Redefining metamorphosis in spiny lobsters: molecular analysis of the phyllosoma to puerulus transition in Sagmariasus verreauxi

The moulting arthropod: a complete genetic toolkit review

Exoskeletons are a defining character of all arthropods that provide physical support for their segmented bodies and appendages as well as protection from the environment and predation. This ubiquitous yet evolutionarily variable feature has been instrumental in facilitating the adoption of a variety of lifestyles and the exploitation of ecological niches across all environments. Throughout the radiation that produced the more than one million described modern species, adaptability afforded by segmentation and exoskeletons has led to a diversity that is unrivalled amongst animals. However, because of the limited extensibility of exoskeleton chitin and cuticle components, they must be periodically shed and replaced with new larger ones, notably to accommodate the growing individuals encased within. Therefore, arthropods grow discontinuously by undergoing periodic moulting events, which follow a series of steps from the preparatory pre-moult phase to ecdysis itself and post-moult maturation of new exoskeletons. Each event represents a particularly vulnerable period in an arthropod's life cycle, so processes must be tightly regulated and meticulously executed to ensure successful transitions for normal growth and development. Decades of research in representative arthropods provide a foundation of understanding of the mechanisms involved. Building on this, studies continue to develop and test hypotheses on the presence and function of molecular components, including neuropeptides, hormones, and receptors, as well as the so-called early, late, and fate genes, across arthropod diversity. Here, we review the literature to develop a comprehensive overview of the status of accumulated knowledge of the genetic toolkit governing arthropod moulting. From biosynthesis and regulation of ecdysteroid and sesquiterpenoid hormones, to factors involved in hormonal stimulation responses and exoskeleton remodelling, we identify commonalities and differences, as well as highlighting major knowledge gaps, across arthropod groups. We examine the available evidence supporting current models of how components operate together to prepare for, execute, and recover from ecdysis, comparing reports from Chelicerata, Myriapoda, Crustacea, and Hexapoda. Evidence is generally highly taxonomically imbalanced, with most reports based on insect study systems. Biases are also evident in research on different moulting phases and processes, with the early triggers and late effectors generally being the least well explored. Our synthesis contrasts knowledge based on reported observations with reasonably plausible assumptions given current taxonomic sampling, and exposes weak assumptions or major gaps that need addressing. Encouragingly, advances in genomics are driving a diversification of tractable study systems by facilitating the cataloguing of putative genetic toolkits in previously under-explored taxa. Analysis of genome and transcriptome data supported by experimental investigations have validated the presence of an "ultra-conserved" core of arthropod genes involved in moulting processes. The molecular machinery has likely evolved with elaborations on this conserved pathway backbone, but more taxonomic exploration is needed to characterise lineage-specific changes and novelties. Furthermore, linking these to transformative innovations in moulting processes across Arthropoda remains hampered by knowledge gaps and hypotheses based on untested assumptions. Promisingly however, emerging from the synthesis is a framework that highlights research avenues from the underlying genetics to the dynamic molecular biology through to the complex physiology of moulting.

Transcriptomic Analysis across Crayfish (Cherax quadricarinatus) Claw Regeneration Reveals Potential Stem Cell Sources for Cultivated Crustacean Meat

In the face of rising global demand and unsustainable production methods, cultivated crustacean meat (CCM) is proposed as an alternative means to produce delicious lobster, shrimp, and crab products. Cultivated meat requires starting stem cells that may vary in terms of potency and the propensity to proliferate or differentiate into myogenic (muscle-related) tissues. Recognizing that regenerating limbs are a non-lethal source of tissue and may harbor relevant stem cells, we selected those of the crayfish Cherax quadricarinatus as our model. To investigate stem cell activity, we conducted RNA-Seq analysis across six stages of claw regeneration (four pre-molt and two post-molt stages), along with histology and real-time quantitative PCR (qPCR). Our results showed that while genes related to energy production, muscle hypertrophy, and exoskeletal cuticle synthesis dominated the post-molt stages, growth factor receptors (FGFR, EGFR, TGFR, and BMPR) and those related to stem cell proliferation and potency (Cyclins, CDKs, Wnts, C-Myc, Klf4, Sox2, PCNA, and p53) were upregulated before the molt. Pre-molt upregulation in several genes occurred in two growth peaks; Stages 2 and 4. We therefore propose that pre-molt limb regeneration tissues, particularly those in the larger Stage 4, present a prolific and non-lethal source of stem cells for CCM development.

