Stimulation of molt by RNA interference of the molt-inhibiting hormone in the crayfish Cherax quadricarinatus

Silencing Multiple Crustacean Hyperglycaemic Hormone-Encoding Genes in the Redclaw Crayfish Cherax quadricarinatus Induces Faster Molt Rates with Anomalies

RNA interference (RNAi)-based biotechnology has been previously implemented in decapod crustaceans. Unlike traditional RNAi methodologies that investigate single gene silencing, we employed a multigene silencing approach in decapods based on chimeric double-stranded RNA (dsRNA) molecules coined 'gene blocks'. Two dsRNA constructs, each targeting three genes of the crustacean hyperglycaemic hormone (CHH) superfamily of neuropeptides, were produced: Type II construct targeting Cq-Molt-inhibiting hormone 1 (MIH1), Cq-MIH-like 1 (MIHL1), and Cq-MIHL2 isoforms and Type I construct targeting Cq-ion transport peptide (Cq-ITP; a putative hybrid of CHH and MIH) and Cq-CHH and Cq-CHH-like (CHHL) isoforms. Both constructs were injected into juvenile redclaw crayfish, Cherax quadricarinatus, to determine the effects of multigene knockdown on molting and developmental processes. A 20-Hydroxyecdysone (20E) enzyme-linked immunosorbent assay (ELISA) and glucose assay were used to determine the effects of RNAi on molting and hemolymph glycemic activities, respectively. Multigene silencing reduced the intermolt interval by 23%. Statistically significant elevated 20E was recorded in treated intermolt individuals, consistent with the reduced intermolt interval as well as unique and abnormal phenotypes related to the molting process, which indicates a shift in 20E-induced cascade. There was no effect of RNAi treatment on hemolymph glucose level or molt increment. Through multigene silencing and subsequent annotation of gene networks, gene blocks may provide a tailored approach to investigate complex polygenic traits with RNAi in a more efficient and scalable manner.

Transcriptome analysis uncovers the expression of genes associated with growth in the gills and muscles of white shrimp (Litopenaeus vannamei) with different growth rates

Litopenaeus vannamei is a crucial species in aquaculture. The gene expression patterns associated with distinct growth rates are not well understood. To investigate this, we used RNA-seq to study the underlying growth mechanism of L. vannamei with varying growth rates. Individuals of higher growth performance (HG), middle growth performance (MG), and lower growth performance (LG) were examined. A total of 8422 and 4560 differentially expressed genes (DEGs) were identified in gill and muscle samples, respectively. Genes related to growth were significantly up-regulated in HG gills, such as cuticle protein, chitin synthase, pupal cuticle protein, titin myosin G heavy chain, and myosin heavy chain 10. The GO enrichment analysis revealed that the DEGs of HG gills were significantly enriched in "structural constituent of cuticle", "primary metabolic process" and "chitin binding". The growth-related genes were highly expressed in HG muscle, such as myosin heavy chain, myosin heavy chain type A and myosin 3. The GO enrichment analysis revealed that the DEGs of HG muscle were significantly enriched in "myosin filament", "myosin complex" and "myofibril". These findings provide insights into mechanisms underlying the growth performance of superior L. vannamei, and identify candidate genes for genetic improvement programs aimed at enhancing this trait.

Temperature-driven changes in the neuroendocrine axis of the blue crab Callinectes sapidus during the molt cycle

Environmental cues such as temperature induce macroscopic changes in the molting cycle of crustaceans, however, the physiological mechanisms behind these changes remain unclearWe aimed to investigate the regulatory mechanisms in the intermolt and premolt stages of the Callinectes sapidus molt cycle in response to thermal stimuli. The concentration of ecdysteroids and lipids in the hemolymph, and the expression of heat shock proteins (HSPs) and molt key genes were assessed at 19 °C, 24 °C and 29 °C. The premolt animals exhibited a much larger response to the colder temperature than intermolt animals. Ecdysteroids decreased drastically in premolt animals, whereas the expression of their hepatopancreas receptor (CasEcR) increased, possibly compensating for the low hemolymphatic levels at 19 °C. This decrease might be due to increased HSPs and inhibited ecdysteroidogenesis in the Y-organ. In addition, the molting-inhibiting hormone expression in the X-organ/sinus gland (XO/SG) remained constant between temperatures and stages, suggesting it is constitutive in this species. Lipid concentration in the hemolymph, and the expression of CasEcR and CasHSP90 in the XO/SG were influenced by the molting stage, not temperature. On the other hand, the expression of HSPs in the hepatopancreas is the result of the interaction between the two factors evaluated in the study. Our results demonstrated that temperature is an effective modulator of responses related to the molting cycle at the endocrine level and that temperature below the control condition caused a greater effect on the evaluated responses compared to the thermostable condition, especially when the animal was in the premolt stage.

Epibiont Cohabitation in Freshwater Shrimp Neocaridina davidi with the Description of Two Species New to Science, Cladogonium kumaki sp. nov. and Monodiscus kumaki sp. nov., and Redescription of Scutariella japonica and Holtodrilus truncatus

This contribution presents the occurrence of epibiotic species associated with Neocaridina davidi shrimp collected in the wild, aquaculture ponds, and aquaria. A total of 900 shrimp are imported from Taiwan, three-quarters of which host at least one of the recorded epibionts. Among those epibionts, two species new to science are discovered, Cladogonium kumaki sp. nov. and Monodiscus kumaki sp. nov., while the other two, Holtodrilus truncatus and Scutariella japonica, are redescribed. The largest number of epibionts is found in shrimp collected from aquaculture ponds and the lowest in individuals from aquaria. Epibiont occurrence differs across designated microhabitats. The epibionts may be introduced alongside their host outside their native range, and their presence may affect shrimp breeding rates. Thus, more control over them should be provided. Their spread can be limited by removal from the host during molting or manually, as well as by using interspecies interactions.

Influence of Garlic (Allium sativum) Clove-Based Selenium Nanoparticles on Status of Nutritional, Biochemical, Enzymological, and Gene Expressions in the Freshwater Prawn Macrobrachium rosenbergii (De Man, 1879)

Selenium (Se) is one of the essential micronutrients for performing vital body functions. This study aims at examining the influence of dietary supplementation of garlic clove-based green-synthesized selenium nanoparticles (GBGS-SeNPs, 48-87 nm) on carcass minerals and trace elements, and growth, biochemical, enzymological, and gene expression analyses in the freshwater prawn, Macrobrachium rosenbergii post larvae (PL). The 96 h LC₅₀ of this GBGS-SeNPs to M. rosenbergii PL was 52.23 mg L^-1. Five different artificial diets without supplementation of GBGS-SeNPs (control, 0.0 mg kg^-1) and with supplementations of GBGS-SeNPs starting from 100 times lower than the LC₅₀ value (0.5, 1.0, 1.5, and 2.0 mg kg^-1) were prepared and fed to M. rosenbergii PL for 90 days. A dose-dependent accumulation of Se was observed in the carcass of experimental prawns. GBGS-SeNPs, up to 1.5 mg kg^-1 significantly influenced the absorption of other trace elements (Ca, Cu, and Fe) and mineral salts (K, Mg, Na, and Zn). GBGS-SeNPs-supplemented diets showed efficient food conversion ratio (FCR) of 1.32 g against 2.71 g, and therefore enhanced the survival rate (85.6% against 78.8% in control) and weight gain (WG) of 1.41 g against 0.46 g of control prawn. GBGS-SeNPs significantly elevated the activities of protease, amylase, and lipase, and the contents of total protein, essential amino acids (EAA), total carbohydrate, total lipid, monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), and ash. These indicate the growth promoting potential of GBGS-SeNPs in prawn. The insignificantly altered activities of glutamic oxaloacetate transaminase (GOT), glutamic pyruvate transaminase (GPT), superoxide dismutase (SOD), and catalase, and the content of malondialdehyde (MDA) up to 1.5 mg kg^-1 suggest its acceptability in prawn. Moreover, a respective down- and upregulated myostatin (MSTN) and crustacean hyperglycemic hormone (CHH) genes confirmed the influence of GBGS-SeNPs on the growth of prawn. In contrast, 2.0 mg kg^-1 GBGS-SeNPs supplementation starts to produce negative effects on prawn (FCR, 1.76 g; survival rate, 82.2%; WG, 0.84 g against respective values of 1.32 g, 85.6%; and 1.41 g observed in 1.5 mg kg^-1 of GBGS-SeNPs-supplemented diet fed prawn). This study recommends a maximum of 1.5 mg kg^-1 GBGS-SeNPs as dietary supplement to attain sustainable growth of M. rosenbergii. This was confirmed through polynomial and linear regression analyses.

