.

MicroRNA sequencing analysis reveals injury-induced immune responses of Scylla paramamosain against cheliped autotomy

During pond culture or intensive culture system of crabs (mainly Eriocheir sinensis, Portunus trituberculatus and Scylla paramamosain), high-density farming has typically contributed to a higher limb autotomy level in juvenile animals, especially in S. paramamosain which has a high level of cannibalism. Due to the high limb autotomy level, the survival and growth rates in S. paramamosain farming are restricted, which limit the growth of the mud crab farming industry. MicroRNAs (miRNAs) are small noncoding RNAs that regulate a series of biological processes including innate immune responses by post-transcriptional suppression of their target genes. MiRNAs are believed to be crucial for innate immune process of host wound healing. Many miRNAs have been verified to be required in host immune responses to repair wound and to defense pathogen after tissue damage. However, to our best knowledge, the miRNAs functions of crustacean innate immune reactions against injury induced by limb autotomy have not been studied yet. Here in this study, for the first time, miRNAs involved in the S. paramamosain immune reactions against injury induced by cheliped autotomy were obtained by high-throughput sequencing. A total of 575 miRNAs (518 known miRNAs and 57 novel predicted miRNAs) were obtained, of which 141 differentially expressed microRNAs (93 up-regulated microRNAs and 48 down-regulated microRNAs) were revealed to be modified against cheliped autotomy, and the qPCR results of randomly selected miRNAs confirmed the expression patterns in the miRNAs sequencing data. Numerous immune-related target genes associated with innate immune system were mediated by miRNAs to induce host humoral immune and cellular immune defense to minimize acute physical damage. Furthermore, the genes expression in hemolymph coagulation and melanization pathways, as well as Toll and Imd signaling pathways were mediated by miRNAs to activate host immune responses including melanization and antimicrobial peptides for rapid wound healing and killing invaded pathogens. These results will help to understand injury-induced immune responses in crabs and to develop an effective control strategy of autotomy rate in crabs farming.

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

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

Evidence from transcriptome analysis unravelled the roles of eyestalk in salinity adaptation in Pacific white shrimp (Litopenaeus vannamei)

Eyestalk is considered the main neuroendocrine organ in crustaceans. Eyestalk regulates reproduction, molting, and energy metabolism by secreting several neurohormones. However, the role of eyestalk in salinity adaptation in crustaceans remains unclear. To reveal the role of eyestalk in salinity adaptation in Litopenaeus vannamei, we performed RNA-seq to compare the transcriptomic response of the eyestalk under low salinity (salinity 3) with that of the control group (salinity 25) for 8 weeks. A total of 479 mRNAs, including 150 upregulated and 329 downregulated mRNAs, were differentially expressed between the two salinity groups. The majority of the differentially expressed genes (DEGs) were enriched in biological pathways related to osmoregulation, metabolism and energy production, and oxidative stress. The most important DEGs associated with osmoregulation were CA4, ATP1A, ATP2B, ABCB1, ABCC4, PhoA, PhoB, NOS1, ACE, ANPEP, and the V-type H⁺-ATPase E-subunit. The metabolism-related DEGs were divided into three main categories: carbohydrate and energy metabolism (i.e., G6PC, UGT), protein and amino acid metabolism (i.e., SLC15A1, AhcY, GFAT), and lipid and fatty acid metabolism (i.e., GPAT3_4, CYP2J). The key DEGs related to the oxidative stress response were UGT, NDUFB1, QCR7, QCR8, P5CDh, COX6B, and CES1. These results provide evidence for the existence of an eyestalk-salinity adaptation-stress endocrine axis in L. vannamei. These findings provide a better understanding of the molecular mechanism underlying salinity adaptation in L. vannamei.

MEK homologue is involved in immune response by regulating antimicrobial peptides expression in Chinese mitten crab Eriocheir sinensis

MEK activates the phosphorylation of downstream molecules involved in various immune responses. In this study, an MEK homologue gene in Chinese mitten crab Eriocheir sinensis (designated as EsMEK) was investigated. EsMEK mRNA was constitutively expressed in all tissues with higher expression in hepatopancreas, hemocytes, and gills. EsMEK protein was mainly localized in the cytoplasm. Lipopolysaccharide (LPS) and Aeromonas hydrophila challenge significantly increased the mRNA levels of EsMEK in hemocytes. In addition, the mRNA expression level of some antimicrobial peptides (AMPs), including EsWAP, EsDWD1, and EsALF decreased significantly due to the inhibition of EsMEK by specific dsRNA in LPS-challenged crabs. Downstream pathway analysis revealed that the phosphorylation of EsERK decreased prominently after EsMEK inhibition. These results suggested that EsMEK played an important role in regulating the expression of antimicrobial peptides in E. sinensis through MEK-ERK pathway.