Identification and Physiological Assays of Crustacean Hyperglycemic Hormones in the Japanese Spiny Lobster, Panulirus japonicus

The Japanese spiny lobster Panulirus japonicus lives on rocky shores and is mainly distributed along the Pacific coast around Japan. Due to the high demand for it, the development of aquaculture systems and increasing its resource volume requires further expansive production. However, a major factor preventing the establishment of aquaculture technology for this lobster is the difficulty with rearing processes from larval to juvenile production. A recent study shed light on the molecular mechanisms underlying larval development from the perspective of physiological functions of endocrine factors such as molting hormones. However, physiological studies of P. japonicus are still lacking. In decapod crustaceans, the X-organ/sinus gland complex is a well-known endocrine system that secretes the crustacean hyperglycemic hormone (CHH)-superfamily peptides that regulate growth, molting, sexual maturation, reproduction, and change in body color. In this study, we identified two CHHs from the sinus glands of P. japonicus using reversed-phase high-performance liquid chromatography in order to elucidate their physiological function for the first time.

Ontogeny of the Cytochrome P450 Superfamily in the Ornate Spiny Lobster (Panulirus ornatus)

Cytochrome P450s (CYP450s) are a versatile superfamily of enzymes known to undergo rapid evolution. They have important roles across growth and development pathways in crustaceans, although it is difficult to characterise orthologs between species due to their sequence diversity. Conserved CYP450s enzymes in crustaceans are those associated with ecdysteroidogenesis: synthesising and breaking down the active moult hormone, 20-hydroxyecdysone. The complex life cycle of the ornate spiny lobster, Panulirus ornatus, relies on moulting in order to grow and develop. Many of these diverse life stages have been analysed to establish a comprehensive transcriptomic database for this species. The transcripts putatively encoding for CYP450s were mapped using transcriptomic analysis and identified across growth and development stages. With the aid of phylogeny, 28 transcripts of 42 putative P. ornatus CYP450s were annotated, including the well conserved Halloween genes, which are involved in ecdysteroidogenesis. Expression patterns across the life stages determined that only a subset of the CYP450s can be detected in each life stage or tissue. Four Shed transcripts show overlapping expression between metamorphosis and adult tissues, suggesting pleotropic functions of the multiple Shed orthologs within P. ornatus.

Unravelling the neuropeptidome of the ornate spiny lobster Panulirus ornatus: A focus on peptide hormones and their processing enzymes expressed in the reproductive tissues

Neuropeptides are commonly produced in the neural tissues yet can have effects on far-reaching targets, with varied biological responses. We describe here the neuropeptidome of the ornate spiny lobster, Panulirus ornatus, a species of emerging importance to closed-system aquaculture, with a focus on peptide hormones produced by the reproductive tissues. Transcripts for a precursor to one neuropeptide, adipokinetic hormone/corazonin-related peptide (ACP) were identified in high numbers in the sperm duct of adult spiny lobsters suggesting a role for ACP in the reproduction of this species. Neuropeptide production in the sperm duct may be linked with physiological control of spermatophore production in the male, or alternatively may function in signalling to the female. The enzymes which process nascent neuropeptide precursors into their mature, active forms have seldom been studied in decapods, and never before at the multi-tissue level. We have identified transcripts for multiple members of the proprotein convertase subtisilin/kexin family in the ornate spiny lobster, with some enzymes showing specificity to certain tissues. In addition, other enzyme transcripts involved with neuropeptide processing are identified along with their tissue and life stage expression patterns.

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.

Signaling Pathways That Regulate the Crustacean Molting Gland

A pair of Y-organs (YOs) are the molting glands of decapod crustaceans. They synthesize and secrete steroid molting hormones (ecdysteroids) and their activity is controlled by external and internal signals. The YO transitions through four physiological states over the molt cycle, which are mediated by molt-inhibiting hormone (MIH; basal state), mechanistic Target of Rapamycin Complex 1 (mTORC1; activated state), Transforming Growth Factor-β (TGFβ)/Activin (committed state), and ecdysteroid (repressed state) signaling pathways. MIH, produced in the eyestalk X-organ/sinus gland complex, inhibits the synthesis of ecdysteroids. A model for MIH signaling is organized into a cAMP/Ca2+-dependent triggering phase and a nitric oxide/cGMP-dependent summation phase, which maintains the YO in the basal state during intermolt. A reduction in MIH release triggers YO activation, which requires mTORC1-dependent protein synthesis, followed by mTORC1-dependent gene expression. TGFβ/Activin signaling is required for YO commitment in mid-premolt. The YO transcriptome has 878 unique contigs assigned to 23 KEGG signaling pathways, 478 of which are differentially expressed over the molt cycle. Ninety-nine contigs encode G protein-coupled receptors (GPCRs), 65 of which bind a variety of neuropeptides and biogenic amines. Among these are putative receptors for MIH/crustacean hyperglycemic hormone neuropeptides, corazonin, relaxin, serotonin, octopamine, dopamine, allatostatins, Bursicon, ecdysis-triggering hormone (ETH), CCHamide, FMRFamide, and proctolin. Contigs encoding receptor tyrosine kinase insulin-like receptor, epidermal growth factor (EGF) receptor, and fibroblast growth factor (FGF) receptor and ligands EGF and FGF suggest that the YO is positively regulated by insulin-like peptides and growth factors. Future research should focus on the interactions of signaling pathways that integrate physiological status with environmental cues for molt control.

