Identification of putative ecdysteroid and juvenile hormone pathway genes in the shrimp Neocaridina denticulata

Effects of molting on the expression of ecdysteroid responsive genes in the crustacean molting gland (Y-organ)

Ecdysteroid molting hormones coordinate arthropod growth and development. Binding of 20-hydroxyecdysone (20E) to ecdysteroid receptor EcR/RXR activates a cascade of nuclear receptor transcription factors that mediate tissue responses to hormone. Insect ecdysteroid responsive and Forkhead box class O (FOXO) transcription factor gene sequences were used to extract orthologs from blackback land crab (Gecarcinus lateralis) Y-organ (YO) transcriptome: Gl-Ecdysone Receptor (EcR), Gl-Broad Complex (Br-C), Gl-E74, Gl-Hormone Receptor 3 (HR3), Gl-Hormone Receptor 4 (HR4), Gl-FOXO, and Gl-Fushi tarazu factor-1 (Ftz-f1). Quantitative polymerase chain reaction quantified mRNA levels in tissues from intermolt animals and in YO of animals induced to molt by multiple limb autotomy (MLA) or eyestalk ablation (ESA). Gl-EcR, Gl-Retinoid X Receptor (RXR), Gl-Br-C, Gl-HR3, Gl-HR4, Gl-E74, Gl-E75, Gl-Ftz-f1, and Gl-FOXO were expressed in all 10 tissues, with Gl-Br-C, Gl-E74, Gl-E75, and Gl-HR4 mRNA levels in the YO lower than those in most of the other tissues. In MLA animals, molting had no effect on Gl-Br-C, Gl-E74, and Gl-Ftz-f1 mRNA levels and little effect on Gl-EcR, Gl-E75, and Gl-HR4 mRNA levels. Gl-HR3 and Gl-FOXO mRNA levels were increased during premolt stages, while Gl-RXR mRNA level was highest during intermolt and premolt stages and lowest at postmolt stage. In ESA animals, YO mRNA levels were not correlated with hemolymph ecdysteroid titers. ESA had no effect on Gl-EcR, Gl-E74, Gl-HR3, Gl-HR4, Gl-Ftz-f1, and Gl-FOXO mRNA levels, while Gl-RXR, Gl-Br-C, and Gl-E75 mRNA levels were decreased at 3 days post-ESA. These data suggest that transcriptional up-regulation of Gl-FOXO and Gl-HR3 contributes to increased YO ecdysteroidogenesis during premolt. By contrast, transcriptional regulation of ecdysteroid responsive genes and ecdysteroidogenesis were uncoupled in the YO of ESA animals.

Comparative transcriptomic characterization of the ovary in the spawning process of the mud crab Scylla paramamosain

Oviposition is induced upon mating in most insects. Spawning is a physiological process that is fundamental for the reproduction of Scylla paramamosain. However, the molecular mechanisms underlying the spawning process in this species are poorly understood. Herein, comprehensive ovary transcriptomic analysis was conducted at the germinal vesicle breakdown stage (GVBD), spawning stage, 0.5 h post-spawning stage, and 24 h post-spawning stage of S. paramamosain for gene discovery. A total of 67,230 unigenes were generated, and 27,975 (41.61%) unigenes were annotated. Meanwhile, the differentially expressed genes (DEGs) between the different groups were identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was subsequently conducted. These results suggested that octopamine (OA) and tyramine (TA) could induce oviposition, while dopamine (DA) and serotonin (5-hydroxytryptamine [5-HT]) inhibit oviposition. The 20-hydroxyecdysone (20E) and methyl farnesoate (MF) signal pathways might be positively associated with oviposition. Furthermore, numerous transcripts that encode neuropeptides and their G-protein-coupled receptors (GPCRs), such as CNMamide, RYamide, ecdysis-triggering hormone (ETH), GPA2/GPB5 receptor, and Moody receptor, appear to be differentially expressed during the spawning process. Eleven unigenes were selected for qRT-PCR and the pattern was found to be consistent with the transcriptome expression pattern. Our work is the first spawning-related investigation of S. paramamosain focusing on the ovary at the whole transcriptome level. These findings assist in improving our understanding of spawning regulation in S. paramamosain and provide information for oviposition studies in other crustaceans.

Proposing Effective Ecotoxicity Test Species for Chemical Safety Assessment in East Asia: A Review

East Asia leads the global chemical industry, but environmental chemical risk in these countries is an emerging concern. Despite this, only a few native species that are representative of East Asian environments are listed as test species in international guidelines compared with those native to Europe and America. This review suggests that Zacco platypus, Misgurnus anguillicaudatus, Hydrilla verticillata, Neocaridina denticulata spp., and Scenedesmus obliquus, all resident to East Asia, are promising test species for ecotoxicity tests. The utility of these five species in environmental risk assessment (ERA) varies depending on their individual traits and the state of ecotoxicity research, indicating a need for different applications of each species according to ERA objectives. Furthermore, the traits of these five species can complement each other when assessing chemical effects under diverse exposure scenarios, suggesting they can form a versatile battery for ERA. This review also analyzes recent trends in ecotoxicity studies and proposes emerging research issues, such as the application of alternative test methods, comparative studies using model species, the identification of specific markers for test species, and performance of toxicity tests under environmentally relevant conditions. The information provided on the utility of the five species and alternative issues in toxicity tests could assist in selecting test species suited to study objectives for more effective ERA.

New insights into the regulation mechanism of Pacific white shrimp (Litopenaeus vannamei) hepatopancreas under 4-nonylphenol exposure using transcriptome analysis

4-Nonylphenol (4-NP) is one of the common endocrine-disrupting chemicals (EDCs) in estuaries and coastal zones, which can exert detrimental effects on the physiological function of aquatic organisms. However, the molecular response triggered by 4-NP remains largely unknown in Pacific white shrimp (Litopenaeus vannamei). In this study, transcriptomic analysis was performed to investigate the underlying mechanisms of 4-NP toxicity in the hepatopancreas of L. vannamei. Nine RNA-Seq libraries were generated from L. vannamei at 0 h, 24 h, and 48 h following exposure to 4-NP. Compared with 0 h vs 24 h, 962 up- and 463 down-regulated differentially expressed genes (DEGs) were identified, indicating that many genes in L. vannamei were induced to resist adverse circumstances by 4-NP exposure. In contrast, 902 up- and 1027 down-regulated DEGs were revealed in the comparison of 0 h vs 48 h, demonstrating that prolonged exposure to the stress from 4-NP resulted in more inhibited genes. To validate the accuracy of the transcriptome data, eight DEGs were selected for quantitative real-time polymerase chain reaction (qRT-PCR), which were consistent with the RNA-Seq results. Through KEGG pathway enrichment analysis, three specific pathways related to hormonal effects and endocrine function of L. vannamei were enriched significantly, including tyrosine metabolism, insect hormone biosynthesis, and melanogenesis. After 4-NP stress, genes involved in tyrosine metabolism (Tyr) and melanogenesis pathway (AC, CBP, Wnt, Frizzled, Tcf, and Ras) were induced to promote melanin pigment to help shrimp resist adverse environments. In the insect hormone biosynthesis, ALDH, CYP15A1, CYP15A1/C1, and JHE genes were activated to synthesize juvenile hormone (JH), while Spook, Phm, Sad, and CYP18A1 were induced to generate molting hormone. There is an enhanced interaction between the molting hormone and JH, with JH playing a dominant role and maintaining its "classic status quo action". Our study demonstrated that 4-NP exposure led to impairments of biological functions in L. vannamei hepatopancreas. The genes and pathways identified provide novel insights into the molecular mechanisms underlying 4-NP toxicity effects in prawns and enrich the information on the toxicity mechanism of crustaceans in response to EDCs exposure.

Evaluation of Phytosterols as an Alternative to Cholesterol in Practical Diets on Growth and Nonspecific Immunity of Litopenaeus vannamei

This study is aimed at evaluating the effectiveness of phytosterols as an alternative to cholesterol in practical diets of Pacific white shrimp Litopenaeus vannamei from the perspective of growth and nonspecific immunity. Five diets were formulated to contain different sterol sources and levels. Two diets were supplemented with 1 g/kg cholesterol (LC (low cholesterol)) or phytosterol (LP (low phytosterol)). Other three experimental diets were supplemented with 2 g/kg cholesterol (HC (high cholesterol)), 2 g/kg phytosterol (HP (high phytosterol)), or mixed sterol source (CP, 1 g/kg cholesterol + 1 g/kg phytosterol), respectively. A total of 750 healthy and uniform-sized shrimp (0.52 ± 0.008 g) were randomly distributed into 5 groups with 3 replicates and fed with the five experimental diets for 60 days. Results showed that the growth performance of shrimp was influenced by the sterol levels and supplementation with 2 g/kg sterol level facilitated the growth of shrimp. The inclusion of phytosterol has a cholesterol-lowering effect on shrimp, as evidenced by a reduction in hemolymph cholesterol and triglyceride contents in the HP group. Besides, supplementation with 2 g/kg phytosterol or mixed sterol sources had positive effects on the hemolymph superoxide dismutase, phenol oxidase, and lysozyme as well as hepatopancreas alkaline phosphatase activities, demonstrating that the nonspecific immunity and antioxidative capacity were improved. In conclusion, phytosterols could be an appropriate alternative to partially replace dietary cholesterol in shrimp feeds. This study preliminarily revealed the effects of different sterol sources and levels on the growth and nonspecific immunity of shrimp and provided a basis for further exploration of the mechanism of phytosterol.