Neural excitotoxicity and the toxic mechanism induced by acute hypoxia in Chinese mitten crab (Eriocheir sinensis)

Hypoxia can induce neural excitotoxicity in mammals, but this adverse effect has not been investigated in aquatic animals to date, especially in crustaceans. This study explored the induction effect and toxic mechanism of acute hypoxia stress (1.0 ± 0.1 mg dissolved oxygen /L) for 24 h on neural excitotoxicity in juvenile Chinese mitten crab, Eriocheir sinensis. The results showed that hemolymph glucose and serum lactic acid content were significantly increased, and the mRNA expression of crustacean hyperglycemic hormone and hypoxia-inducible factor 1α were significantly up-regulated in the hypoxia group compared with control. RNA-Seq results confirmed that acute hypoxia stress had a more significant impact on carbohydrate metabolism than lipid and protein metabolism. In addition, the TUNEL assay showed that the apoptosis rate of nerve cells was significantly higher in the hypoxia group than in the control, and similar trends were observed in the expression of apoptosis-related genes. RNA-Seq results also showed that acute hypoxia stress-induced neuronal apoptosis by regulating multiple apoptosis-related pathways. Moreover, free glutamate and GABA contents in the nerve tissue of thoracic ganglia were significantly higher in the hypoxia group than in the control group. Furthermore, the mRNA expression of NMDA related receptors was significantly up-regulated in the hypoxia group compared with the control. Similar trends were observed in the expression of calcium-dependent degrading enzymes and endogenous antioxidant-related proteins or enzymes. Meanwhile, the mRNA expression level of high-affinity neuronal glutamate transporter in the hypoxia group was significantly up-regulated compared with the control, whereas the vesicular glutamate transporter was significantly down-regulated. Furthermore, NMDA-R antagonists (MK-801 and Ro25-6981) injection showed that NMDA-R served as the bridge and core position of glutamate-induced neural neurotoxicity. This study provides a new perspective and theoretical guidance for exploring the regulation of hypoxic tolerance in E. sinensis.

Impact of imidacloprid exposure on the biochemical responses, transcriptome, gut microbiota and growth performance of the Pacific white shrimp Litopenaeus vannamei

The widespread use of neonicotinoid insecticides, such as imidacloprid, in agriculture is one of the key factors for the drop in the survival of invertebrates, including decapod crustaceans. However, there is currently a lack of comprehensive studies on the chronic toxicity mechanisms in decapod crustaceans. Here, the concentration-dependent effects of imidacloprid on the physiology and biochemistry, gut microbiota and transcriptome of L. vannamei , and the interaction between imidacloprid, gut microbiota and genes were studied. Imidacloprid caused oxidative stress, leading to reduced growth and to immunity and tissue damage in L. vannamei . Imidacloprid increased the gut pathogenic microbiota abundance and broke the steady state of the gut microbiota interaction network, resulting in microbiota function disorders. Chronic imidacloprid exposure induced overall transcriptome changes in L. vannamei . Specifically, imidacloprid caused a large number of differentially expressed genes (DEGs) to be significantly downregulated. The inhibition of autophagy-related pathways revealed the toxic process of imidacloprid to L. vannamei . The changes in phase I and II detoxification gene expression clarified the formation of a detoxification mechanism in L. vannamei . The disturbance of circadian rhythm (CLOCK) caused by imidacloprid is one of the reasons for the increase in gut pathogenic microbiota abundance.