RNA interference analysis of potential functions of cyclin A in the reproductive development of male oriental river prawns (Macrobrachium nipponense)

Cyclin A (CycA) plays essential roles in regulating multiple steps of the cell cycle, and it affects gonad development in mammals and invertebrates. Previous RNA interference (RNAi) analysis revealed that knocking-down the expression of CycA in female oriental river prawns (Macrobrachium nipponense) inhibited ovarian development. CycA was also predicted to have regulatory roles in reproductive development of male M. nipponense based on significant changes of Mn-CycA expression after eyestalk ablation. The goal of this study was to investigate the potential functions of CycA in the reproductive development of male M. nipponense using RNAi and histological observations. Quantitative real-time PCR analysis revealed that both single-side and double-side eyestalk ablation stimulated the expressions of Mn-CycA, and the expression was higher in prawns with double-side eyestalk ablation (p < 0.05). Mn-CycA expression was significantly higher in the testis and androgenic gland during the reproductive season than during the non-reproductive season (p < 0.05). In the RNAi analysis, Mn-CycA expression significantly decreased after prawns were injected with dsCycA, and the expression of insulin-like androgenic gland hormone (Mn-IAG) also decreased as Mn-CycA expression decreased. This result indicated that CycA positively regulated the expression of IAG in M. nipponense. Histological observations revealed that the number of sperm decreased dramatically to <5% of the total cells in the testis of the dsCycA-treated group compared to that of control group on day 14, indicating that knockdown of Mn-CycA expression inhibited testis development by affecting the expression of Mn-IAG in M. nipponense. These results highlighted the functions of CycA in male reproductive development of M. nipponense, which can be applied to future studies of male reproduction in other crustacean species.

RNA Interference Analysis of the Functions of Cyclin B in Male Reproductive Development of the Oriental River Prawn (Macrobrachium nipponense)

Cyclin B (CycB) plays essential roles in cell proliferation and promotes gonad development in many crustaceans. The goal of this study was to investigate the regulatory roles of this gene in the reproductive development of male oriental river prawns (Macrobrachium nipponense). A phylo-genetic tree analysis revealed that the protein sequence of Mn-CycB was most closely related to those of freshwater prawns, whereas the evolutionary distance from crabs was much longer. A quantitative PCR analysis showed that the expression of Mn-CycB was highest in the gonad of both male and female prawns compared to that in other tissues (p < 0.05), indicating that this gene may play essential roles in the regulation of both testis and ovary development in M. nipponense. In males, Mn-CycB expression in the testis and androgenic gland was higher during the reproductive season than during the non-reproductive season (p < 0.05), implying that CycB plays essential roles in the reproductive development of male M. nipponense. An RNA interference analysis revealed that the Mn-insulin-like androgenic gland hormone expression decreased as the Mn-CycB expression decreased, and that few sperm were detected 14 days after the dsCycB treatment, indicating that CycB positively affects testis development in M. nipponense. The results of this study highlight the functions of CycB in M. nipponense, and they can be applied to studies of male reproductive development in other crustacean species.

A Tale of Two Lobsters—Transcriptomic Analysis Reveals a Potential Gap in the RNA Interference Pathway in the Tropical Rock Lobster Panulirus ornatus

RNA interference (RNAi) has been widely utilised in many invertebrate models since its discovery, and in a majority of instances presents as a highly efficient and potent gene silencing mechanism. This is emphasized in crustaceans with almost all taxa having the capacity to trigger effective silencing, with a notable exception in the spiny lobsters where repeated attempts at dsRNA induced RNAi have demonstrated extremely ineffective gene knockdown. A comparison of the core RNAi machinery in transcriptomic data from spiny lobsters (Panulirus ornatus) and the closely related slipper lobsters (Thenus australiensis, where silencing is highly effective) revealed that both lobsters possess all proteins involved in the small interfering and microRNA pathways, and that there was little difference at both the sequence and domain architecture level. Comparing the expression of these genes however demonstrated that T. australiensis had significantly higher expression in the transcripts encoding proteins which directly interact with dsRNA when compared to P. ornatus, validated via qPCR. These results suggest that low expression of the core RNAi genes may be hindering the silencing response in P. ornatus, and suggest that it may be critical to enhance the expression of these genes to induce efficient silencing in spiny lobsters.

17β-Estradiol (E2) may be involved in the mode of crustacean female sex hormone (CFSH) action in the blue crab, Callinectes sapidus

17β-estradiol (E2) has been proved to control reproduction, sexual differentiation, and the development of the secondary sexual characteristics of vertebrate females. In decapod crustacean species, crustacean female sex hormone (CFSH), a protein hormone, is required for developing adult-specific ovigerous setae for embryo brooding and gonophores for mating at the blue crab Callinectes sapidus puberty molting. However, it is unclear that whether the mode of CFSH action involves a vertebrate-type sex steroid hormone in crustaceans. To this end, E2 levels were first measured using a competitive ELISA in the hemolymph and the potential CFSH target tissues from both prepuberty and adult females; the presence of E2 was further confirmed with a liquid chromatography tandem mass spectrometry method. Then, the cDNAs of the following genes known to be associated with vertebrate steroidogenic pathways were isolated: StAR-related lipid transfer protein 3 (StAR3); 3β-hydroxysteroid dehydrogenase (3βHSD); two isoforms of 17β-hydroxysteroid dehydrogenase 8 (17βHSD8); and, estradiol-related receptor (ERR). RT-PCR analysis revealed that these genes were widely distributed in the eyestalk ganglia, hepatopancreas, brain, ovary, spermathecae, ovigerous and plumose setae tissues of adult females. The 17βHSD8 transcripts were localized in the follicle cells, the periphery of the nuclear membrane of primary oocytes, and yolk granules of the vitellogenic oocytes using in situ hybridization, and the corresponding protein was detected in the follicle cells and ooplasm of primary oocytes using immunohistochemistry. Furthermore, the adult females injected with CFSH-dsRNA (n = 30 times) had E2 and StAR3 transcripts levels lower in the ovigerous and plumose setae, spermathecae than controls. These results suggested that the mode of CFSH action in C. sapidus might involve E2 in these adult-female-specific tissues.