Sesquiterpenoid pathway in the mandibular organ of Penaeus monodon: Cloning, expression, characterization of PmJHAMT and its alteration response to eyestalk ablation

Methyl farnesoate (MF), a crustacean equivalent of juvenile hormone (JH) of insects, is known to be produced from the mandibular organ (MO). This study reports transcriptome analysis of Penaeus monodon MO and identifies putative genes encoding enzymes in the sesquiterpenoid pathway. A total of 44,490,420 clean reads were obtained and utilized for subsequent analysis. De novo assembly created 31,201 transcripts and 31,167 unigenes. To archive the functional annotation, all unigenes were annotated with KOG, KEGG, and GO. Putative genes encoding enzymes and regulatory proteins involved in the sesquiterpenoid pathway were obtained from the MO transcriptome data based on the conserved domains and sequence homology. They included S-adenosylmethionine synthetase, farnesyl pyrophosphate synthase, short chain dependent dehydrogenase/reductase (SDR), NAD(P) + -dependent aldehyde dehydrogenase, S-adenosylmethionine-dependent methyltransferases or juvenile hormone acid-O-methyl transferase (JHAMT), farnesoic acid O-methyl transferase (FAMeT), juvenile hormone binding protein, cytochrome C/P-450 family 15 (CRYP15A1)/methylfarnesoate epoxidase (MFE), juvenile hormone epoxide hydrolase (JHEH), and juvenile hormone esterase (JHE). We first identified and characterized JHAMT orthologs inP. monodon(PmJHAMT). The complete cDNA sequence ofPmJHAMTconsisted of 1,221 nt encoded 271 amino acids with a conserved S-adenosyl methionine (SAM) binding domain. Phylogenetic analysis clusteredPmJHAMTinto the group JHAMT with the same clade of the crabPortunus trituberculausJHAMT. Moreover, the predicted three-dimensional structure of PmJHAMT showed remarkable similarity with the recent crystal structure ofthe Bombyx moriJHAMT homodimer. RT-PCR analysis revealed that PmJHAMT was exclusively expressed in MO and initially expressed at stage 3 postlarvae. In situ hybridization with a specific probe to PmJHAMT validated the specific expression of this gene in MO cells. Finally, we evaluated the regulation of MO by eyestalk inhibitory peptides. Diminishing MO inhibitory hormone through unilateral eyestalk ablation resulted in a significantly higher expression ofPmJHAMTin MO by quantitative PCR. This result indicated that the eyestalk inhibitory hormone inhibited MF synthesis byPmJHAMTgene suppression in the MO. This finding provides insight into the crustacean sesquiterpenoid pathway and improves our understanding of crustacean endocrinology.

Identification and characterization of two types of triacylglycerol lipase genes from Neocaridina denticulata sinensis

Triacylglycerol lipases (TGLs) can catalyze the hydrolysis reaction of triacylglycerol serving multiple functions in most organisms. Based on the genomic and transcriptomic databases of Neocaridina denticulata sinensis, two TGL genes from N. denticulata sinensis designated NdTGL1 and NdTGL2 were identified and characterized. NdTGL1 showed the highest expression in the stomach, followed by the testis and hepatopancreas, and NdTGL2 exhibited the maximum expression in the hepatopancreas, followed by the stomach and heart. Under the stimulation of copper ion, the expression of NdTGL1 peaked at 12 h and the expression of NdTGL2 elevated significantly at 24 h after stimulation (P < 0.05). It is speculated that NdTGLs may play an important role in the stress response of N. denticulata sinensis. Challenged with Vibrio parahaemolyticus, the expression profiles of NdTGL1 and NdTGL2 in the hepatopancreas was different, which indicates that the immune response of the V. parahaemolyticus challenge might lead to changes in triglyceride metabolism. The recombinant NdTGL (recNdTGL1 and recNdTGL2) were obtained and the enzymatic characterization of recNdTGL1 and recNdTGL2 were determined. The common maximum activity and stability of the recNdTGL1 and recNdTGL2 were observed at 45 °C and 10 °C, respectively. Both recNdTGL1 and recNdTGL2 exhibited the highest activity at pH 10.0. Furthermore, the recNdTGL1 and recNdTGL2 displayed the maximum stability at pH 5.0 and pH 8.0, respectively. In presence of different metal ions, the enzyme activity of recNdTGL1 and recNdTGL2 were inhibited by Cu²⁺ and Zn²⁺, and decreased by about 25%. Studies on the triacylglycerol lipases of N. denticulata sinensis provide theoretical support for studies related to fat metabolism in crustaceans and studies on response mechanism of digestive enzymes to microbial pathogens.

Dietary cholesterol promotes growth and ecdysone signalling pathway by modulating cholesterol transport in swimming crabs (Portunus trituberculatus)

Cholesterol, as an indispensable nutrient, regulates molting and growth in crustacean. As crustaceans are unable to biosynthesize cholesterol de novo, it is central to understand how dietary cholesterol affects molting in crustaceans. An 8-week feeding trial was conducted to evaluate the effects of dietary cholesterol level (0.12%, 0.43%, 0.79%, 1.00%, 1.30% and 2.50%) on growth, cholesterol metabolism and expression of genes related to lipid and ecdysone metabolism in female swimming crabs (Portunus trituberculatus). A total of 192 crabs (1.41 ± 0.05 g) were randomly distributed into 192 aquaria. Each treatment had 4 replicates with each replicate containing 8 crabs. Crabs fed the 1.00% cholesterol diet showed best growth performance, and thus based on percent weight gain, the optimal dietary cholesterol requirement was calculated at 1.01%. Tissue cholesterol concentrations were positively correlated with dietary cholesterol level. The contents of functional fatty acids in hepatopancreas significantly increased as dietary cholesterol increased from 0.12% to 2.50% (P < 0.05). The expression levels of genes related to lipogenesis pathway, lipid catabolism and fatty acid oxidation were significantly down-regulated with increased dietary cholesterol level (P < 0.05). The highest expression levels of cholesterol transport genes, low-density lipoprotein receptor (ldlr) and low-density lipoprotein receptor-related protein 2 (lrp2) occurred in crabs fed the 1.30% cholesterol diet. Moreover, hormones related to molting such as crustacean hyperglycemic hormone (CHH), methyl farnesoate (MF), molt-inhibiting hormone (MIH), and ecdysone in hemolymph were significantly influenced by dietary cholesterol level (P < 0.05). The highest expression levels of ecdysone receptor (ecr) and chitinase 1 (chi1) in eyestalk and hepatopancreas were found in crabs fed the diet containing 1.00% cholesterol (P < 0.05). In conclusion, the optimal dietary level was beneficial to functional fatty acid accumulation, regulated lipid metabolism, promoted the ecdysone signalling pathway by improving the cholesterol transport, and improved the molting rate and growth of swimming crabs.

Identification and Evolution Analysis of the Complete Methyl Farnesoate Biosynthesis and Related Pathway Genes in the Mud Crab, Scylla paramamosain

The sesquiterpenoid hormone methyl farnesoate (MF) plays a vital role during crustacean development, which is mainly evidenced by its varied titers during different developmental stages. However, the biosynthesis pathways of MF remain obscure to some extent. In this study, we identified the complete MF biosynthesis and related pathway genes in Scylla paramamosain, including three involved in acetyl-CoA metabolism, eight in the mevalonate pathway, five in the sesquiterpenoids synthesis pathway, and five in the methionine cycle pathway. Bioinformatics, genomic structure, and phylogenetic analysis indicated that the JH biosynthesis genes might have experienced evolution after species differentiation. The mRNA tissue distribution analysis revealed that almost all genes involving in or relating to MF syntheses were highly expressed in the mandibular organ (MO), among which juvenile hormone acid methyltransferase was exclusively expressed in the MO, suggesting that most of these genes might mainly function in MF biosynthesis and that the methionine cycle pathway genes might play a crucial regulatory role during MF synthesis. In addition, the phylogenetic and tissue distribution analysis of the cytochrome P450 CYP15-like gene suggested that the epoxidized JHs might exist in crustaceans, but are mainly synthesized in hepatopancreas rather than the MO. Finally, we also found that betaine-homocysteine S-methyltransferase genes were lost in insects while methionine synthase was probably lost in most insects except Folsomia candida, indicating a regulatory discrepancy in the methionine cycle between crustaceans and insects. This study might increase our understanding of synthetic metabolism tailored for sesquiterpenoid hormones in S. paramamosain and other closely related species.