Biological scaling analyses are more than statistical line fitting

The magnitude of many biological traits relates strongly and regularly to body size. Consequently, a major goal of comparative biology is to understand and apply these 'size-scaling' relationships, traditionally quantified by using linear regression analyses based on log-transformed data. However, recently some investigators have questioned this traditional method, arguing that linear or non-linear regression based on untransformed arithmetic data may provide better statistical fits than log-linear analyses. Furthermore, they advocate the replacement of the traditional method by alternative specific methods on a case-by-case basis, based simply on best-fit criteria. Here, I argue that the use of logarithms in scaling analyses presents multiple valuable advantages, both statistical and conceptual. Most importantly, log-transformation allows biologically meaningful, properly scaled (scale-independent) comparisons of organisms of different size, whereas non-scaled (scale-dependent) analyses based on untransformed arithmetic data do not. Additionally, log-based analyses can readily reveal biologically and theoretically relevant discontinuities in scale invariance during developmental or evolutionary increases in body size that are not shown by linear or non-linear arithmetic analyses. In this way, log-transformation advances our understanding of biological scaling conceptually, not just statistically. I hope that my Commentary helps students, non-specialists and other interested readers to understand the general benefits of using log-transformed data in size-scaling analyses, and stimulates advocates of arithmetic analyses to show how they may improve our understanding of scaling conceptually, not just statistically.

The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation

The infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. Here we report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crab Eriocheir sinensis, a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. We show the expansion of specific gene families in the crab, including F-ATPase, which enhances our knowledge on the adaptive plasticity of this successful invasive species. Our analysis of spatio-temporal transcriptomes and the genome of E. sinensis and other decapods shows that brachyurization development is associated with down-regulation of Hox genes at the megalopa stage when tail shortening occurs. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics. These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general.

Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus cyaneus

The ancient Lake Baikal is the largest source of liquid freshwater on Earth and home to a unique fauna. Several hundred mostly cold-adapted endemic amphipod species inhabit Baikal, an ecosystem that is already being influenced by global change. In this study, we characterized the core proteome and heat stress-induced changes in a temperature-tolerant endemic amphipod, Eulimnogammarus cyaneus, using a proteogenomic approach (PRIDE dataset PXD013237) to unravel the molecular mechanisms of the observed adverse effects. As males were previously found to be much more tolerant to thermal stress, we placed special emphasis on differences between the sexes. For both sexes, we observed adaption of energy metabolism, cytoskeleton, lipid, and carbohydrate metabolism upon heat stress. In contrast, significant differences were determined in the molecular chaperone response. Females from the control conditions possessed significantly higher levels of heat shock proteins (HSP70, HSPb1, Hsc70-3), which, in contrast to males, were not further increased in response to heat stress. The inability of females to further increase heat shock protein synthesis in response to temperature stress may be due to sex-specific processes, such as egg production, requiring a large proportion of the available energy. As ovigerous females synthesize generally higher amounts of protein, they also need higher levels of molecular chaperones for the folding of these new proteins. Thus, the higher sensitivity of females to heat shock may be due to the lack of molecular chaperone molecules to counteract the heat-induced protein denaturation.

Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis

Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in Crustacea. Functional analysis, although essential, has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, transcriptome sequencing was conducted on 59 samples representing diverse developmental stages (fertilized eggs, zoea, megalopa, three sub-stages of larvae, juvenile crabs, and adult crabs) and different tissues (eyestalk, hepatopancreas, and muscle from juvenile crabs, and eyestalk, hepatopancreas, muscle, heart, stomach, gill, thoracic ganglia, intestine, ovary, and testis from adult crabs) of E. sinensis. A comprehensive reference transcriptome was assembled, including 19,023 protein-coding genes. Hierarchical clustering based on 128 differentially expressed cuticle-related genes revealed two distinct expression patterns during the early larval developmental stages, demonstrating the distinct roles of these genes in “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting. Phylogenetic analysis of 1406 one-to-one orthologous gene families identified from seven arthropod species and Caenorhabditis elegans strongly supported the hypothesis that Malacostraca and Branchiopoda do not form a monophyletic group. Furthermore, Branchiopoda is more phylogenetically closely related to Hexapoda, and the clade of Hexapoda and Branchiopoda and the clade of Malacostraca belong to the Pancrustacea. This study offers a high-quality transcriptome resource for E. sinensis and demonstrates the evolutionary relationships of major arthropod groups. The differentially expressed genes identified in this study facilitate further investigation of the cuticle-related gene expression networks which are likely associated with “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting.