Identification of potential functions of polo-like kinase 1 in male reproductive development of the oriental river prawn (Macrobrachium nipponense) by RNA interference analysis

Polo-like kinase 1 (Plk1) has multiple functions in the cell cycle, including in the maturation of centrosomes during the G2/M transition, the separation of centrosomes, and the activation of cyclin-dependent kinase 1 expression and spindle assembly. In this study, we investigated the potential regulatory roles of Plk1 in the reproductive development of the male oriental river prawn (Machrobrachium nipponense). The full cDNA sequence of Mn-Plk1 was 2360 base pairs long, with an open reading frame of 1836 base pairs encoding 611 amino acids. Protein sequence alignment identified a conserved serine/threonine kinase domain and two Polo-boxes. Phylogenetic tree analysis revealed that Mn-Plk1 had the closest evolutionary distance with Plk1s of freshwater prawns and then with those of crustacean species, whereas the evolutionary distance with mollusks was much more distant. Quantitative PCR analysis predicted that Mn-Plk1 plays essential roles in the regulation of gonad development. RNA interference analysis and histological observations showed that expression of insulin-like androgenic gland hormone decreased as the expression of Mn-Plk1 decreased, and fewer than 5% of cells were sperm cells at day 14 in the dsPlk1 injected prawns. This result indicated that Plk1 positively regulated testis development in M. nipponense by affecting the expression of this hormone. Our results highlight the functions of Plk1 in M. nipponense and provide valuable information that can be applied to establish artificial techniques to regulate testis development in this species.

Calcium signaling and regulation of ecdysteroidogenesis in crustacean Y-organs

Crustacean Y-organs secrete ecdysteroid molting hormones. Ecdysteroids are released in increased amount during premolt, circulate in hemolymph, and stimulate the events in target cells that lead to molting. During much of the molting cycle, ecdysteroid production is suppressed by molt-inhibiting hormone (MIH), a peptide neurohormone produced in the eyestalks. The suppressive effect of MIH is mediated by a cyclic nucleotide second messenger. A decrease in circulating MIH is associated with an increase in the hemolymphatic ecdysteroid titer during pre-molt. Nevertheless, it has long been hypothesized that a positive regulatory signal or stimulus is also involved in promoting ecdysteroidogenensis during premolt. Data reviewed here are consistent with the hypothesis that an intracellular Ca²⁺ signal provides that stimulus. Pharmacological agents that increase intracellular Ca²⁺ in Y-organs promote ecdysteroidogenesis, while agents that lower intracellular Ca²⁺ or disrupt Ca²⁺ signaling suppress ecdysteroidogenesis. Further, an increase in the hemolymphatic ecdysteroid titer after eyestalk ablation or during natural premolt is associated with an increase in intracellular free Ca²⁺ in Y-organ cells. Several lines of evidence suggest elevated intracellular calcium is linked to enhanced ecdysteroidogenesis through activation of Ca²⁺/calmodulin dependent cyclic nucleotide phosphodiesterase, thereby lowering intracellular cyclic nucleotide second messenger levels and promoting ecdysteroidogenesis. Results of transcriptomic studies show genes involved in Ca²⁺ signaling are well represented in Y-organs. Several recent studies have focused on Ca²⁺ transport proteins in Y-organs. Complementary DNAs encoding a plasma membrane Ca²⁺ ATPase (PMCA) and a sarcoplasmic/endoplasmic reticulum Ca²⁺ ATPase (SERCA) have been cloned from crab Y-organs. The relative abundance of PMCA and SERCA transcripts in Y-organs is elevated during premolt, a time when Ca²⁺ levels in Y-organs are likewise elevated. The results are consistent with the notion that these transport proteins act to maintain the Ca²⁺ gradient across the cell membrane and re-set the cell for future Ca²⁺ signals.

An outbreak of crayfish rickettsiosis caused by Coxiella cheraxi in redclaw crayfish (Cherax quadricarinatus) imported to Israel from Australia

The redclaw crayfish (Cherax quadricarinatus) is a freshwater decapod crustacean, cultured in numerous countries worldwide for both food and ornamental purposes. Redclaw crayfish has become an important aquaculture species due to its physical and biological traits, relatively easy breeding, and a short growing-out period to reach commercial size. Bacterial infections are the second-most studied pathogens of freshwater crayfish. However, redclaw crayfish rickettsiosis, caused by Coxiella cheraxi, was reported in only a few scientific papers in the early 2000s, in Australia and Ecuador. Coxiella cheraxi is a rod-shaped intracellular bacterium that can cause mortality of 22%-80% in naturally infected crayfish. In experimental infections, mortality rates may be even higher (40%-90%). Coxiella cheraxi is closely related to Coxiella burnetii, the agent of Q-fever, which affects ruminants (goats, sheep, and cattle) and occasionally may cause zoonotic infections. According to the scientific knowledge available, C. cheraxi is a species-specific pathogen because it has been only detected in Cherax quadricarinatus and thus far, there is no evidence of a zoonotic potential. In this study, we describe an outbreak of rickettsiosis in a batch of redclaw crayfish imported to Israel from an Australian hatchery, observed 2 months after introduction in a quarantine facility. Initial mortality was evaluated through histopathology, revealing infection by rickettsia-like organisms (RLO) that were subsequently investigated by molecular analysis and transmission electron microscopy examination. Phylogenetic analysis revealed that the detected RLO were closely related to C. cheraxi from a single source (Australian strain TO98), available in free publicly accessible databases. After 5 months in quarantine, almost 99% of the crayfish population had died. Our findings raise valuable questions related to aquatic animal trade and the importance of mitigation measures, such as quarantine and routine diagnostic procedures, to limit the spread of infectious diseases.

Identification of candidate genes from androgenic gland in Macrobrachium nipponense regulated by eyestalk ablation

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.

Biological insights into the rapid tissue regeneration of freshwater crayfish and crustaceans

The freshwater crayfish is capable of regenerating limbs, following autotomy, injury and predation. In arthropod species, regeneration and moulting are two processes linked and strongly regulated by ecdysone. The regeneration of crayfish limbs is divided into wound healing, blastema formation, cellular reprogramming and tissue patterning. Limb blastema cells undergo proliferation, dedifferentiation and redifferentiation. A limb bud, containing folded segments of the regenerating limb, is encased within a cuticular sheath. The functional limb regenerates, in proecdysis, in two to three consecutive moults. Rapid tissue growth is regulated by hormones, limb nerves and local cells. The TGF-β/activin signalling pathway has been determined in the crayfish, P. fallax f. virginalis, and is suggested as a potential regulator of tissue regeneration. In this review article, we discuss current understanding of tissue regeneration in the crayfish and various crustaceans. A thorough understanding of the cellular, genetic and molecular pathways of these biological processes is promising for the development of therapeutic applications for a wide array of diseases in regenerative medicine.