The juvenile hormone epoxide hydrolase homolog in Penaeus vannamei plays immune-related functions

Juvenile hormone epoxide hydrolase (JHEH) participates in the degradation of juvenile hormone and also involved in the development and molting process in insects. Here, the JHEH homolog in Pennaus vannamei was cloned and found to consist of a full-length cDNA of 2543 bp and an open reading frame (ORF) of 1386 bp. Transcripts of PvJHEH1 were expressed in most tissues of healthy shrimp with the highest found in the hepatopancreas and lowest in hemocytes. Both Gram-negative (Vibrio parahaemolyticus) and Gram-positive (Streptococcus iniae) bacteria induced PvJHEH1 expression in shrimp hemocytes and hepatopancreas, suggesting the involvement of PvJHEH1 in P. vannamei immune responses. Moreover, the mRNA levels of ecdysone inducible nuclear transcription factor PvE75 and crustacean hyperglycemic hormone (PvCHH), two endocrine-related genes with roles in shrimp innate immune response, decreased significantly in shrimp hemocytes after PvJHEH1 knockdown. Shrimp survival was also affected after PvJHEH1 knockdown followed by V. parahaemolyticus challenge, indicating that JHEH1 plays an essential role in shrimp survival during bacterial infection.

Rethinking Sesquiterpenoids: A Widespread Hormone in Animals

The sesquiterpenoid hormone juvenile hormone (JH) controls development, reproduction, and metamorphosis in insects, and has long been thought to be confined to the Insecta. While it remains true that juvenile hormone is specifically synthesized in insects, other types or forms of sesquiterpenoids have also been discovered in distantly related animals, such as the jellyfish. Here, we combine the latest literature and annotate the sesquiterpenoid biosynthetic pathway genes in different animal genomes. We hypothesize that the sesquiterpenoid hormonal system is an ancestral system established in an animal ancestor and remains widespread in many animals. Different animal lineages have adapted different enzymatic routes from a common pathway, with cnidarians producing farnesoic acid (FA); non-insect protostomes and non-vertebrate deuterostomes such as cephalochordate and echinoderm synthesizing FA and methyl farnesoate (MF); and insects producing FA, MF, and JH. Our hypothesis revolutionizes the current view on the sesquiterpenoids in the metazoans, and forms a foundation for a re-investigation of the roles of this important and yet neglected type of hormone in different animals.

Molecular Characterization of the Cytochrome P450 Epoxidase (CYP15) in the Swimming Crab Portunus trituberculatus and Its Putative Roles in Methyl Farnesoate Metabolism

CYP15, which encodes a microsomal cytochrome P450 enzyme, could be involved in juvenile hormone biosynthesis in insects. In this study, a full-length cDNA of CYP15 was cloned from the swimming crab Portunus trituberculatus. This PtCYP15 amino acid sequence contains six conserved domains, which is a typical feature of the cytochrome P450 family. Phylogenetic tree analysis results showed that PtCYP15 clusters in a single branch of crustacean species, suggesting that CYP15 may be more widely present in crustaceans. The PtCYP15 mRNA has a broad pattern of tissue expression in P. trituberculatus, including high levels of expression in the hepatopancreas of both sexes and in the ovary of female crabs. During ovarian development stages, PtCYP15 mRNA is highly expressed in stages I and II and less so in stages III and IV in the hepatopancreas and the ovary of the female crabs. These expression profiles are opposite those of methyl farnesoate in hemolymph, suggesting that PtCYP15 might be involved in methyl farnesoate metabolism. In vitro studies show that only methyl farnesoate upregulated vitellogenin expression in the hepatopancreas, suggesting that methyl farnesoate might be the equivalent of juvenile hormone III in crustaceans. Methyl farnesoate treatment increased levels of PtCYP15 in explants of the hepatopancreas and ovary, while juvenile hormone III treatment reduced levels of PtCYP15 mRNA in ovary explants, suggesting that PtCYP15 might be involved in degrading methyl farnesoate. Furthermore, PtCYP15 mRNA expression levels were inhibited by adding juvenile hormone III to ovary explants. These findings provide foundational information for future research on methyl farnesoate metabolism in crustaceans.

Juvenile hormone synthesis and signaling disruption triggering male offspring induction and population decline in cladocerans (water flea): Review and adverse outcome pathway development

Juvenile hormone (JH) are a family of multifunctional hormones regulating larval development, molting, metamorphosis, reproduction, and phenotypic plasticity in arthropods. Based on its importance in arthropod life histories, many insect growth regulators (IGRs) mimicking JH have been designed to control harmful insects in agriculture and aquaculture. These JH analogs (JHAs) may also pose hazards to nontarget species by causing unexpected endocrine-disrupting (ED) effects such as molting and metamorphosis defects, larval lethality, and disruption of the sexual identity. This critical review summarizes the current knowledge of the JH-mediated effects in the freshwater cladoceran crustaceans such as Daphnia species on JHA-triggered endocrine disruptive outputs to establish a systematic understanding of JHA effects. Based on the current knowledge, adverse outcome pathways (AOPs) addressing the JHA-mediated ED effects in cladoceran leading to male offspring production and subsequent population decline were developed. The weight of evidence (WoE) of AOPs was assessed according to established guidelines. The review and AOP development aim to present the current scientific understanding of the JH pathway and provide a robust reference for the development of tiered testing strategies and new risk assessment approaches for JHAs in future ecotoxicological research and regulatory processes.

Comparative Metabolomics and Lipidomics of Four Juvenoids Application to Scylla paramamosain Hepatopancreas: Implications of Lipid Metabolism During Ovarian Maturation

This study was the first to evaluate multiple hormonal manipulations to hepatopancreas over the ovarian development stages of the mud crab, Scylla paramamosain. A total of 1258 metabolites in 75 hepatopancreas explants from five female crabs were induced by juvenile hormone III (JH III), methyl farnesoate (MF), farnesoic acid (FA) and methoprene (Met), as identified from combined metabolomics and lipidomics (LC-MS/MS). 101 significant metabolites and 47 significant pathways were selected and compared for their comprehensive effects to ovarian maturation. While MF played an extensive role in lipid accumulation, JH III and Met shared similar effects, especially in the commonly and significantly elevated triglycerides and lysophospholipids (fold change≥2 and ≤0.5, VIP≥1). The significant upregulation of β-oxidation and key regulators in lipid degradation by FA (P ≤ 0.05) resulted in less lipid accumulation from this treatment, with a shift toward lipid export and energy consumption, unlike the effects of MF, JH III and Met. It was possible that MF and FA played their own unique roles and acted in synergy to modulate lipid metabolism during crab ovarian maturation. Our study yielded insights into the MF-related lipid metabolism in crustacean hepatopancreas for the overall regulation of ovarian maturation, and harbored the potential use of juvenoids to induce reproductive maturity of this economic crab species.

Susceptibility of the Non-Targeted Crustacean Eurytemora affinis to the Endocrine Disruptor Tebufenozide: A Transcriptomic Approach

Copepods are zooplanktonic crustaceans ubiquitously widespread in aquatic systems. Although they are not the target, copepods are exposed to a wide variety of pollutants such as insect growth regulators (IGRs). The aim of this study was to investigate the molecular response of a non-targeted organism, the copepod Eurytemora affinis, to an IGR. Adult males and females were exposed to two sub-lethal concentrations of tebufenozide (TEB). Our results indicate a sex-specific response with a higher sensitivity in males, potentially due to a differential activation of stress response pathways. In both sexes, exposure to TEB triggered similar pathways to those found in targeted species by modulating the transcription of early and late ecdysone responsive genes. Among them were genes involved in cuticle metabolism, muscle contraction, neurotransmission, and gametogenesis, whose mis-regulation could lead to moult, locomotor, and reproductive impairments. Furthermore, genes involved in epigenetic processes were found in both sexes, which highlights the potential impact of exposure to TEB on future generations. This work allows identification of (i) potential biomarkers of ecdysone agonists and (ii) further assessment of putative physiological responses to characterize the effects of TEB at higher biological levels. The present study reinforces the suitability of using E. affinis as an ecotoxicological model.

Juvenile hormone in spiders. Is this the solution to a mystery?