Multi-Tissue Transcriptome Analysis Identifies Key Sexual Development-Related Genes of the Ornate Spiny Lobster (Panulirus ornatus)

Sexual development involves the successive and overlapping processes of sex determination, sexual differentiation, and ultimately sexual maturation, enabling animals to reproduce. This provides a mechanism for enriched genetic variation which enables populations to withstand ever-changing environments, selecting for adapted individuals and driving speciation. The molecular mechanisms of sexual development display a bewildering diversity, even in closely related taxa. Many sex determination mechanisms across animals include the key family of "doublesex- and male abnormal3-related transcription factors" (Dmrts). In a few exceptional species, a single Dmrt residing on a sex chromosome acts as the master sex regulator. In this study, we provide compelling evidence for this model of sex determination in the ornate spiny lobster Panulius ornatus, concurrent with recent reports in the eastern spiny lobster Sagmariasus verreauxi. Using a multi-tissue transcriptomic database established for P. ornatus, we screened for the key factors associated with sexual development (by homology search and using previous knowledge of these factors from related species), providing an in-depth understanding of sexual development in decapods. Further research has the potential to close significant gaps in our understanding of reproductive development in this ecologically and commercially significant order.

Physiological status and nutritional condition of cultured juvenile Thenus australiensis over the moult cycle

The moult cycle is arguably the most critical aspect of crustacean biology and is associated with dramatic changes in behaviour, physiology and condition. Here we describe the first detailed investigation of the combined changes in morphology, physiological status and nutritional condition over the moult cycle of juvenile T. australiensis. Haemolymph refractive index (measured as Brix) was evaluated as a non-destructive method for predicting physiological status and nutritional condition. Post-moult, inter-moult and pre-moult stages were identifiable by microscopic examination of the pleopod distal tips, though differentiation of the pre-moult substages was not possible using this technique. Monitoring of ecdysial suture lines on the exoskeleton gill chambers was found to be highly useful for visually determining progression through the pre-moult stage and predicting the timing of ecdysis. A classical pattern of inter-moult growth was observed where size and wet weight remained relatively uniform over the moult cycle while highly significant changes in whole-body composition were simultaneously observed over time. Growth was most evident by changes in dry weight and dry matter content which more than doubled by the onset of pre-moult. Changes in dry matter content were generally mirrored by Brix and whole-body crude protein, total lipid and gross energy content. Brix strongly correlated with dry matter content and significant correlations were also found for all other primary measures of nutritional condition. Typical moult-related changes were also found for circulating ecdysteroids. This study clearly demonstrates pronounced cyclical changes in physiology and condition of juvenile T. australiensis over a typical moult cycle. The significant correlations between haemolymph and whole-body composition validates Brix as a practical and non-destructive method to objectively assess physiological status, nutritional condition and quality in T. australiensis and further demonstrates its potential for individual crustacean assessment in experimental research and practical commercial applications.

Neural remodelling in spiny lobster larvae is characterized by broad neuropeptide suppression

Neuropeptides are ancient endocrine components which have evolved to regulate many aspects of biology across the animal kingdom including behaviour, development and metabolism. To supplement current knowledge, we have utilized a transcriptome series describing larval development in the ornate spiny lobster, Panulirus ornatus. The biology of this animal has been leveraged to provide insights into the roles of molting, metamorphosis and metabolism across the neuropeptide family. We report an extensive list of neuropeptides across three distinct life phases of the animal. We show distinct groups of neuropeptides with differential expression between larval phases, indicating phase-specific roles for these peptides. For selected neuropeptides, we describe and discuss expression profiles throughout larval development and report predicted peptide cleavage sites and mature peptide sequences. We also report the neuropeptide nesfatin for the first time in a crustacean, and report secondary peptide products with a level of evolutionary conservation similar to the conventional mature peptide nesfatin-1, indicating a conserved role in these secondary products which are widely regarded as biologically inactive. In addition, we report a trend of downregulation in the neuropeptides as the animal undergoes extensive neural remodelling in fulfillment of metamorphosis. We suggest that this downregulation in neuropeptides relates to the brief, yet dramatic changes in morphology experienced by the central nervous system in the process of metamorphosis.

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.

Transcriptional profiling of spiny lobster metamorphosis reveals three new additions to the nuclear receptor superfamily

Background

The Crustacea are an evolutionarily diverse taxon which underpins marine food webs and contributes significantly to the global economy. However, our knowledge of crustacean endocrinology and development is far behind that of terrestrial arthropods. Here we present a unique insight into the molecular pathways coordinating crustacean metamorphosis, by reconciling nuclear receptor (NR) gene activity from a 12-stage, 3-replicate transcriptome in the ornate spiny lobster (Panulirus ornatus) during larval development.