Transcriptome Profiling Analysis of the Testis After Eyestalk Ablation for Selection of the Candidate Genes Involved in the Male Sexual Development in Macrobrachium nipponense

The eyestalk of crustacean species secretes many hormones, affecting the process of reproduction, molting, metabolism of glucose, and other functions in crustaceans. In this study, important metabolic pathways and candidate genes involved in the male sexual development were identified through performing the transcriptome profiling analysis of the testis after the ablation of eyestalk from Macrobrachium nipponense. The histological observations revealed that the testis development became vigorous after eyestalk ablation, indicating that the hormones secreted by the eyestalk have negative effects on the testis development in M. nipponense. Transcriptome profiling analysis revealed that 1,039, 1,226, and 3,682 differentially expressed genes (DEGs) were identified between normal prawns (CG) vs single-side eyestalk ablation prawns (SS), SS vs double-side eyestalk ablation prawns (DS), and CG vs DS, respectively, indicating that the ablation of double-side eyestalk has more significant regulatory roles on male sexual development than that of single-side ablation, which was consistent with the histological observations. Lysosome, Apoptosis, Glycolysis/Gluconeogenesis, and Insulin signaling pathway were the main enriched metabolic pathways in all of these three comparisons, and the important genes from these metabolic pathways were also selected. The qPCR verifications of 10 DEGs from these metabolic pathways were the same as those of RNA-seq. The qPCR, in situ hybridization, and RNA interference analysis of Mn-NF_kBα revealed that NF_kBα has a positive regulatory effect on testis development. This study provided new insights on male sexual development in M. nipponense, promoting the studies on male sexual development in other crustaceans as well.

Comparative Analysis of the Intermolt and Postmolt Hepatopancreas Transcriptomes Provides Insight into the Mechanisms of Procambarus clarkii Molting Process

In the present study, we used RNA-Seq to investigate the expression changes in the transcriptomes of two molting stages (postmolt (M) and intermolt (NM)) of the red swamp crayfish and identified differentially expressed genes. The transcriptomes of the two molting stages were de novo assembled into 139,100 unigenes with a mean length of 675.59 bp. The results were searched against the NCBI, NR, KEGG, Swissprot, and KOG databases, to annotate gene descriptions, associate them with gene ontology terms, and assign them to pathways. Furthermore, using the DESeq R package, differentially expressed genes were evaluated. The analysis revealed that 2347 genes were significantly (p > 0.05) differentially expressed in the two molting stages. Several genes and other factors involved in several molecular events critical for the molting process, such as energy requirements, hormonal regulation, immune response, and exoskeleton formation were identified and evaluated by correlation and KEGG analysis. The expression profiles of transcripts detected via RNA-Seq were validated by real-time PCR assay of eight genes. The information presented here provides a transient view of the hepatopancreas transcripts available in the postmolt and intermolt stage of crayfish, hormonal regulation, immune response, and skeletal-related activities during the postmolt stage and the intermolt stage.

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.

Identification of two genes potentially related to myogenesis and muscle growth in Fenneropenaeus chinensis: Activin receptor II and Follistatin-like protein

Activin receptor (ActR) and follistatin-like (FSTL) genes, which are involved in the Myostatin (Mstn) related TGF-β/Smad signaling pathway, play important roles in regulating the muscle generation, development and growth of muscle in vertebrate. Our previous studies have confirmed that Mstn negatively regulates muscle development and growth in Fenneropenaeus chinensis as that in vertebrate. However, the roles of ActR and FSTL in muscle development and growth in invertebrate remains unclear. In the present study, type II ActR(FcActRII) and FSTL (FcFSTL) genes from F. chinensis were cloned and characterized, and their functions on muscle development and growth were investigated. The full-length cDNAs of FcActRII and FcFSTL were 2366 bp that encoded 572 amino acids and 2474 bp that encoded 717 amino acids, respectively. Sequence analysis revealed that the overall protein sequences of the two genes shared 97% and 96% identities with Penaeus vannamei and 50%-59% and 35%-36% identities with vertebrates, respectively. In the early development stages, muscles firstly appeared in nauplius stage and developed gradually until post larval, and the mRNA expressions of FcActRII increased from gastrula to zoea stage and then decreased from zoea stage to post larval stage while that of FcFSTL was lowest in gastrula stage and increased rapidly in nauplius stage and then expressed stably from nauplius stage to post-larval stage. In the adult shrimp, the two genes were widely distributed in the examined tissues. The FcActRII expression in muscle of L group was significantly lower than that of S group, but the FcFSTL expression showed an opposite result. After down-regulating the expression of FcMstn by RNAi, FcActRII expression was significantly down-regulated while that of FcFSTL was up-regulated. The present study suggested that FcActRII and FcFSTL, regulated by FcMstn, might be involved in myogenesis and muscle growth.

From sporadic single genes to a broader transcriptomic approach: Insights into the formation of the biomineralized exoskeleton in decapod crustaceans

One fundamental character common to pancrustaceans (Crustacea and Hexapoda) is a mineralized rigid exoskeleton whose principal organic components are chitin and proteins. In contrast to traditional research in the field that has been devoted to the structural and physicochemical aspects of biomineralization, the present study explores transcriptomic aspects of biomineralization as a first step towards adding a complementary molecular layer to this field. The rigidity of the exoskeleton in pancrustaceans dictates essential molt cycles enabling morphological changes and growth. Thus, formation and mineralization of the exoskeleton are concomitant to the timeline of the molt cycle. Skeletal proteinaceous toolkit elements have been discovered in previous studies using innovative molt-related binary gene expression patterns derived from transcriptomic libraries representing the major stages comprising the molt cycle of the decapod crustacean Cherax quadricarinatus. Here, we revisited some prominent exoskeleton-related structural proteins encoding and, using the above molt-related binary pattern methodology, enlarged the transcriptomic database of C. quadricarinatus. The latter was done by establishing a new transcriptomic library of the cuticle forming epithelium and molar tooth at four different molt stages (i.e., inter-molt, early pre-molt, late pre-molt and post-molt) and incorporating it to a previous transcriptome derived from the gastroliths and mandible. The wider multigenic approach facilitated by the newly expanded transcriptomic database not only revisited single genes of the molecular toolkit, but also provided both scattered and specific information that broaden the overview of proteins and gene clusters which are involved in the construction and biomineralization of the exoskeleton in decapod crustaceans.

The Crustacean Hyperglycemic Hormone Superfamily: Progress Made in the Past Decade

Early studies recognizing the importance of the decapod eyestalk in the endocrine regulation of crustacean physiology-molting, metabolism, reproduction, osmotic balance, etc.-helped found the field of crustacean endocrinology. Characterization of putative factors in the eyestalk using distinct functional bioassays ultimately led to the discovery of a group of structurally related and functionally diverse neuropeptides, crustacean hyperglycemic hormone (CHH), molt-inhibiting hormone (MIH), gonad-inhibiting hormone (GIH) or vitellogenesis-inhibiting hormone (VIH), and mandibular organ-inhibiting hormone (MOIH). These peptides, along with the first insect member (ion transport peptide, ITP), constitute the original arthropod members of the crustacean hyperglycemic hormone (CHH) superfamily. The presence of genes encoding the CHH-superfamily peptides across representative ecdysozoan taxa has been established. The objective of this review is to, aside from providing a general framework, highlight the progress made during the past decade or so. The progress includes the widespread identification of the CHH-superfamily peptides, in particular in non-crustaceans, which has reshaped the phylogenetic profile of the superfamily. Novel functions have been attributed to some of the newly identified members, providing exceptional opportunities for understanding the structure-function relationships of these peptides. Functional studies are challenging, especially for the peptides of crustacean and insect species, where they are widely expressed in various tissues and usually pleiotropic. Progress has been made in deciphering the roles of CHH, ITP, and their alternatively spliced counterparts (CHH-L, ITP-L) in the regulation of metabolism and ionic/osmotic hemostasis under (eco)physiological, developmental, or pathological contexts, and of MIH in the stimulation of ovarian maturation, which implicates it as a regulator for coordinating growth (molt) and reproduction. In addition, experimental elucidation of the steric structure and structure-function relationships have given better understanding of the structural basis of the functional diversification and overlapping among these peptides. Finally, an important finding was the first-ever identification of the receptors for this superfamily of peptides, specifically the receptors for ITPs of the silkworm, which will surely give great impetus to the functional study of these peptides for years to come. Studies regarding recent progress are presented and synthesized, and prospective developments remarked upon.