The juvenile hormone (JH) plays a crucial role in arthropod physiological processes, e.g., the regulation of metamorphosis, development, and reproduction (the vitellogenesis, the development of gonads, egg production). Still, data about this sesquiterpenoid hormone in spiders (Araneae) are rudimentary and equivocal. The presence of the JH or its precursors (e.g. methyl farnesoate) is not confirmed in spiders. The site of synthesis of its is still undetermined. No receptors of the JH are identified in spiders and thus, the molecular mechanism of action of this group of hormones is still unknown. Here we show by using the phylogenetic analysis and qPCR method the presence of the transcript of the enzyme catalyzing the last phase of the JH biosynthesis pathway (epox CYP15A1), the JH receptor (Met), and a possible candidate to the methyl farnesoate receptor (USP) in the various tissues and stages of ontogenesis in both sexes of spider Parasteatoda tepidariorum. Our results indicate that the juvenile hormone and/or methyl farnesoate presence is possible in the species of spider P. tepidariorum. The presence of the Ptepox CYP15A1 gene suggests that the main site of the juvenile hormone synthesis can be the integument and not the Schneider organ 2. It also seems that the juvenile hormone and/or methyl farnesoate can be hormones with biological activity due to the presence of the transcript of insect and crustacean JH/MG receptor - Met. The Ptepox CYP15A1, PtMet, and Ptusp expression are sex-, tissue-and time-specific. This study is the first report about the presence of the Ptepox CYP15A1 and PtMet transcripts in the Arachnida, which may indicate the presence of the juvenile hormone and/or methyl farnesoate in spiders.

Genomic insights into the sessile life and biofouling of barnacles (Crustacea: Cirripedia)

Members of the infraclass Cirripedia, commonly called barnacles, are unique among the subphylum Crustacea in that they exhibit a biphasic life cycle with a planktonic larval stage and a sessile adult stage. Understanding their unique sessile life and mechanisms of attachment are hampered by the lack of genomic resources. Here, we present a 746 Mb genome assembly of Lepas anserifera – the first sequenced stalked barnacle genome. We estimate that Cirripedia first arose ~495 million years ago (MYA) and further diversified since Mesozoic. A demographic analysis revealed remarkable population changes of the barnacle in relation to sea-level fluctuations in the last 2 MYA. Comparative genomic analyses revealed the expansion of a number of developmental related genes families in barnacle genomes, such as Br–C, PCP20 and Lola, which are potentially important for the evolution of metamorphosis, cuticle development and central nervous system. Phylogenetic analysis and tissue expression profiling showed the possible roles of gene duplication, functional diversification and co-option in shaping the genomic evolution of barnacles. Overall, our study provides not only a valuable draft genome for comparative genomic analysis of crustacean evolution, but also facilitates studies of biofouling control.

Identification, characterization and mRNA transcript abundance profiles of the carboxylesterase (CXE5) gene in Eriocheir sinensis suggest that it may play a role in methyl farnesoate degradation

The sesquiterpenoid methyl farnesoate (MF) is a de-epoxidized form of insect juvenile hormone (JH) III in crustaceans, and its precise titer plays important roles in regulating many critical physiological processes, including reproduction and ovarian maturation. Understanding the synthetic and degradation pathways of MF is equally important for determining how to maintain MF titers at appropriate levels and thus for potential applications in crab aquaculture. Although the synthetic pathway of MF has been well established, little is known about MF degradation. Previous research proposed that specific carboxylesterases (CXEs) that degrade MF in crustaceans are conserved from those of JH III. In this study, we identified a novel Es-CXE5 gene from Eriocheir sinensis. The Es-CXE5 protein contains some conserved motifs, including catalytic triad and oxyanion hole, which are characteristics of the biologically active CXE family. The phylogenetic analysis showed that Es-CXE5 belongs to the hormone/semiochemical processing group of the CXE family. Moreover, Tissue and stage-specific expression results suggested that Es-CXE5 expression in hepatopancreas was highest and associated with the hemolymph MF titer. Furthermore, Es-CXE5 mRNA transcripts were detected in both in vitro and in vivo experiments and ESA experiment in the hepatopancreas and ovary. The results of this study showed that Es-CXE5 mRNA abundance in the hepatopancreas was notably induced by MF addition but had no effect on the ovary. Taken together, our results suggest that Es-CXE5 may degrade MF in the hepatopancreas and may thus be involved in ovarian development in E. sinensis.

The genome of the European estuarine calanoid copepod Eurytemora affinis: Potential use in molecular ecotoxicology

In this study, we sequenced and assembled the genome of a European estuarine calanoid copepod using Oxford Nanopore PromethION and Illumina HiSeq 2500 platforms. The length of the assembled genome was 776.1 Mb with N50 = 474.9 kb (BUSCO 85.9%), and the genome consisted of 2473 contigs. A total of 18,014 genes were annotated and orthologous gene clusters were analyzed in comparison to other copepods. In addition, genome-wide identification of cytochrome P450s, glutathione S-transferases, and ATP-binding cassette transporters in E. affinis was performed to determine gene repertoire of these detoxification-related gene families. Results revealed the presence of species-specific gene inventories, indicating that these gene families have evolved through species-specific gene loss/expansion processes, possibly due to adaptation to different environmental stressors. Our study provides a new inventory of the European estuarine calanoid copepod E. affinis genome with emphasis on phase I, II, and III detoxification systems.

Sex Determination and Differentiation in Decapod and Cladoceran Crustaceans: An Overview of Endocrine Regulation

Mechanisms underlying sex determination and differentiation in animals are known to encompass a diverse array of molecular clues. Recent innovations in high-throughput sequencing and mass spectrometry technologies have been widely applied in non-model organisms without reference genomes. Crustaceans are no exception. They are particularly diverse among the Arthropoda and contain a wide variety of commercially important fishery species such as shrimps, lobsters and crabs (Order Decapoda), and keystone species of aquatic ecosystems such as water fleas (Order Branchiopoda). In terms of decapod sex determination and differentiation, previous approaches have attempted to elucidate their molecular components, to establish mono-sex breeding technology. Here, we overview reports describing the physiological functions of sex hormones regulating masculinization and feminization, and gene discovery by transcriptomics in decapod species. Moreover, this review summarizes the recent progresses of studies on the juvenile hormone-driven sex determination system of the branchiopod genus Daphnia, and then compares sex determination and endocrine systems between decapods and branchiopods. This review provides not only substantial insights for aquaculture research, but also the opportunity to re-organize the current and future trends of this field.

The genome of the marine water flea Diaphanosoma celebensis: Identification of phase I, II, and III detoxification genes and potential applications in marine molecular ecotoxicology

To assemble the genome of the marine water flea Diaphanosoma celebensis, a sentinel model for marine environmental monitoring, we constructed a high-quality genome using PromethION and HiSeq 2500 platforms. The total length of the assembled genome was 100.08 Mb, with N50 = 2.56 Mb (benchmarking universal single-copy orthologs, 96.9%) and consisted of 179 scaffolds. A total of 15,427 genes were annotated, and orthologous gene clusters in D. celebensis were analyzed and compared with those of the cladocerans Daphnia magna and Daphnia pulex. In addition, phase I, II, and III detoxification gene families of cytochrome P450s, glutathione S-transferases, and ATP-binding cassette were fully identified and revealed lineage-specific gene loss and/or expansion, suggesting that the evolution of detoxification gene families likely modulates fitness and susceptibility in response to environmental stressors. The study improves our understanding of the detoxification-related gene system and should contribute to future studies of molecular ecotoxicology in cladoceran species and their responses to emerging pollutants.

Characterization of Shed genes encoding ecdysone 20-monooxygenase (CYP314A1) in the Y-organ of the blackback land crab, Gecarcinus lateralis

Molting in decapod crustaceans is controlled by ecdysteroid hormones synthesized and secreted by the molting gland, or Y-organ (YO). Halloween genes encode cytochrome P450 enzymes in the ecdysteroid synthetic pathway. The current paradigm is that YOs secrete an inactive precursor (e.g., ecdysone or E), which is hydroxylated at the #20 carbon to form an active hormone (20-hydroxyecdysone or 20E) by a mitochonrial 20-monooxygenase (CYP314A1) in peripheral tissues. 20-Monooxygenase is encoded by Shed in decapods and Shade in insects. We used eastern spiny lobster Shed sequences to extract six orthologs in the G. lateralis YO transcriptome. Phylogenetic analysis of the deduced amino acid sequences from six decapod species organized the Sheds into seven classes (Sheds 1-7), resulting in the assignment of the G. lateralis Sheds to Gl-Shed1, 2, 4A, 4B, 5A, and 5B. The mRNA levels of the six Gl-Sheds in the YO of intermolt animals were comparable to those in nine other tissues that included hepatopancreas and muscle. qPCR was used to compare the effects of molt induction by multiple leg autotomy (MLA) and eyestalk ablation (ESA) on Gl-Shed mRNA levels in the YO. Molt stage had little effect on Gl-Shed1 and Gl-Shed5B expression in the YO of MLA animals. Gl-Shed5A was expressed at the highest mRNA levels in the YO and was significantly increased during early and mid premolt stages. By contrast, ESA ± SB431542 had no effect on Gl-Shed expression at 1, 3, 5, and 7 days post-ESA. SB431542, which inhibits Transforming Growth Factor-β/activin signaling and blocks YO commitment, decreased Gl-Shed2 and Gl-Shed4A mRNA levels at 14 days post-ESA. A targeted metabolomic analysis showed that YOs cultured in vitro secreted E and 20E to the medium. These data suggest that the YO expresses 20-monooygenases that can convert E to 20E, which may contribute to the increase in active hormone in the hemolymph during premolt.