Results

We annotated 18 distinct nuclear receptor genes, including three novel NRs which are upregulated prior to metamorphosis and have hence been named the “molt-associated receptors” (MARs). We also demonstrate the ecdysone-responsive expression of several known molt-related NRs including ecdysone receptor, fushi-tarazu-F1 and E75. Phylogenetic analysis of the curated NR family confirmed gene annotations and suggested that the MARs are a recent addition to the crustacean superfamily, occurring across the Malacostraca from the Stomatopoda to the Decapoda. The ligand-binding domain of these receptors appears to be less conserved than that of typical group-1 NRs. Expression data from two other crustacean species was utilized to examine MAR expression. The Y-organ of the tropical land crab showed a decline in expression of all MARs from intermolt to post-molt. Tissue distributions showed gonad-enriched expression in the Eastern rock lobster and antennal gland-enriched expression in the tropical land crab, although expression was evident across most tissues.

Conclusion

By mining transcriptome data, we have curated an extensive list of NR genes expressed during the metamorphic molts of P. ornatus, including three novel crustacean NRs which appear to play a role in the molting process. Divergence of the E-region of these new receptors indicates that they may have adopted a function that is unconventional for NRs. Based on expression patterns, we can confirm that a number of NRs play a role in the ecdysone cassette which regulates molting in crustaceans. This study describes in detail the molecular events surrounding crustacean molting and metamorphosis by taking advantage of the distinctive life history unique to achelatan crustaceans.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5925-5) contains supplementary material, which is available to authorized users.

Crustacean larval factor shares structural characteristics with the insect-specific follicle cell protein

Literature on the cuticle formation in larval stages of the diverse group of decapod crustaceans is lacking, as opposed to a wealth of knowledge in several insect groups. Here we provide the first glimpse of the cuticular organisation in larvae of the eastern spiny lobster Sagmariasus verreauxi. A bioinformatic approach applied to S. verreauxi transcriptome through metamorphosis identified for the first time a small secreted protein with multiple isoforms that is highly expressed in crustacean larvae. This protein, named crustacean larval factor (Clf) shares structural characteristics with insect follicle cell protein 3 (FCP3), an insect-specific, rapidly evolving protein, with spatial-temporal regulated expression that is restricted to follicular cells during the production of the vitellin coat. Furthermore, we identified the FCP3 domain in additional structural proteins in multiple arthropod groups. Recombinant Clf inhibited in vitro calcium carbonate crystalline precipitation, in keeping with the finding that the spiny lobster larval cuticle is mainly composed of amorphous calcium carbonate. In addition, the recombinant Clf was shown to bind chitosan. Taken together, this research identifies two novel structural domains with lineage-specific expansion across arthropods. In crustaceans, Clf is found predominantly in larvae and the spatial-temporal regulated FCP3 factor occurs as a domain identified in multiple structural proteins across arthropods. Given the shared ten cysteines backbone between the Clf and FCP domains, a shared evolution is suggested and should be further explored.

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.

Morphometric relationships and seasonal variation in size, weight, and a condition index of post-settlement stages of the Caribbean spiny lobster

Spiny lobsters have a protracted pelagic, oceanic larval phase. The final larval stage metamorphoses into a non-feeding postlarva (puerulus) that actively swims towards the coast to settle in shallow habitats and does not resume feeding until after the molt into the first-stage juvenile. Therefore, the body dimensions and nutritional condition of both settled pueruli and first juveniles are likely to vary over time, potentially playing a crucial role in the recruitment to the benthic population. We compared carapace length (CL), height (CH), and width (CW); total length (TL), and body weight (W) between pueruli and first juveniles of the Caribbean spiny lobster, Panulirus argus, as well as morphometric relationships between both developmental stages. Except for CL, all other dimensions were larger in first juveniles, but more markedly CH and W. The slopes of the CH vs CL, CW vs CL, and W vs CL regressions differed significantly between stages, and all log-transformed relationships showed isometry in both stages, except for the CH vs CL relationship, which showed positive allometry. These results reflect a morphological change from the flatter, more streamlined body of the puerulus, to the heavier, more cylindrical body of the juvenile. We also analyzed seasonal variations in CL, W, the W/CL index (a morphometric condition index), and a modified W/CL index (i.e. after controlling for a significant effect of CL) of both stages using individuals monthly collected over 12 consecutive seasons (Autumn 2010–Summer 2013). In both stages, all three variables exhibited significant seasonal variation. For pueruli, the modified W/CL index differed from average in only two seasons, winter 2011 (higher) and summer 2013 (lower), but showed great within-season variation (larger coefficients of variation, CV), potentially reflecting variability in nutritional condition of larvae prior to metamorphosis and in the distances swum by individual pueruli to the settlement habitats. For first juveniles, the modified W/CL index was higher than average in winter and spring 2011, and lower in autumn 2011 and winter 2012, but showed less within season variation (smaller CVs), suggesting a combination of carry-over effects of puerulus condition and effects of local conditions (e.g., food availability and predation risk). These findings warrant further investigation into factors potentially decoupling settlement from recruitment processes.