Double-Stranded RNA Binding Proteins in Serum Contribute to Systemic RNAi Across Phyla-Towards Finding the Missing Link in Achelata

RNA interference (RNAi) has become a widely utilized method for studying gene function, yet despite this many of the mechanisms surrounding RNAi remain elusive. The core RNAi machinery is relatively well understood, however many of the systemic mechanisms, particularly double-stranded RNA (dsRNA) transport, are not. Here, we demonstrate that dsRNA binding proteins in the serum contribute to systemic RNAi and may be the limiting factor in RNAi capacity for species such as spiny lobsters, where gene silencing is not functional. Incubating sera from a variety of species across phyla with dsRNA led to a gel mobility shift in species in which systemic RNAi has been observed, with this response being absent in species in which systemic RNAi has never been observed. Proteomic analysis suggested lipoproteins may be responsible for this phenomenon and may transport dsRNA to spread the RNAi signal systemically. Following this, we identified the same gel shift in the slipper lobster Thenus australiensis and subsequently silenced the insulin androgenic gland hormone, marking the first time RNAi has been performed in any lobster species. These results pave the way for inducing RNAi in spiny lobsters and for a better understanding of the mechanisms of systemic RNAi in Crustacea, as well as across phyla.

Molecular characterization, RNA interference and recombinant protein approach to study the function of the putative Molt Inhibiting Hormone (FmMIH1) gene from the shrimp Fenneropenaeus merguiensis

The Molt Inhibiting Hormone gene and cDNA of the banana shrimp Fenneropenaeus merguiensis (FmMIH1) has been cloned and characterized. FmMIH1 possesses most of the characteristics of the eyestalk CHH/MIH/GIH family subtype-II neuropeptides. FmMIH1 open reading frame consists of 315 bp encoding for 105 amino acid residues. The mature peptide of FmMIH1 consists of 76 amino acid residues, a glycine residue at position 11 of the mature peptide and 6 cysteine residues located in the conserved position. In addition to eyestalk, high levels of FmMIH1 transcript could also be detected in the intestine. FmMIH1 transcript level is low throughout the post-molt, early to mid-intermolt and premolt. However, a sharp increase could be observed in late intermolt (C3 stage). Both alignment and phylogenetic analysis reveal that FmMIH1 is most similar to the MIH1 of other shrimps. For functional assay, RNA interference results show that a significant 2.3 days (P < 0.05) reduction in molt cycle duration could be observed in shrimp receiving dsFmMIH1 injection. Surprisingly, injection of recombinant FmMIH1 could also cause a significant reduction of the molt cycle (average 1.9 days, P < 0.05). We hypothesize that the recombinant protein is biological inactive but it competes with the endogenous MIH for carrier protein binding and consequently reduces the amount of biological MIH that could reach the targets. In conclusion, the result of this study will provide us new insight in molting/growth control in crustacean.

Genomic organization of the molt-inhibiting hormone gene in the red swamp crayfish Procambarus clarkii and characterization of single-nucleotide polymorphisms associated with growth

Molt-inhibiting hormone (MIH), a neuropeptide synthesized in the eyestalk in crustaceans, is mainly responsible for the molting by negatively controlling the ecdysteroids secretion. Although there are several reports of the isolation and protein sequencing of MIH in the red swamp crayfish, little is known about the nucleotide sequence and gene organization of this neuropeptide, even less about the association of MIH polymorphisms and growth traits. Here, a 1237 bp full-length MIH cDNA was obtained from the crayfish eyestalk, which encodes a putative protein of 106 amino acids, with a 191 bp 5'-UTR and a 728 bp 3'-UTR. The MIH genomic DNA sequence is 4205 bp in length, which includes three exons interrupted by two introns, and a 929 bp 5'-flanking region. Potential transcription initiation site and transcription factor binding sites were identified in the 5'-flanking region, implying a potential role in transcriptional regulation. Seventeen SNPs in the 5'-flanking region and 3'-UTR were identified, and the associations between these SNPs and growth traits were evaluated with a two-stage design. A SNPs g. -12C > G that showed a significant association with body weight was identified. Individuals with GG genotype had a significantly higher body weight than those with CC genotype (43.98 ± 9.82 g vs. 34.27 ± 6.87 g; P ﹤ 0.001), indicating a beneficial effect of the G allele on the growth of red swamp crayfish. The obtained MIH gene, as well as the identified SNPs, may serve as targets for molecular marker-aided selection in growth improvement of the red swamp crayfish in future studies.

Mycobacterium gordonae infecting redclaw crayfish Cherax quadricarinatus

The redclaw crayfish Cherax quadricarinatus (von Martens, 1868) is one of the most commonly exploited freshwater crayfish species worldwide. Redclaw crayfish are susceptible to a number of pathogens but none have been linked to widespread epizootics. Mycobacterial infections have been sporadically reported in crayfish. In the case described, histopathology and bacterial identification confirmed an opportunistic infection caused by Mycobacterium gordonae in a hatchery of C. quadricarinatus in Israel. Intranuclear inclusion bodies, recorded in cells of the tubular epithelium of the hepatopancreas by histopathology, indicate a co-infection with a viral agent, referable to C. quadricarinatus bacilliform virus (CqBV). To the best of our knowledge this is the first description of mycobacteriosis in redclaw crayfish.

Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing?

Loss-of-function technologies, such as morpholino- and RNAi-mediated gene knockdown, and TALEN- and CRISPR/Cas9-mediated gene knockout, are widely used to investigate gene function and its physiological significance. Here, we provide a general overview of the various knockdown and knockout technologies commonly used in comparative physiology and discuss the merits and drawbacks of these technologies with a particular focus on research conducted in zebrafish. Despite their widespread use, there is an ongoing debate surrounding the use of knockdown versus knockout approaches and their potential off-target effects. This debate is primarily fueled by the observations that, in some studies, knockout mutants exhibit phenotypes different from those observed in response to knockdown using morpholinos or RNAi. We discuss the current debate and focus on the discrepancies between knockdown and knockout phenotypes, providing literature and primary data to show that the different phenotypes are not necessarily a direct result of the off-target effects of the knockdown agents used. Nevertheless, given the recent evidence of some knockdown phenotypes being recapitulated in knockout mutants lacking the morpholino or RNAi target, we stress that results of knockdown experiments need to be interpreted with caution. We ultimately argue that knockdown experiments should not be discontinued if proper control experiments are performed, and that with careful interpretation, knockdown approaches remain useful to complement the limitations of knockout studies (e.g. lethality of knockout and compensatory responses).