Identification of Functional SSR Markers in Freshwater Ornamental Shrimps Neocaridina denticulata Using Transcriptome Sequencing

The amazing colors and patterns are fascinating characteristics in all of the aquarium species. However, genetic and breeding molecular investigations of ornamental shrimps are rather limited. Here, we present the first transcriptomic analysis and application of microsatellites based on the chromatophore-encoded genes of Neocaridina denticulata to assist freshwater ornamental shrimp germplasm enhancement and its extensive applications. A total of 65,402 unigenes were annotated, and 4706 differentially expressed genes were screened and identified between super red shrimp and chocolate shrimp strains. Several gene ratios were examined to put in perspective possible genetic markers for the different strains of normal pigmentation development, including flotillin-2-like, keratin, the G protein-coupled receptor Mth2-like, annexin A7, and unconventional myosin-IXb-like. Five simple sequence repeat markers were effective for colored shrimps and were used to develop a marker-assisted selection platform for systematic breeding management program to maintain genetic diversity of the species. These markers could also be used to assist the identification of pure strains and increase the genetic stability of ornamental shrimp color phenotypes. Consequently, our results of microsatellite marker development are valuable for assisting shrimp genetic and selection breeding studies on freshwater ornamental shrimp and related crystal shrimp species.

Diversity and evolution of the P450 family in arthropods

The P450 family (CYP genes) of arthropods encodes diverse enzymes involved in the metabolism of foreign compounds and in essential endocrine or ecophysiological functions. The P450 sequences (CYPome) from 40 arthropod species were manually curated, including 31 complete CYPomes, and a maximum likelihood phylogeny of nearly 3000 sequences is presented. Arthropod CYPomes are assembled from members of six CYP clans of variable size, the CYP2, CYP3, CYP4 and mitochondrial clans, as well as the CYP20 and CYP16 clans that are not found in Neoptera. CYPome sizes vary from two dozen genes in some parasitic species to over 200 in species as diverse as collembolans or ticks. CYPomes are comprised of few CYP families with many genes and many CYP families with few genes, and this distribution is the result of dynamic birth and death processes. Lineage-specific expansions or blooms are found throughout the phylogeny and often result in genomic clusters that appear to form a reservoir of catalytic diversity maintained as heritable units. Among the many P450s with physiological functions, six CYP families are involved in ecdysteroid metabolism. However, five so-called Halloween genes are not universally represented and do not constitute the unique pathway of ecdysteroid biosynthesis. The diversity of arthropod CYPomes has only partially been uncovered to date and many P450s with physiological functions regulating the synthesis and degradation of endogenous signal molecules (including ecdysteroids) and semiochemicals (including pheromones and defense chemicals) remain to be discovered. Sequence diversity of arthropod P450s is extreme, and P450 sequences lacking the universally conserved Cys ligand to the heme have evolved several times. A better understanding of P450 evolution is needed to discern the relative contributions of stochastic processes and adaptive processes in shaping the size and diversity of CYPomes.

Transgenerational inheritance of chemical-induced signature: A case study with simvastatin

The hypothesis that exposure to certain environmental chemicals during early life stages may disrupt reproduction across multiple non-exposed generations has significant implications for understanding disease etiology and adverse outcomes. We demonstrate here reproductive multi and transgenerational effects, at environmentally relevant levels, of one of the most prescribed human pharmaceuticals, simvastatin, in a keystone species, the amphipod Gammarus locusta. The transgenerational findings has major implications for hazard and risk assessment of pharmaceuticals and other contaminants of emerging concern given that transgenerational effects of environmental chemicals are not addressed in current hazard and risk assessment schemes. Considering that the mevalonate synthesis, one of the key metabolic pathways targeted by simvastatin, is highly conserved among metazoans, these results may also shed light on the potential transgenerational effects of simvastatin on other animals, including humans.

Combined effects of exposure to sub-lethal concentration of the insecticide chlorpyrifos and the herbicide glyphosate on the biochemical changes in the freshwater crayfish Pontastacus leptodactylus

Glyphosate is an herbicide that inhibits the growth of weed plants, while chlorpyrifos is an insecticide commonly applied to control the pests' population. This study aimed to investigate the combined effects of chlorpyrifos and glyphosate on biochemical, immunological parameters, and oxidative stress biomarkers in freshwater crayfish Pontastacus leptodactylus for 21 days. The experimental design of this study was factorial (3 × 3), including 0.0, 0.4, and 0.8 mg L-1 glyphosate and 0.0, 2.5, and 5 µg L-1 chlorpyrifos. The exposure to chlorpyrifos, glyphosate alone and a mixture of them significantly decreased acetylcholinesterase, alkaline phosphatase, phenoloxidase activities, and total protein levels. The lactate dehydrogenase, glutamic-pyruvic-transaminase, and catalase activities, the contents of glucose, and malondialdehyde levels were increased in the crayfish. No significant changes were detected in glutamic-oxaloacetic-transaminase (SGOT) activity, triglyceride, and total antioxidant (TAO) levels in the crayfish treated with 0.4 mg L-1 glyphosate and the control group. Co-exposure of crayfish to chlorpyrifos and glyphosate increased SGOT activity and TAO levels. Although chlorpyrifos combined with glyphosate decreased the γ-Glutamyltransferase (GGT) activity, the GGT activity was significantly increased in the P. leptodactylus exposed during 21 days to 5 µg L-1 chlorpyrifos alone and 0.8 mg L-1 glyphosate alone. In comparison with the reference group, no significant changes were evidenced in the cholesterol levels in the P. leptodactylus treated with 2.5 µg L-1 chlorpyrifos, but its levels were significantly increased in the other treatment groups. In conclusion, the mix of glyphosate and chlorpyrifos exhibited synergic effects on the different toxicological biomarkers in the narrow-clawed crayfish. Co-exposure to pesticides may result in disruption of homeostasis in the crayfish by altering the biochemical and immunological parameters.

Roles of and cross-talk between ecdysteroid and sesquiterpenoid pathways in embryogenesis of branchiopod crustacean Daphnia magna

The ecdysteroid and sesquiterpenoid pathways control growth, developmental transition, and embryogenesis in insects. However, the function of orthologous genes and the cross-talk between both pathways remain largely uncharacterized in non-insect arthropods. Spook (Spo) and Juvenile hormone acid o-methyltransferase (Jhamt) have been suggested to function as rate-limiting factors in ecdysteroid and sesquiterpenoid biosynthesis, respectively, in insects. In this study, we report on the functions of Spo and Jhamt and the cross-talk between them in embryos of the branchiopod crustacean Daphnia magna. Spo expression was activated at the onset of gastrulation, with the depletion of Spo transcript by RNAi resulting in developmental arrest at this stage. This phenotype could be partially rescued by supplementation with 20-hydroxyecdysone, indicating that Spo may play the same role in ecdysteroid biosynthesis in early embryos, as reported in insects. After hatching, Spo expression was repressed, while Jhamt expression was activated transiently, despite its silencing during other embryonic stages. Jhamt RNAi showed little effect on survival, but shortened the embryonic period. Exposure to the sesquiterpenoid analog Fenoxycarb extended the embryonic period and rescued the Jhamt RNAi phenotype, demonstrating a previously unidentified role of sesquiterpenoid in the repression of precocious embryogenesis. Interestingly, the knockdown of Jhamt resulted in the derepression of ecdysteroid biosynthesis genes, including Spo, similar to regulation during insect hormonal biosynthesis. Sesquiterpenoid signaling via the Methoprene-tolerant gene was found to be responsible for the repression of ecdysteroid biosynthesis genes. It upregulated an ortholog of CYP18a1 that degrades ecdysteroid in insects. These results illuminate the conserved and specific functions of the ecdysteroid and sesquiterpenoid pathways in Daphnia embryos. We also infer that the common ancestor of branchiopod crustaceans and insects exhibited antagonism between the two endocrine hormones before their divergence 400 million years ago.