Can metamorphosis survival during larval development in spiny lobster Sagmariasus verreauxi be improved through quantitative genetic inheritance?

Background

One of the major impediments to spiny lobster aquaculture is the high cost of hatchery production due to the long and complex larval cycle and poor survival during the many moult stages, especially at metamorphosis. We examined if the key trait of larval survival can be improved through selection by determining if genetic variance exists for this trait. Specifically, we report, for the first time, genetic parameters (heritability and correlations) for early survival rates recorded at five larval phases; early-phyllosoma stages (instars 1–6; S1), mid-phyllosoma stages (instars; 7–12; S2), late-phyllosoma stages (instars 13–17; S3), metamorphosis (S4) and puerulus stage (S5) in hatchery-reared spiny lobster Sagmariasus verreauxi.

Results

The data were collected from a total of 235,060 larvae produced from 18 sires and 30 dams over nine years (2006 to 2014). Parentage of the offspring and full-sib families was verified using ten microsatellite markers. Analysis of variance components showed that the estimates of heritability for all the five phases of larval survival obtained from linear mixed model were generally similar to those obtained from threshold logistic generalised models (0.03–0.47 vs. 0.01–0.50). The heritability estimates for survival traits recorded in the early larval phases (S1 and S2) were higher than those estimated in later phases (S3, S4 and S5). The existence of the additive genetic component in larval survival traits indicate that they could be improved through selection. Both phenotypic and genetic correlations among the five survival measures studied were moderate to high and positive. The genetic associations between successive rearing periods were stronger than those that are further apart.

Conclusions

Our estimates of heritability and genetic correlations reported here in a spiny lobster species indicate that improvement in the early survival especially during metamorphosis can be achieved through genetic selection in this highly economic value species.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0621-z) contains supplementary material, which is available to authorized users.

Y-linked iDmrt1 paralogue (iDMY) in the Eastern spiny lobster, Sagmariasus verreauxi: The first invertebrate sex-linked Dmrt

Sex determination pathways are extensively diverse across species, with the master sex-determinants being the most variable element. Despite this, there is a family of DM-domain transcription factors (Dmrts), which hold a highly conserved function in sexual development. This work is the first to describe a heterogametic sex-linked Dmrt in an invertebrate species, the Eastern spiny lobster, Sagmariasus verreauxi. We have termed the Y-linked, truncated paralogue of the autosomal iDmrt1, Sv-iDMY. Considering the master sex-determining function of both DMY in medaka and DM-W in frog, we hypothesised a similar function of Sv-iDMY. By conducting temporal expression analyses during embryogenesis we have identified a putative male sex-determining period during which iDMY>iDmrt1. Employing a GAL4-transactivation assay we then demonstrate the dominant negative suppression of iDMY over its autosomal iDmrt1 paralogue, suggesting the mechanism with which iDMY determines sex. Comparative analyses of Sv-iDMY, DM-W and medaka DMY, highlight the C'-mediated features of oligomerisation and transactivation as central to the mechanism that each exerts. Indeed, these features may underpin the plasticity facilitating the convergent emergence of these three sporadic sex-linked master-Dmrts.

CYP450s analysis across spiny lobster metamorphosis identifies a long sought missing link in crustacean development

Cytochrome P450s (CYP450s) are a rapidly evolving family of enzymes, making it difficult to identify bona fide orthologs with notable lineage-specific exceptions. In ecdysozoans, a small number of the most conserved orthologs include enzymes which metabolize ecdysteroids. Ecdysone pathway components were recently shown in a decapod crustacean but with a notable absence of shade, which is important for converting ecdysone to its active form, 20-hydroxyecdysone (20HE), suggesting that another CYP450 performs a similar function in crustaceans. A CYPome temporal expression analysis throughout metamorphosis performed in this research highlights several un-annotated CYP450s displaying differential expression and provides information into expression patterns of annotated CYP450s. Using the expression patterns in the Eastern spiny lobster Sagmariasus verreauxi, followed by 3D modelling and finally activity assays in vitro, we were able to conclude that a group of CYP450s, conserved across decapod crustaceans, function as the insect shade. To emphasize the fact that these genes share the function with shade but are phylogenetically distinct, we name this enzyme system Shed.