Ecdysone inducible gene E75 from black tiger shrimp Penaeus monodon: Characterization and elucidation of its role in molting

Molting is controlled by ecdysteroids, which are synthesized and secreted by the Y-organ in crustaceans. Ecdysone inducible gene, E75, is an early-response gene in the 20-hydroxyecdysone (20E) signaling pathway, with crucial roles in arthropod development. Complementary DNA (cDNA) encoding Penaeus monodon E75 (PmE75) was cloned using RT-PCR and RACE. PmE75 cDNA was 3526 bp long and encoded a 799-amino acid protein. Tissue distribution analysis showed that PmE75 was expressed ubiquitously in selected tissues, and was relatively abundant in the epidermis, muscle, and hepatopancreas. Developmental expression revealed that PmE75 was expressed throughout its life cycle. Silencing PmE75 significantly decreased PmE75 expression. Shrimps injected with PBS and dsGFP started molting on Day 7 and had almost completed molting on Day 9, whereas dsPmE75-injected shrimp presented no signs of molting. These results suggested that PmE75 might be involved in molting. In situ hybridization results support this hypothesis. To explore the role of 20E and eyestalks in the regulation of molting in P. monodon, exogenous 20E injection and eyestalk ablation (ESA) were performed, and showed that 20E can induce the transcription and expression of PmE75 in the hepatopancreas, epidermis, and muscle, which were significantly elevated after ESA. These results provide further insights into our understanding of molting.

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.

Characterization, expression patterns of molt-inhibiting hormone gene of Macrobrachium nipponense and its roles in molting and growth

The oriental river prawn, Macrobrachium nipponense, is an important commercial aquaculture resource in China. In order to overwinter, M. nipponense displays decreased physiological activity and less consumption of energy. Sudden warming would trigger molting and cause an extensive death, resulting in huge economic losses. Therefore, it is of great practical significance to study the molting mechanism of oriental river prawns. Molt-inhibiting hormone gene (MIH) plays a major role in regulating molting in crustaceans. In this study, a full length MIH cDNA of M. nipponense (Mn-MIH) was cloned from the eyestalk. The total length of the Mn-MIH was 925 bp, encoding a protein of 119 amino acids. Tissue distribution analysis showed that Mn-MIH was highly expressed in the eyestalk, and that it had relatively low expression in gill, ovary, and abdominal ganglion. Mn-MIH was detected in all developmental stages, and changed regularly in line with the molting cycle of the embryo and larva. Mn-MIH varied in response to the molting cycle, suggesting that Mn-MIH negatively regulates ecdysteroidogenesis. Mn-MIH inhibition by RNAi resulted in a significant acceleration of molting cycles in both males and females, confirming the inhibitory role of MIH in molting. After long-term RNAi males, but not females had significant weight gain, confirming that Mn-MIH plays an important role in growth of M. nipponense. Our work contributes to a better understanding of the role of Mn-MIH in crustacean molting and growth.

Molecular cloning and characterization of a sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) from Y-organs of the blue crab (Callinectes sapidus)

Existing data indicate that a Ca²⁺ signal stimulates ecdysteroid hormone production by crustacean molting glands (Y-organs). Ca²⁺ signaling is dependent on a tightly regulated Ca²⁺ gradient, with intracellular free Ca²⁺ maintained at a low basal level (typically sub-micromolar). This is achieved through the action of proteins intrinsic to the plasma membrane and the membranes of organelles. One such protein, the sarco/endoplasmic reticulum Ca²⁺ ATPase (SERCA), pumps Ca²⁺ from cytosol to the lumen of the endoplasmic reticulum. As a step toward understanding Ca²⁺-mediated regulation of ecdysteroidogenesis, we have begun investigating Ca²⁺ transport proteins in Y-organs. In studies reported here, we used a PCR-based strategy to clone from Y-organs of the blue crab (Callinectes sapidus) a cDNA encoding a putative SERCA protein. The cloned Cas-SERCA cDNA (3806 bp) includes a 3057-bp open reading frame that encodes a 1019-residue protein (Cas-SERCA). The conceptually translated protein has a predicted molecular mass of 111.42 × 10³ and contains all signature domains of an authentic SERCA, including ten transmembrane domains and a phosphorylation site at aspartate 351. A homology model of Cas-SERCA closely resembles models of related SERCA proteins. Phylogenetic analysis shows Cas-SERCA clusters with SERCA proteins from other arthropods. An assessment of tissue distribution indicates the Cas-SERCA transcript is widely distributed across tissues. Studies using quantitative PCR showed Cas-SERCA transcript abundance increased significantly in Y-organs activated by eyestalk ablation, a pattern consistent with the hypothesis that Cas-SERCA functions to maintain Ca²⁺ homeostasis in Y-organs.

Functional analysis of the promoter of the molt-inhibiting hormone (mih) gene in mud crab Scylla paramamosain

In this study, the 5'-flanking region of molt-inhibiting hormone (MIH) gene was cloned by Tail-PCR. It is 2024 bp starting from the translation initiation site, and 1818 bp starting from the predicted transcription start site. Forecast analysis results by the bioinformatics software showed that the transcription start site is located at 207 bp upstream of the start codon ATG, and TATA box is located at 240 bp upstream of the start codon ATG. Potential transcription factor binding sites include Sp1, NF-1, Oct-1, Sox-2, RAP1, and so on. There are two CpG islands, located at -25- +183 bp and -1451- -1316 bp respectively. The transfection results of luciferase reporter constructs showed that the core promoter region was located in the fragment -308 bp to -26 bp. NF-kappaB and RAP1 were essential for mih basal transcriptional activity. There are three kinds of polymorphism CA in the 5'-flanking sequence, and they can influence mih promoter activity. These findings provide a genetic foundation of the further research of mih transcription regulation.

Transcriptomic analysis of the hepatopancreas induced by eyestalk ablation in shrimp, Litopenaeus vannamei

Although eyestalk ablation (ESA) is currently considered the most effective method to facilitate molting and maturation, its physiological responses are still not clearly explained in decapod crustaceans. In this study, we analyzed the hepatopancreatic transcriptomes of Litopenaeus vannamei after ESA using the Illumina Miseq platform. After screening 53,029 contigs with high cutoff values (fold change>|10|; P-value<0.05; RPKM>1), we were able to identify 105 differentially expressed genes (DEGs), of which 100 were up-regulated and five were down-regulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that many DEGs were involved in the synthetic pathways for glycerol and trehalose, which are known to function as the major protectants under conditions of low temperature and osmotic stress in arthropods. Additional analysis of the other DEGs enabled us to classify them in four categories: immunity; cellular trafficking; transcriptional regulation; molting and maturation. Many DEGs were involved in immunity and stress responses, in particular the proPO activation system, which is the major immune and wound-healing system in arthropods. In addition to immunity and stress responses, we were also able to identify DEGs involved in molting and maturation processes (e.g., group I chitinase), as well as those involved in hormone metabolism and trafficking. Collectively, based on the transcriptomic analysis, ESA causes not only stress and immune responses, but also molting and maturation in L. vannamei. The DEGs identified in this study could be useful markers to understand the physiological responses that ESA induces in shrimp, such as molting, maturation, and immunity.