Hormonal control of the crustacean molting gland: Insights from transcriptomics and proteomics

Endocrine control of molting in decapod crustaceans involves the eyestalk neurosecretory center (X-organ/sinus gland complex), regenerating limbs, and a pair of Y-organs (YOs), as molting is induced by eyestalk ablation or multiple leg autotomy and suspended in early premolt by limb bud autotomy. Molt-inhibiting hormone (MIH) and crustacean hyperglycemic hormone (CHH), produced in the X-organ/sinus gland complex, inhibit the YO. The YO transitions through four physiological states over the molt cycle: basal in intermolt; activated in early premolt; committed in mid- and late premolt; and repressed in postmolt. We assembled the first comprehensive YO transcriptome over the molt cycle in the land crab, Gecarcinus lateralis, showing that as many as 23 signaling pathways may interact in controlling ecdysteroidogenesis. A proposed model of the MIH/cyclic nucleotide pathway, which maintains the basal YO, consists of cAMP/Ca²⁺ triggering and nitric oxide (NO)/cGMP summation phases. Mechanistic target of rapamycin (mTOR) signaling is required for YO activation in early premolt and affects the mRNA levels of thousands of genes. Transforming Growth Factor-β (TGFβ)/Activin signaling is required for YO commitment in mid-premolt and high ecdysteroid titers at the end of premolt may trigger YO repression. The G. lateralis YO expresses 99 G protein-coupled receptors, three of which are putative receptors for MIH/CHH. Proteomic analysis shows the importance of radical oxygen species scavenging, cytoskeleton, vesicular secretion, immune response, and protein homeostasis and turnover proteins associated with YO function over the molt cycle. In addition to eyestalk ganglia, MIH mRNA and protein are present in brain, optic nerve, ventral nerve cord, and thoracic ganglion, suggesting that they are secondary sources of MIH. Down-regulation of mTOR signaling genes, in particular Ras homolog enriched in brain or Rheb, compensates for the effects of elevated temperature in the YO, heart, and eyestalk ganglia in juvenile Metacarcinus magister. Rheb expression increases in the activated and committed YO. These data suggest that mTOR plays a central role in mediating molt regulation by physiological and environmental factors.

Impacts of Methyl Farnesoate and 20-Hydroxyecdysone on Larval Mortality and Metamorphosis in the Kuruma Prawn Marsupenaeus japonicus

Physiological functions of juvenile hormone (JH) and molting hormone have been demonstrated in insects. JH, molting hormone and their mimics (insect growth regulators, IGRs) show endocrine-disrupting effects not only on target pest insects but also on other arthropod species such as crustaceans. However, little is known about the endocrine-disrupting effects of IGRs on benthic crustaceans. In this study, laboratory experiments were conducted to investigate effects of representative innate JH in crustaceans (methyl farnesoate, MF) and molting hormone (20-hydroxyecdysone, 20E, active form of ecdysteroid) on larval stages of the kuruma prawn Marsupenaeus japonicus, which is a decapod crustacean living in warm seawater. Larval development of kuruma prawn progresses in the order of nauplius, zoea, mysis, and then post-larvae with molting and metamorphosis, but it is unknown whether both MF and 20E have crucial roles in metamorphosis and molting of this species. Treatments of either MF or 20E on shrimp larvae were attempted at each developmental stage and those effects were validated. In terms of EC50 values between mortality and metamorphosis, there were apparent differences in the transition from nauplius to zoea (MF: 7.67 and 0.12 μM; 20E: 3.84 and 0.06 μM in survival and metamorphic rates, respectively). In contrast, EC50 values in MF and 20E treatments showed high consistency in the transitions between zoea to mysis (EC50 values for survival; MF: 1.25 and 20E: 0.22 μM), and mysis to post-larvae (EC50 values for survival; MF: 0.65 and 20E: 0.46 μM). These data suggest that nauplius has strong resistance against exposure to MF and 20E. Moreover, both chemicals induced high mortality triggered by the disruption of molting associated with metamorphosis. To our knowledge, this is the first experimental evidence that investigates in vivo physiological functions of MF and 20E in the larval stages of kuruma prawn, shedding light on not only ecotoxicological impacts of IGRs released into nature, but also endocrine mechanisms underlying larval development with metamorphosis in benthic decapod crustaceans.

Ecdysteroid-mimicking compounds act as both agonists and antagonists to the crustacean ecdysone receptor

To characterize the potential endocrine-disrupting chemicals (EDCs) in the environment that interact with the crustacean ecdysone receptor (EcR), we established a method involving in silico modeling/molecular docking and in vitro reporter gene assay. Cherry shrimp (Neocaridina davidi) EcR (NdEcR) and retinoid X receptor (NdRxR) were identified and cloned for use in this method. A theoretical 3D model of NdEcR ligand-binding domain (LBD) was built in silico based on sequence homology with the established X-ray structure of insect EcR. The interaction of the NdEcR LBD with ecdysteroids, diacylhydrazine (DAH) pesticides, and other potential EDCs was evaluated using molecular docking programs. The results revealed that the ligand-binding pocket in the NdEcR LBD was flexible and adaptive for accommodating ligands of different shapes. The agonistic and antagonistic activities of the candidate compounds were further assessed by in vitro reporter gene assay using human cell lines transiently transfected with NdEcR and NdRxR expression plasmids and a reporter plasmid containing synthesized ecdysone response element. The assay was validated by the dose-dependent responses of EcR-mediated gene transcription after treating the transfected cell lines with ecdysteroids, 20-hydroxyecdysone, and ponasterone A. Examination of the candidate compounds using the reporter gene assay revealed restricted functional specificity to ecdysteroids and DAHs. Three of the tested DAH pesticides originally targeting the insect EcR were found to be weak agonists and strong antagonists of NdEcR. These results suggest that DAHs are potential EDCs for crustaceans that disrupt their ecdysteroid signals by functioning as EcR agonists or antagonists.

Genome-wide survey of cytochrome P450 genes in the salmon louse Lepeophtheirus salmonis (Krøyer, 1837)

Background

The salmon louse (Lepeophtheirus salmonis) infests farmed and wild salmonid fishes, causing considerable economic damage to the salmon farming industry. Infestations of farmed salmon are controlled using a combination of non-medicinal approaches and veterinary drug treatments. While L. salmonis has developed resistance to most available salmon delousing agents, relatively little is known about the molecular mechanisms involved. Members of the cytochrome P450 (CYP) superfamily are typically monooxygenases, some of which are involved in the biosynthesis and metabolism of endogenous compounds, while others have central roles in the detoxification of xenobiotics. In terrestrial arthropods, insecticide resistance can be based on the enhanced expression of CYPs. The reported research aimed to characterise the CYP superfamily in L. salmonis and assess its potential roles in drug resistance.

Methods

Lepeophtheirus salmonis CYPs were identified by homology searches of the genome and transcriptome of the parasite. CYP transcript abundance in drug susceptible and multi-resistant L. salmonis was assessed by quantitative reverse transcription PCR, taking into account both constitutive expression and expression in parasites exposed to sublethal levels of salmon delousing agents, ecdysteroids and environmental chemicals.

Results

The above strategy led to the identification of 25 CYP genes/pseudogenes in L. salmonis, making its CYP superfamily the most compact characterised for any arthropod to date. Lepeophtheirus salmonis possesses homologues of a number of arthropod CYP genes with roles in ecdysteroid metabolism, such as the fruit fly genes disembodied, shadow, shade, spook and Cyp18a1. CYP transcript expression did not differ between one drug susceptible and one multi-resistant strain of L. salmonis. Exposure of L. salmonis to emamectin benzoate or deltamethrin caused the transcriptional upregulation of certain CYPs. In contrast, neither ecdysteroid nor benzo[a]pyrene exposure affected CYP transcription significantly.

Conclusions

The parasite L. salmonis is demonstrated to possess the most compact CYP superfamily characterised for any arthropod to date. The complement of CYP genes in L. salmonis includes conserved CYP genes involved in ecdysteroid biosynthesis and metabolism, as well as drug-inducible CYP genes. The present study does not provide evidence for a role of CYP genes in the decreased susceptibility of the multiresistant parasite strain studied.

Effects of two juvenile hormone analogue insecticides, fenoxycarb and methoprene, on Neocaridina davidi

Juvenile hormone analogue (JHA) insecticides are endocrine disrupters that interfere with hormonal action in insects by mimicking their juvenile hormones (JH). As the structure and functions of methyl farnesoate in crustaceans are similar to those of JH in insects, exogenous JHA insecticides could have adverse effects on the development and reproduction of crustaceans. This study examined the toxic effects of two JHA insecticides, fenoxycarb and methoprene, on a freshwater shrimp model of cherry shrimp, Neocaridina davidi. Both insecticides had detrimental effects on cherry shrimp, but fenoxycarb was more toxic than methoprene. Chronic exposure to these insecticides reduced the shrimp's body length and molting frequency. Based on transcriptome annotations for N. davidi, we identified important gene homologues that were active in both insect JH biosynthetic and degradative pathways as well as JH and ecdysteroid signaling pathways. Chronic treatments with JHAs had significant effects on these genes in N. davidi. Our transcriptomic analysis showed that genes involved in the pathways related to cuticle development, serine protease activity, and carbohydrate, peptide and lipid metabolic processes were differentially expressed in shrimp exposed to JHAs. These results demonstrate the toxicity of fenoxycarb and methoprene to freshwater crustaceans and indicate the need to monitor the use of JHA insecticides.