Biomolecular changes that occur in the antennal gland of the giant freshwater prawn (Machrobrachium rosenbergii)

In decapod crustaceans, the antennal gland (AnG) is a major primary source of externally secreted biomolecules, and some may act as pheromones that play a major role in aquatic animal communication. In aquatic crustaceans, sex pheromones regulate reproductive behaviours, yet they remain largely unidentified besides the N-acetylglucosamine-1,5-lactone (NAGL) that stimulates male to female attraction. In this study, we used an AnG transcriptome of the female giant freshwater prawn (Macrobrachium rosenbergii) to predict the secretion of 226 proteins, including the most abundantly expressed transcripts encoding the Spaetzle protein, a serine protease inhibitor, and an arthropodial cuticle protein AMP 8.1. A quantitative proteome analysis of the female AnG at intermolt, premolt and postmolt, identified numerous proteins of different abundances, such as the hemocyanin subunit 1 that is most abundant at intermolt. We also show that hemocyanin subunit 1 is present within water surrounding females. Of those metabolites identified, we demonstrate that the NAGL and N-acetylglucosamine (NAG) can bind with high affinity to hemocyanin subunit 1. In summary, this study has revealed components of the female giant freshwater prawn AnG that are released and contribute to further research towards understanding crustacean conspecific signalling.

Resistance to starvation of first-stage juveniles of the Caribbean spiny lobster

The non-feeding postlarva (puerulus) of spiny lobsters actively swims from the open ocean to the coastal habitats where it settles and molts to the first-stage juvenile (JI). Because pueruli use much of their energy reserves swimming and preparing for the post-settlement molt, the survival of JIs presumably depends on resuming feeding as soon as possible. To test this hypothesis, the resistance to starvation of JIs of the Caribbean spiny lobster, Panulirus argus, was evaluated by measuring their point-of-no-return (PNR, minimum time of initial starvation preventing recovery after later feeding) and point-of-reserve-saturation (PRS, minimum time of initial feeding allowing for food-independent development through the rest of the molting cycle) in a warm and a cold season. Each experiment consisted of eight groups: a continuously fed control (FC) group, a continuously starved control (SC) group, and six groups subjected to differential periods of either initial starvation and subsequent feeding (PNR experiments) or initial feeding and subsequent starvation (PSR experiments). No JIs molted under continuous absence of food (SC). In both PNR experiments (temperature in warm season: 29.79 ± 0.07°C, mean ± 95% CI; in cold season: 25.63 ± 0.12°C) mortality increased sharply after 9 d of initial starvation and intermolt periods increased with period of initial starvation, but were longer in the cold season. The PNR₅₀ was longer in the warm season (12.1 ± 1.2 d, mean ± 95% CI) than in the cold season (9.5 ± 2.1 d). In PRS experiments (temperature in warm season: 29.54 ± 0.07 °C; in cold season: 26.20 ± 0.12 °C), JIs that molted did so near the end of the feeding period; all JIs initially fed for up to 6 d succumbed, and no JIs molted after 13 d of starvation despite having fed previously. The PRS₅₀ did not differ between the cold (13.1 ± 0.7 d) and warm seasons (12.1 ± 1.1 d). JIs of P. argus exhibit a remarkable resistance to starvation considering that the previous non-feeding, energy-demanding puerulus phase lasts for ∼3 weeks. However, JIs appear to have a relatively higher degree of dependence on food to complete development to JII during the cold season than during the warm season. Therefore, JIs of P. argus would appear to be more resistant to starvation during the warm season.

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.

Deep sequencing of transcriptomes from the nervous systems of two decapod crustaceans to characterize genes important for neural circuit function and modulation

BACKGROUND

Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and performed de novo assembly for the nervous system transcriptomes of two decapod crustaceans: the Jonah crab (Cancer borealis) and the American lobster (Homarus americanus).

RESULTS

Forty-two thousand, seven hundred sixty-six and sixty thousand, two hundred seventy-three contigs were assembled from C. borealis and H. americanus respectively, representing 9,489 and 11,061 unique coding sequences. From these transcripts, genes associated with neural function were identified and manually curated to produce a characterization of multiple gene families important for nervous system function. This included genes for 34 distinct ion channel types, 17 biogenic amine and 5 GABA receptors, 28 major transmitter receptor subtypes including glutamate and acetylcholine receptors, and 6 gap junction proteins - the Innexins.

CONCLUSION

With this resource, crustacean model systems are better poised for incorporation of modern genomic and molecular biology technologies to further enhance the interrogation of fundamentals of nervous system function.