Transcriptome analysis on the exoskeleton formation in early developmetal stages and reconstruction scenario in growth-moulting in Litopenaeus vannamei

Exoskeleton construction is an important issue in shrimp. To better understand the molecular mechanism of exoskeleton formation, development and reconstruction, the transcriptome of the entire developmental process in Litopenaeus vannamei, including nine early developmental stages and eight adult-moulting stages, was sequenced and analysed using Illumina RNA-seq technology. A total of 117,539 unigenes were obtained, with 41.2% unigenes predicting the full-length coding sequence. Gene Ontology, Clusters of Orthologous Group (COG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and functional annotation of all unigenes gave a better understanding of the exoskeleton developmental process in L. vannamei. As a result, more than six hundred unigenes related to exoskeleton development were identified both in the early developmental stages and adult-moulting. A cascade of sequential expression events of exoskeleton-related genes were summarized, including exoskeleton formation, regulation, synthesis, degradation, mineral absorption/reabsorption, calcification and hardening. This new insight on major transcriptional events provide a deep understanding for exoskeleton formation and reconstruction in L. vannamei. In conclusion, this is the first study that characterized the integrated transcriptomic profiles cover the entire exoskeleton development from zygote to adult-moulting in a crustacean, and these findings will serve as significant references for exoskeleton developmental biology and aquaculture research.

Transcriptomic characterization and curation of candidate neuropeptides regulating reproduction in the eyestalk ganglia of the Australian crayfish, Cherax quadricarinatus

The Australian redclaw crayfish (Cherax quadricarinatus) has recently received attention as an emerging candidate for sustainable aquaculture production in Australia and worldwide. More importantly, C. quadricarinatus serves as a good model organism for the commercially important group of decapod crustaceans as it is distributed worldwide, easy to maintain in the laboratory and its reproductive cycle has been well documented. In order to better understand the key reproduction and development regulating mechanisms in decapod crustaceans, the molecular toolkit available for model organisms such as C. quadricarinatus must be expanded. However, there has been no study undertaken to establish the C. quadricarinatus neuropeptidome. Here we report a comprehensive study of the neuropeptide genes expressed in the eyestalk in the Australian crayfish C. quadricarinatus. We characterised 53 putative neuropeptide-encoding transcripts based on key features of neuropeptides as characterised in other species. Of those, 14 neuropeptides implicated in reproduction regulation were chosen for assessment of their tissue distribution using RT-PCR. Further insights are discussed in relation to current knowledge of neuropeptides in other species and potential follow up studies. Overall, the resulting data lays the foundation for future gene-based neuroendocrinology studies in C. quadricarinatus.

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

High-throughput RNA sequencing (RNA-seq) technology has become an important tool for studying physiological responses of organisms to changes in their environment. De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence. The contributions from the "Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology" symposium in this issue show the successes and limitations of using RNA-seq in the study of crustaceans. In conjunction with the symposium, the Animal Genome to Phenome Research Coordination Network collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Many were unaware of the bioinformatics analysis resources currently available on the CyVerse platform. Our analysis of community responses led to three recommendations for advancing the field: (1) integration of genomic and RNA-seq sequence assemblies for crustacean gene annotation and comparative expression; (2) development of methodologies for the functional analysis of genes; and (3) information and training exchange among laboratories for transmission of best practices. The field lacks the methods for manipulating tissue-specific gene expression. The decapod crustacean research community should consider the cherry shrimp, Neocaridina denticulata, as a decapod model for the application of transgenic tools for functional genomics. This would require a multi-investigator effort.

Whole Transcriptome Analysis Provides Insights into Molecular Mechanisms for Molting in Litopenaeus vannamei

Molting is one of the most important biological processes in shrimp growth and development. All shrimp undergo cyclic molting periodically to shed and replace their exoskeletons. This process is essential for growth, metamorphosis, and reproduction in shrimp. However, the molecular mechanisms underlying shrimp molting remain poorly understood. In this study, we investigated global expression changes in the transcriptomes of the Pacific white shrimp, Litopenaeus vannamei, the most commonly cultured shrimp species worldwide. The transcriptome of whole L. vannamei was investigated by RNA-sequencing (RNA-seq) throughout the molting cycle, including the inter-molt (C), pre-molt (D0, D1, D2, D3, D4), and post-molt (P1 and P2) stages, and 93,756 unigenes were identified. Among these genes, we identified 5,117 genes differentially expressed (log2ratio ≥1 and FDR ≤0.001) in adjacent molt stages. The results were compared against the National Center for Biotechnology Information (NCBI) non-redundant protein/nucleotide sequence database, Swiss-Prot, PFAM database, the Gene Ontology database, and the Kyoto Encyclopedia of Genes and Genomes database in order to annotate gene descriptions, associate them with gene ontology terms, and assign them to pathways. The expression patterns for genes involved in several molecular events critical for molting, such as hormone regulation, triggering events, implementation phases, skelemin, immune responses were characterized and considered as mechanisms underlying molting in L. vannamei. Comparisons with transcriptomic analyses in other arthropods were also performed. The characterization of major transcriptional changes in genes involved in the molting cycle provides candidates for future investigation of the molecular mechanisms. The data generated in this study will serve as an important transcriptomic resource for the shrimp research community to facilitate gene and genome annotation and to characterize key molecular processes underlying shrimp development.

The Involvement of Hemocyte Prophenoloxidase in the Shell-Hardening Process of the Blue Crab, Callinectes sapidus

Cuticular structures of arthropods undergo dramatic molt-related changes from being soft to becoming hard. The shell-hardening process of decapod crustaceans includes sclerotization and mineralization. Hemocyte PPO plays a central role in melanization and sclerotization particularly in wound healing in crustaceans. However, little is known about its role in the crustacean initial shell-hardening process. The earlier findings of the aggregation of heavily granulated hemocytes beneath the hypodermis during ecdysis imply that the hemocytes may be involved in the shell-hardening process. In order to determine if hemocytes and hemocyte PPO have a role in the shell-hardening of crustaceans, a knockdown study using specific CasPPO-hemo-dsRNA was carried out with juvenile blue crabs, Callinectes sapidus. Multiple injections of CasPPO-hemo-dsRNA reduce specifically the levels of CasPPO-hemo expression by 57% and PO activity by 54% in hemocyte lysate at the postmolt, while they have no effect on the total hemocyte numbers. Immunocytochemistry and flow cytometry analysis using a specific antiserum generated against CasPPO show granulocytes, semigranulocytes and hyaline cells as the cellular sources for PPO at the postmolt. Interestingly, the type of hemocytes, as the cellular sources of PPO, varies by molt stage. The granulocytes always contain PPO throughout the molt cycle. However, semigranulocytes and hyaline cells become CasPPO immune-positive only at early premolt and postmolt, indicating that PPO expression in these cells may be involved in the shell-hardening process of C. sapidus.

A crayfish molar tooth protein with putative mineralized exoskeletal chitinous matrix properties

Some crustaceans possess exoskeletons that are reinforced with calcium carbonate. In the crayfish Cherax quadricarinatus, the molar tooth, which is part of the mandibular exoskeleton, contains an unusual crystalline enamel-like apatite layer. As this layer resembles vertebrate enamel in composition and function, it offers an interesting example of convergent evolution. Unlike other parts of the crayfish exoskeleton, which is periodically shed and regenerated during the molt cycle, molar mineral deposition takes place during the pre-molt stage. The molar mineral composition transforms continuously from fluorapatite through amorphous calcium phosphate to amorphous calcium carbonate and is mounted on chitin. The process of crayfish molar formation is entirely extracellular and presumably controlled by proteins, lipids, polysaccharides, low-molecular weight molecules and calcium salts. We have identified a novel molar protein termed Cq-M15 from C. quadricarinatus and cloned its transcript from the molar-forming epithelium. Its transcript and differential expression were confirmed by a next-generation sequencing library. The predicted acidic pI of Cq-M15 suggests its possible involvement in mineral arrangement. Cq-M15 is expressed in several exoskeletal tissues at pre-molt and its silencing is lethal. Like other arthropod cuticular proteins, Cq-M15 possesses a chitin-binding Rebers-Riddiford domain, with a recombinant version of the protein found to bind chitin. Cq-M15 was also found to interact with calcium ions in a concentration-dependent manner. This latter property might make Cq-M15 useful for bone and dental regenerative efforts. We suggest that, in the molar tooth, this protein might be involved in calcium phosphate and/or carbonate precipitation.