The crustacean ecdysone cassette: A gatekeeper for molt and metamorphosis

Arthropods have long been utilized as models to explore molecular function, and the findings derived from them can be applied throughout metazoa, including as a basis for medical research. This has led to the adoption of many representative insect models beyond Drosophila, as each lends its own unique perspective to questions in endocrinology and genetics. However, non-insect arthropods are yet to be realised for the potential insight they may provide in such studies. The Crustacea are among the most ancient arthropods from which insects descended, comprising a huge variety of life histories and ecological roles. Of the events in a typical crustacean development, metamorphosis is perhaps the most ubiquitous, challenging and highly studied. Despite this, our knowledge of the endocrinology which underpins metamorphosis is rudimentary at best; although several key molecules have been identified and studied in depth, the link between them is quite nebulous and leans heavily on well-explored insect models, which diverged from the Pancrustacea over 450 million years ago. As omics technologies become increasingly accessible, they bring the prospect of explorative molecular research which will allow us to uncover components and pathways unique to crustaceans. This review reconciles known components of crustacean metamorphosis and reflects on our findings in insects to outline a future search space, with focus given to the ecdysone cascade. To expand our knowledge of this ubiquitous endocrine system not only aids in our understanding of crustacean metamorphosis, but also provides a deeper insight into the adaptive capacity of arthropods throughout evolution.

Juvenile hormone and sesquiterpenoids in arthropods: Biosynthesis, signaling, and role of MicroRNA

Arthropod molting and reproduction are precisely controlled by the levels of sesquiterpenoids, a class of C15 hormones derived from three isoprene units. The two major functional arthropod sesquiterpenoids are juvenile hormone (JH) and methyl farnesoate (MF). In hemimetabolous insects (such as the aphids, bugs, and cockroaches) and holometabolous insects (such as beetles, bees, butterflies, and flies), dramatic decrease in the titers of JH and/or MF promote metamorphosis from larvae to adults either directly or through an intermediate pupal stage, respectively. JH is absent in crustaceans (lobster, shrimp, crab) and other arthropods (chelicerates such as ticks, mites, spiders, scorpions and myriapods such as millipede and centipedes). In some crustaceans, molting and reproduction is dependent on changing levels of MF. The regulation of sesquiterpenoid production is thus crucial in the life cycle of arthropods. Dynamic and complex mechanisms have evolved to regulate sesquiterpenoid production. Noncoding RNAs such as the microRNAs are primary regulators. This article provides an overview of microRNAs that are known to regulate sesquiterpenoid production in arthropods.

Identification of target genes for RNAi-mediated control of the Twospotted Spider Mite

RNA interference (RNAi) is being developed for the management of pests that destroy crops. The twospotted Spider Mite (TSSM), Tetranychus urticae is a worldwide pest due to its unique physiological and behavioral characteristics including extraordinary ability to detoxify a wide range of pesticides and feed on many host plants. In this study, we conducted experiments to identify target genes that could be used for the development of RNAi-based methods to control TSSM. Leaf disc feeding assays revealed that knockdown in the expression genes coding for proteins involved in the biosynthesis and action of juvenile hormone (JH) and action of ecdysteroids [Methoprene-tolerant (Met), retinoid X receptor β, farnesoic acid O-methyltransferase, and CREB-binding protein] caused 35-56% mortality. Transgenic tobacco plants expressing hairpin dsRNA targeting Met gene were generated and tested. About 48% mortality was observed in TSSM raised on transgenic tobacco plants expressing dsMet. These studies not only broaden our knowledge on understanding hormone action in TSSM but also identified target genes that could be used in RNAi-mediated control of TSSM.

Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems

In the field of crustacean biology, usage of RNA-seq to study gene expression is rapidly growing. Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to insect and vertebrate model organisms, however, information on the organization of crustacean genomes is virtually nonexistent, making de novo transcriptome assembly, annotation and quantification problematic and challenging. We present here a summary of the methodologies and software analyses employed in 23 recent publications, which describe de novo transcriptome assembly, annotation, and differential gene expression in a variety of crustacean experimental systems. We focus on establishing a series of best practices that will allow for investigators to produce datasets that are understandable, reproducible, and of general utility for related analyses and cross-study comparisons.

Identification, expression, and endocrine-disruption of three ecdysone-responsive genes in the sentinel species Gammarus fossarum

Taking advantage of a large transcriptomic dataset recently obtained in the sentinel crustacean amphipod Gammarus fossarum, we developed an approach based on sequence similarity and phylogenetic reconstruction to identify key players involved in the endocrine regulation of G. fossarum. Our work identified three genes of interest: the nuclear receptors RXR and E75, and the regulator broad-complex (BR). Their involvement in the regulation of molting and reproduction, along with their sensitivity to chemical contamination were experimentally assessed by studying gene expression during the female reproductive cycle, and after laboratory exposure to model endocrine disrupting compounds (EDCs): pyriproxyfen, tebufenozide and piperonyl butoxide. RXR expression suggested a role of this gene in ecdysis and post-molting processes. E75 presented two expression peaks that suggested a role in vitellogenesis, and molting. BR expression showed no variation during molting/reproductive cycle. After exposure to the three EDCs, a strong inhibition of the inter-molt E75 peak was observed with tebufenozide, and an induction of RXR after exposure to pyriproxyfen and piperonyl butoxide. These results confirm the implication of RXR and E75 in hormonal regulation of female reproductive cycles in G. fossarum and their sensitivity towards EDCs opens the possibility of using them as specific endocrine disruption biomarkers.

Juvenile hormone regulates the differential expression of putative juvenile hormone esterases via methoprene-tolerant in non-diapause-destined and diapause-destined adult female beetle

Juvenile hormone (JH) plays an essential role in regulating molting, metamorphosis, reproduction, and diapause (dormancy), in many insects and crustaceans. JH esterases (JHEs) can control JH titer by regulating JH degradation. Although the biochemistry and structure of JHEs have been well studied, regulation of their expression remains unclear. We identified three putative JHEs (JHE1, JHE2, JHE3) in the cabbage beetle Colaphellus bowringi, and investigated the regulation of their expression by JH signaling in non-diapause-destined (NDD, reproductive) and diapause-destined (DD) female adults. Sequence and phylogenetic tree analyses indicate that the three putative JHEs shared conserved motifs with the JHEs of other insects and one crustacean, and were similar to Coleopteran, Dipteran, Orthopteran, Hymenopteran, and Decapodan JHEs. They were, however, less closely related to Hemipteran and Lepidopteran JHEs. JHEs were more highly expressed in NDD female adults than in DD female adults. JH analog induction in DD female adults significantly upregulated the expression of JHE1 and JHE2, but had no effect on the expression of JHE3. Knockdown of the JH candidate receptor methoprene-tolerant (Met) in NDD female adults downregulated the expression of all three JHEs. These results suggest that JHE expression is positively correlated with JH signaling, and that Met may be involved in the JH-mediated differential expression of JHE in DD and NDD adult female C. bowringi.

Transcriptomic information from Pacific white shrimp (Litopenaeus vannamei) ovary and eyestalk, and expression patterns for genes putatively involved in the reproductive process

The increased use of massive sequencing technologies has enabled the identification of several genes known to be involved in different mechanisms associated with reproduction that so far have only been studied in vertebrates and other model invertebrate species. In order to further investigate the genes involved in Litopenaeus vannamei reproduction, cDNA and SSH libraries derived from female eyestalk and gonad were produced, allowing the identification of expressed sequences tags (ESTs) that potentially have a role in the regulation of gonadal maturation. In the present study, different transcripts involved in reproduction were identified and a number of them were characterized as full-length. These transcripts were evaluated in males and females in order to establish their tissue expression profiles during developmental stages (juvenile, subadult and adult), and in the case of females, their possible association with gonad maturation was assessed through expression analysis of vitellogenin. The results indicated that the expression of vitellogenin receptor (vtgr) and minichromosome maintenance (mcm) family members in the female gonad suggest an important role during previtellogenesis. Additionally, the expression profiles of genes such as famet, igfbp and gpcr in brain tissues suggest an interaction between the insulin/insulin-like growth factor signaling pathway (IIS) and methyl farnesoate (MF) biosynthesis for control of reproduction. Furthermore, the specific expression pattern of farnesoic acid O-methyltransferase suggests that final synthesis of MF is carried out in different target tissues, where it is regulated by esterase enzymes under a tissue-specific hormonal control. Finally, the presence of a vertebrate type steroid receptor in hepatopancreas and intestine besides being highly expressed in female gonads, suggest a role of that receptor during sexual maturation.