Comparative transcriptome analysis reveals the impact of the daily rhythm on the hemolymph of the Chinese mitten crab (Eriocheir sinensis)

The daily rhythm affects a series of physiological functions in crustaceans. To study its effect on the physiological function in Eriocheir sinensis, a crustacean species of high economic value, we analyzed the hemolymph transcriptome during the daily rhythm by high-throughput sequencing. We sampled the hemolymph from crabs at four time points in a single day (06:00, 12:00, 18:00, and 24:00 h) and identified 3,01,661 and 1,03,998 transcripts and unigenes, respectively; some of the unigenes were annotated as core clock genes. Moreover, 15,564 differentially expressed genes (DEGs) were divided into nine different clusters. Functional enrichment analysis of DEGs indicated that the molting, metabolism, and immunity processes in E. sinensis were impacted by its daily rhythm. In addition, we mapped the DEGs involved in the daily entrainment pathway. To the best of our knowledge, this is the first comparative transcriptome analysis of crustacean hemolymph during the day-night cycle, and provides multi-level information for unraveling the finer regulatory effects of the daily cycle in crustaceans.

The Single-molecule long-read sequencing of Scylla paramamosain

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

Antioxidative status, immunological responses, and heat shock protein expression in hepatopancreas of Chinese mitten crab, Eriocheir sinensis under the exposure of glyphosate

As a broad-spectrum herbicide, glyphosate was extensively utilised in China for several decades. The contradiction between glyphosate spraying and crab breeding in the rice-crab co-culture system has become more obvious. In this study, the antioxidative status and immunological responses of Chinese mitten crab, Eriocheir sinensis, under sublethal exposure of glyphosate were investigated by detecting the antioxidative and immune-related enzyme activity, acetylcholinesterase (AChE) activity and relative mRNA expression of heat shock proteins (HSPs) in hepatopancreas. The results showed that high concentrations of glyphosate (44 and 98 mg/L) could induce significant alteration of superoxide dismutase (SOD), peroxidase (POD), acid phosphatase (ACP), alkaline phosphatase (AKP), and phenoloxidase (PO) activities by first rising then falling during the exposure. However, AChE activity in all treatments including 4.4 mg/L was inhibited markedly after 6 h of exposure. In addition, the relative mRNA expression of HSP 60, HSP 70, and HSP 90 was significantly upregulated at both 48 h and 96 h. These results revealed that glyphosate has a prominent toxic effect on E. sinensis based on antioxidative and immunological response inhibition and AChE activity reduction even at the lowest concentration of 4.4 mg/L, and a protective response by upregulation of HSPs was carried out by the species to ease the environmental stress.

Dietary L-Tryptophan Modulates the Hematological Immune and Antibacterial Ability of the Chinese Mitten Crab, Eriocheir sinensis, Under Cheliped Autotomy Stress

In pond cultures of juvenile Eriocheir sinensis, limb autotomy stress seriously affects and restricts the quality and economic benefits of aquaculture. This study was designed to evaluate the effects of dietary supplementation of L-tryptophan on E. sinensis under the cheliped autotomy stress. In the present study, 252 crabs were divided into four groups: dietary L-trp supplementation with 0.28, 0.40, 0.53, and 0.70%, and their hematological immunity, antioxidant capacity, anti-stress, and antibacterial ability were evaluated after 14 days of using biochemical analysis, flow cytometry, and molecular biology techniques. First, we counted the mortality after 14 days of feeding and found that compared with other treatments, dietary supplementation of 0.53 and 0.70% L-trp significantly lowered the mortality of E. sinensis. Moreover, the total hemocyte count (THC), hemocyanin, and glutathione (GSH) content, and glutathione peroxidase (GSH-Px) activity significantly increased at 7 and 14 d with dietary supplementation of 0.53 and 0.70% L-trp, in contrast with the significant decrease in malondialdehyde (MDA) content at 14 d in the same dietary groups (P<0.05). Next, the bacterial challenge test after 14 days of feeding showed that the THC levels, phagocytic rate, and acid phosphatase (ACP) and alkaline phosphatase (ALP) activity were significantly higher with dietary supplementation of 0.53 and 0.70% L-trp after 12 and 24 h of Aeromonas hydrophila injection, along with a significant improvement in the antioxidant capacity (P<0.05). Further, we measured the expression of antibacterial-related protein genes (EslecB and HSP 90) and found that they were significant up-regulated in the hepatopancreas, hemocytes, intestine, and gill in the groups with dietary supplementation of 0.53% and 0.70% L-trp after 12 h or 24 h of A. hydrophila injection (P<0.05). Taken together, the observations in this study indicate that dietary supplementation of L-trp can enhance the antioxidant capacity and improve the hematological immune status and antibacterial ability of E. sinensis under the cheliped autotomy stress, thereby increasing the survival rate of E. sinensis under cheliped autotomy stress.