Differential regulation of hepatopancreatic vitellogenin (VTG) gene expression by two putative molt-inhibiting hormones (MIH1/2) in Pacific white shrimp (Litopenaeus vannamei)

Molt-inhibiting hormone (MIH), a peptide member of the crustacean hyperglycemic hormone (CHH) family, is commonly considered as a negative regulator during the molt cycle in crustaceans. Phylogenetic analysis of CHH family peptides in penaeidae shrimps suggested that there is no significant differentiation between MIH and vitellogenesis-inhibiting hormone (VIH, another peptide member of CHH family), by far the most potent negative regulator of crustacean vitellogenesis known. Thus, MIH may also play a role in regulating vitellogenesis. In this study, two previously reported putative MIHs (LivMIH1 and LivMIH2) in the Pacific white shrimp (Litopenaeus vannamei) were expressed in Escherichia coli, purified by immobilized metal ion affinity chromatography (IMAC) and further confirmed by western blot. Regulation of vitellogenin (VTG) mRNA expression by recombinant LivMIH1 and LivMIH2 challenge was performed by both in vitro hepatopancreatic primary cells culture and in vivo injection approaches. In in vitro primary culture of shrimp hepatopancreatic cells, only LivMIH2 but not LivMIH1 administration could improve the mRNA expression of VTG. In in vivo injection experiments, similarly, only LivMIH2 but not LivMIH1 could stimulate hepatopancreatic VTG gene expression and induce ovary maturation. Our study may provide evidence for one isoform of MIH (MIH2 in L. vannamei) may serve as one of the mediators of the physiological progress of molting and vitellogenesis. Our study may also give new insight in CHH family peptides regulating reproduction in crustaceans, in particular penaeidae shrimps.

A novel chitin binding crayfish molar tooth protein with elasticity properties

The molar tooth of the crayfish Cherax quadricarinatus is part of the mandible, and is covered by a layer of apatite (calcium phosphate). This tooth sheds and is regenerated during each molting cycle together with the rest of the exoskeleton. We discovered that molar calcification occurs at the pre-molt stage, unlike calcification of the rest of the new exoskeleton. We further identified a novel molar protein from C. quadricarinatus and cloned its transcript from the molar-forming epithelium. We termed this protein Cq-M13. The temporal level of transcription of Cq-M13 in an NGS library of molar-forming epithelium at different molt stages coincides with the assembly and mineralization pattern of the molar tooth. The predicted protein was found to be related to the pro-resilin family of cuticular proteins. Functionally, in vivo silencing of the transcript caused molt cycle delay and a recombinant version of the protein was found to bind chitin and exhibited elastic properties.

An insulin-like growth factor found in hepatopancreas implicates carbohydrate metabolism of the blue crab Callinectes sapidus

Hyperglycemia that is caused by the release of crustacean hyperglycemic hormone (CHH) from the sinus gland to hemolymph is one of the hallmark physiological phenomena, occurring in decapod crustaceans experiencing stressful conditions. However, the mechanism(s) by which such elevated glucose levels return to resting levels is still unknown. Interestingly, noted is a difference in the clearance rate of hemolymph glucose between adult females and adult males of the blue crab, Callinectes sapidus: the former with more rapid clearance than the latter. The presence of an endogenous-insulin-like molecule is suggested in C. sapidus because an injection of bovine insulin, significantly reduces the levels of hemolymph glucose that were previously elevated by emersion stress or the glucose injection. Using 5' and 3' RACE, the full-length cDNA of an insulin-like molecule is isolated from the hepatopancreas of an adult female C. sapidus and shows the same putative sequence of an insulin-like androgenic gland factor (IAG) but differs in 5' and 3' UTR sequences. A knock-down study using five injections of double-stranded RNA of CasIAG-hep (dsRNA-CasIAG-hep, 10μg/injection) over a 10-day period reduces CasIAG-hep expression by ∼50%. The levels of hemolymph glucose are also kept higher in dsRNA-CasIAG-hep injected group than those treated with dsRNA-green fluorescent protein (dsRNA-IAG-hep) or saline. Most importantly, the hepatopancreas of dsRNA-CasIAG-hep injected animals contains amounts of carbohydrate (glucose, trehalose, and glycogen) significantly lower than those of control groups, indicating that the function of CasIAG-hep in carbohydrate metabolism in crustaceans is similar to carbohydrate metabolism in vertebrates.

Gene silencing in crustaceans: from basic research to biotechnologies

Gene silencing through RNA interference (RNAi) is gaining momentum for crustaceans, both in basic research and for commercial development. RNAi has proven instrumental in a growing number of crustacean species, revealing the functionality of novel crustacean genes essential among others to development, growth, metabolism and reproduction. Extensive studies have also been done on silencing of viral transcripts in crustaceans, contributing to the understanding of the defense mechanisms of crustaceans and strategies employed by viruses to overcome these. The first practical use of gene silencing in aquaculture industry has been recently achieved, through manipulation of a crustacean insulin-like androgenic gland hormone. This review summarizes the advancements in the use of RNAi in crustaceans, and assesses the advantages of this method, as well as the current hurdles that hinder its large-scale practice.

An androgenic gland membrane-anchored gene associated with the crustacean insulin-like androgenic gland hormone

Crustacean male sexual differentiation is governed by the androgenic gland (AG) and specifically by the secreted insulin-like AG hormone (IAG), thus far identified in several decapod species including the Australian red claw crayfish Cherax quadricarinatus (termed Cq-IAG). While a few insulin-like AG genes have been identified in crustaceans, other AG-specific genes have not been documented until now. In the present study, we describe the recent identification of a non-IAG AG-specific transcript obtained from the C. quadricarinatus AG cDNA library. This transcript, termed C. quadricarinatus membrane-anchored AG-specific factor (Cq-MAG), was fully sequenced and found to encode a putative product of 189 amino acids including a signal anchoring peptide. Expression of a recombinant GFP fusion protein lacking the signal anchor encoding sequence dramatically affected recombinant protein localization pattern. While the expression of the deleterious fusion protein was observed throughout most of the cell, the native GFP::Cq-MAG fusion protein was observed mainly surrounding the periphery of the nucleus, demonstrating an endoplasmic reticulum (ER)-like localization pattern. Moreover, co-expression of the wild-type Cq-MAG (fused to GFP) and the Cq-IAG hormone revealed that these peptides indeed co-localize. This study is the first to report a protein specifically associated with the insulin-like AG hormone in addition to the finding of another AG-specific transcript in crustaceans. Previous knowledge suggests that insulin/insulin-like factor secretion involves tissue-specific transcripts and membrane-anchored proteins. In this regard, Cq-MAG's tissue specificity, anchoring properties and intracellular co-localization with Cq-IAG suggest that it may play a role in the processing and secretion of this insulin-like AG hormone.