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.

Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015

Despite their economic, ecological, and experimental importance, genomic resources remain scarce for crustaceans. In lieu of genomes, many researchers have taken advantage of technological advancements to instead sequence and assemble crustacean transcriptomes de novo However, there is little consensus on what standard operating procedures are, or should be, for the field. Here, we systematically reviewed 53 studies published during 2014-2015 that utilized transcriptomic resources from this taxonomic group in an effort to identify commonalities as well as potential weaknesses that have applicability beyond just crustaceans. In general, these studies utilized RNA-Seq data, both novel and publicly available, to characterize transcriptomes and/or identify differentially expressed genes (DEGs) between treatments. Although the software suite Trinity was popular in assembly pipelines and other programs were also commonly employed, many studies failed to report crucial details regarding bioinformatic methodologies, including read mappers and the utilized parameters in identifying and characterizing DEGs. Annotation percentages for assembled transcriptomic contigs were low, averaging 32% overall. While other metrics, such as numbers of contigs and DEGs reported, correlated with the number of sequence reads utilized per sample, these did reach apparent saturation with increasing sequencing depth. Most disturbingly, a number of studies (55%) reported DEGs based on non-replicated experimental designs and single biological replicates for each treatment. Given this, we suggest future RNA-Seq experiments targeting transcriptome characterization conduct deeper (i.e., 50-100 M reads) sequencing while those examining differential expression instead focus more on increased biological replicates at shallower (i.e., ∼10-20 M reads/sample) sequencing depths. Moreover, the community must avoid submitting for review, or accepting for publication, non-replicated differential expression studies. Finally, mining the ever growing publicly available transcriptomic data from crustaceans will allow future studies to focus on hypothesis-driven research instead of continuing to simply characterize transcriptomes. As an example of this, we utilized neurotoxin sequences from the recently described remipede venom gland transcriptome in conjunction with publicly available crustacean transcriptomic data to derive preliminary results and hypotheses regarding the evolution of venom in crustaceans.

Role of Halloween genes in ecdysteroids biosynthesis of the swimming crab (Portunus trituberculatus): Implications from RNA interference and eyestalk ablation

Molting, including metamorphosis molting in arthropods are controlled by the ecdysteroids that are synthesized and secreted by the crustacean Y-organ (YO) or the insect prothoracic gland (PG). The Halloween genes encoding the enzymes mainly involved in the biosynthesis of ecdysteroids are well studied in insects but not in crustaceans. Given the importance of Halloween genes in ecdysteroids biosynthesis, we have previously reported the cDNA cloning of disembodied (Dib) in P. trituberculatus. Here, cDNA sequences of another two Halloween genes, Spook (Spo) and Shadow (Sad), were further identified and characterized. The predicted amino acid sequences for these two Halloween genes of Portunus trituberculatus were compared to those of several other arthropods, and several typical domains of the cytochrome P450 mono-oxygenase (CYP) were identified. Similar to the tissue distribution of Dib, the Spo and Sad also showed high specificity to the YO. RNA interference (RNAi) of these 3 genes indicated they all play essential role in ecdysteroids biosynthesis. To investigate the relationships of the Halloween genes to the eyestalk neuropeptides such as molt-inhibiting hormone (MIH), effects of eyestalk ablation (ESA) on the expression of Dib, Spo and Sad were detected. Expression of Dib and Sad, but not Spo, was significantly induced by ESA. The result indicated that the inhibition of MIH in ecdysteroids biosynthesis may be partly through the transcriptional regulation of certain Halloween genes, such as Dib and Sad, while the Spo might not be the target for MIH signal.

The retinoid X receptor from mud crab: new insights into its roles in ovarian development and related signaling pathway

In arthropods, retinoid X receptor (RXR) is a highly conserved nuclear hormone receptor. By forming a heterodimeric complex with the ecdysone receptor (EcR), RXR is known to be vital importance for various physiological processes. However, in comparison to EcR, the RXR signaling pathway and its roles in crustacean reproduction are poorly understood. In the present study, the RXR mRNA was detected in the ovarian follicular cells of mud crab Scylla paramamosain (SpRXR) and during ovarian maturation, its expression level was found to increase significantly. In vitro experiment showed that both SpRXR and vitellogenin (SpVg) mRNA in the ovarian explants were significantly induced by 20-hydroxyecdysone (20E) but not methyl farnesoate (MF). However, differing from the in vitro experiment, injection of MF in in vivo experiment significantly stimulated the expressions of SpRXR and SpVg in female crabs at early vitellogenic stage, but the ecdysone and insect juvenile hormone (JH) signaling pathway genes were not induced. The results together suggest that both MF and SpRXR play significant roles in regulating the expression of SpVg and ovarian development of S. paramamosain through their own specific signaling pathway rather than sharing with the ecdysone or the insect JH.

In silico prediction of the G-protein coupled receptors expressed during the metamorphic molt of Sagmariasus verreauxi (Crustacea: Decapoda) by mining transcriptomic data: RNA-seq to repertoire

Against a backdrop of food insecurity, the farming of decapod crustaceans is a rapidly expanding and globally significant source of food protein. Sagmariasus verreauxi spiny lobster, the subject of this study, are decapods of underdeveloped aquaculture potential. Crustacean neuropeptide G-protein coupled receptors (GPCRs) mediate endocrine pathways that are integral to animal fecundity, growth and survival. The potential use of novel biotechnologies to enhance GPCR-mediated physiology may assist in improving the health and productivity of farmed decapod populations. This study catalogues the GPCRs expressed in the early developmental stages, as well as adult tissues, with a view to illuminating key neuropeptide receptors. De novo assembled contiguous sequences generated from transcriptomic reads of metamorphic and post metamorphic S. verreauxi were filtered for seven transmembrane domains, and used as a reference for iterative re-mapping. Subsequent putative GPCR open reading frames (ORFs) were BLAST annotated, categorised, and compared to published orthologues based on phylogenetic analysis. A total of 85 GPCRs were digitally predicted, that represented each of the four arthropod subfamilies. They generally displayed low-level and non-differential metamorphic expression with few exceptions that we examined using RT-PCR and qPCR. Two putative CHH-like neuropeptide receptors were annotated. Three dimensional structural modelling suggests that these receptors exhibit a conserved extracellular ligand binding pocket, providing support to the notion that these receptors co-evolved with their ligands across Decapoda. This perhaps narrows the search for means to increase productivity of farmed decapod populations.

The potential role of juvenile hormone acid methyltransferase in methyl farnesoate (MF) biosynthesis in the swimming crab, Portunus trituberculatus

Juvenile hormone (JH) and methyl farnesoate (MF) play essential roles in the development and reproduction of insects and crustaceans respectively. Juvenile hormone acid methyltransferase (JHAMT) catalyzes the methyl esterification in insect JH biosynthesis, while the corresponding step in crustacean MF biosynthesis was long thought to be catalyzed by farnesoic acid O-methyltransferase (FAMeT). However, the new discovery of JHAMT orthologs in crustaceans indicates that JHAMT may also play essential role in the MF biosynthesis in crustaceans. Here we cloned and characterized the full-length cDNA encoding JHAMT in the swimming crab Portunus trituberculatus (PtJHAMT). Sequence and structure analysis of PtJHAMT revealed that it was composed of a 6-stranded β sheet with 9 α helices, and contained a signature Sadenosyl-L-methionine (SAM) binding motif, which is the hallmark in all SAM dependent methyltransferases (SAM-MTs). Several active sites that are critical for the interaction of SAM and JH/FA substrate were also conserved in PtJHAMT. The gene expression of PtJHAMT was highly specific to the mandibular organ, which is the sole site of MF synthesis. PtJHAMT expression significantly increased in the late-vitellogenic stage and mature stage, which suggests a possible role of PtJHAMT in modulating ovarian development. The role of PtJHAMT and PtFAMeT in MF biosynthesis was further investigated by RNA interfering (RNAi). Injection of PtJHAMT and PtFAMeT dsRNA both led to a decrease in hemolymph MF titers. Injection of PtHMGR dsRNA caused the decrease in PtJHAMT expression, but had no effect on mRNA level of PtFAMeT. Together these results suggested that JHAMT and FAMeT are both involved in the MF biosynthesis in crustaceans, while the JHAMT is highly specific to FA substrate, and FAMeT may have more catalytic functions.