Developmental Transcriptomics of the Hawaiian Anchialine Shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Atyidae)

Many crustacean species progress through a series of metamorphoses during the developmental transition from embryo to adult. The molecular genetic basis of this transition, however, is not well characterized for a large number of crustaceans. Here, we employ multiple RNA-Seq methodologies to identify differentially expressed genes (DEGs) between "early" (i.e., Z₁ - Z₂) as well as "late" (i.e., Z₃ - Z₄) larval and adult developmental stages of Halocaridina rubra Holthuis (1963), an atyid shrimp endemic to the environmentally variable anchialine ecosystem of the Hawaiian Islands. Given the differences in salinity tolerance (narrow vs. wide range), energy acquisition (maternal yolk-bearing vs. microphagous grazing), and behavior (positively phototactic vs. not) between larvae and adults, respectively, of this species, we hypothesized the recovery of numerous DEGs belonging to functional categories relating to these characteristics. Consistent with this and regardless of methodology, hundreds of DEGs were identified, including upregulation of opsins and other light/stimulus detection genes and downregulation of genes related to ion transport, digestion, and reproduction in larvae relative to adults. Furthermore, isoform-switching, which has been largely unexplored in crustacean development, appears to be pervasive between H. rubra larvae and adults, especially among structural and oxygen-transport genes. Finally, by comparing RNA-Seq methodologies, we provide recommendations for future crustacean transcriptomic studies, including a demonstration of the pitfalls associated with identifying DEGs from single replicate samples as well as the utility of leveraging "prepackaged" bioinformatics pipelines.

Applying the Power of Transcriptomics: Understanding Male Sexual Development in Decapod Crustacea

The decapod Crustacea are the most species-rich order of the Crustacea and include some of the most charismatic and highly valued commercial species. Thus the decapods draw a significant research interest in relation to aquaculture, as well as gaining a broader understanding of these species' biology. However, the diverse physiology of the group considered with the lack of a model species have presented an obstacle for comparative analyses. In reflection of this, the recent integration of comparative transcriptomics has rapidly advanced our understanding of key regulatory pathways and developmental phenomena, an example being our understanding of sexual development. We discuss our work in the Eastern spiny lobster, Sagmariasus verreauxi, in the context of what is currently known about male sexual development in the decapods, highlighting the importance of transcriptomic techniques in achieving our recent advancements. We describe the progression made in our understanding of male sexual differentiation and maturation, as mediated by the insulin-like androgenic gland hormone (IAG), integrating the role of regulatory binding proteins (IGFBPs), a tyrosine kinase insulin receptor (TKIR), as well as the upstream effect of neuroendocrine hormones (GIH and MIH). We then consider the less well understood mechanism of male sex determination, with an emphasis on what we believe to be the key regulatory factors, the Dsx- and mab-3-related transcription factors (Dmrts). Finally, we discuss the function of the antennal gland (AnG) in sexual development, relating to the emergence of male-biased upregulation in the AnG in later sexual maturation and the sexually dimorphic expression of two key genes Sv-TKIR and Sv-Dmrt1 We then present the AnG as a case study to illustrate how comparative transcriptomic techniques can be applied to guide preliminary analyses, like the hypothesis that the AnG may function in pheromone biosynthesis. In summary, we describe the power of transcriptomics in facilitating the progress made in our understanding of male sexual development, as illustrated by the commercial decapod species, S. verreauxi Considering future directions, we suggest that the integration of multiple omics-based techniques offers the most powerful tool to ensure we continue to piece together the biology of the important group of decapod Crustacea.

Production of recombinant insulin-like androgenic gland hormones from three decapod species: In vitro testicular phosphorylation and activation of a newly identified tyrosine kinase receptor from the Eastern spiny lobster, Sagmariasus verreauxi

In crustaceans the insulin-like androgenic gland hormone (IAG) is responsible for male sexual differentiation. To date, the biochemical pathways through which IAG exerts its effects are poorly understood and could be elucidated through the production of a functional recombinant IAG (rIAG). We have successfully expressed glycosylated, biologically active IAG using the Pichia pastoris yeast expression system. We co-expressed recombinant single-chain precursor molecules consisting of the B and A chains (the mature hormone) tethered by a flexible linker, producing rIAGs of the following commercially important species: Eastern spiny lobster Sagmariasus verreauxi (Sv), redclaw crayfish Cherax quadricarinatus (Cq) and giant freshwater prawn Macrobrachium rosenbergii (Mr). We then tested the biological activity of each, through the ability to increase phosphorylation in the testis; both Sv and Cq rIAGs significantly elevated phosphorylation specific to their species, and in a dose-dependent manner. Mr rIAG was tested on Macrobrachium australiense (Ma), eliciting a similar response. Moreover, using bioinformatics analyses of the de novo assembled spiny lobster transcriptome, we identified a spiny lobster tyrosine kinase insulin receptor (Sv-TKIR). We validated this discovery with a receptor activation assay in COS-7 cells expressing Sv-TKIR, using a reporter SRE-LUC system designed for RTKs, with each of the rIAG proteins acting as the activation ligand. Using recombinant proteins, we aim to develop specific tools to control sexual development through the administration of IAG within the critical sexual differentiation time window. The biologically active rIAGs generated might facilitate commercially feasible solutions for the long sought techniques for sex-change induction and monosex population culture in crustaceans and shed new light on the physiological mode of action of IAG in crustaceans.

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.