Chemoreceptor proteins in the Caribbean spiny lobster, Panulirus argus: Expression of Ionotropic Receptors, Gustatory Receptors, and TRP channels in two chemosensory organs and brain

Identification of transient receptor potential channel genes from the swimming crab, Portunus Trituberculatus, and their expression profiles under acute temperature stress

BACKGROUND

Temperature is an important environment factor that is critical to the survival and growth of crustaceans. However, the mechanisms by which crustaceans detect changes in temperature are still unclear. The transient receptor potential (TRP) channels are non-selective cation channels well known for properties in temperature sensation. However, comprehensive understandings on TRP channels as well as their temperature sensing functions are still lacking in crustaceans.

RESULTS

In this study, a total of 26 TRP genes were identified in the swimming crab, Portunus trituberculatus, which can be classified into TRPA, TRPC, TRPP, TRPM, TRPML, TRPN and TRPV. Tissue expression analysis revealed a wide distribution of these TRP genes in P. trituberculatus, and antennules, neural tissues, and ovaries were the most commonly expressed tissues. To investigate the responsiveness of TRP genes to the temperature change, 18 TRPs were selected to detect their expression after high and low temperature stress. The results showed that 12 TRPs showed induced gene expression in both high and low temperature groups, while 3 were down-regulated in the low temperature group, and 3 showed no change in expression in either group.

CONCLUSIONS

This study characterized the TRP family genes in P. trituberculatus, and explored their involvement in response to temperature stress. Our results will enhance overall understanding of crustacean TRP channels and their possible functions.

Identification of sex pheromone of red swamp crayfish Procambarus clarkii and exploration of the chemosensory mechanism of their antennae

Red swamp crayfish, Procambarus clarkii, is a globally invasive species, which has caused great damage to biodiversity, agriculture, and fishing. Therefore, the development of effective management methods, such as pheromone control, is necessary for biological control and biodiversity protection. However, the components of P. clarkii sex pheromones have not yet been explored, and the chemosensory mechanism of the P. clarkii antennae after stimulation by sex pheromone also remains unknown. In this study, we isolated and identified the candidate bioactive component of the female P. clarkii sex pheromone using ultrafiltration centrifugation, semi-preparative liquid phase separation and omics technologies and conducted bioassays to determine its attraction ability. Meanwhile, RNA-Seq technology was used to analyze the potential chemosensory mechanism of antennae. Our results indicated that the male P. clarkii were uniaxially attracted to the female crude conditioned water (FCW), medium fraction (MF, isolated by ultrafiltration centrifugation), and preparative fragment 6 of females (PFF6, isolated by semi-preparative liquid phase separation). Metabolomic analysis revealed the presence of 18 differential metabolites between the PFF6 and PFM6 samples, among which 15 were significantly upregulated in the PFF6 sample. Bioassay test also showed that mestranol, especially at concentrations of 10-5-10-2 mol∙l-1, could significantly attract P. clarkii males; therefore, mestranol was identified as the candidate sex pheromone component of P. clarkii females. Furthermore, RNA-Seq results showed that most differentially expressed genes (DEGs) enriched in lipid metabolism and signal transduction pathways were up-regulated in P. clarkii males. In addition, high expressions of Ca2+-binding protein and ion transporting ATPases may enhance the sensitivity of the antennae of P. clarkii males towards sex pheromones. Our study provides data on P. clarkii sex pheromone composition and reveals the molecular mechanism of sex pheromone response in P. clarkii. Moreover, our study provides a referable method for the isolation of candidate bioactive molecules from the P. clarkii sex pheromone.

Tropical rock lobster (Panulirus ornatus) uses chemoreception via the antennular lateral flagellum to identify conspecific ecdysis

The tropical rock lobster, Panulirus ornatus, is a commercially important aquaculture species exhibiting complex social interactions in laboratory culture, including cannibalism of moulting conspecifics. Cannibalism of soft-shelled post-moult stage individuals is a major limitation during the juvenile stage of culture. Not limited to P. ornatus, cannibalism is widespread across farmed decapods, limiting stocking densities in crab, freshwater crayfish, and prawn species. To understand the mechanisms driving this behaviour and reduce its prevalence, we have investigated the role of chemoreception via the aesthetasc-bearing region of the lateral antennular flagellum, in the recognition of conspecific moulting cues. Differential expression analysis of several tissues in P. ornatus shows an upregulation of 70 ionotropic receptor isoforms, including co-receptors (IR25a and IR93a) and divergent receptors (IR4, IR7, and IR21a) in the aesthetasc-bearing region of the antennules. Deafferentation of the aesthetascs via deionised water exposure prevents juveniles from responding to conspecific moulting cues in a two-current choice flume, suggesting chemoreception, possibly olfaction, plays a role in identifying moulting juveniles. This is the first step in understanding the mechanisms via which cannibalism is triggered in juvenile P. ornatus culture. Further work in this area will help discover means to limit cannibalism in laboratory and commercial culture.

Ocean acidification alters foraging behaviour in Dungeness crab through impairment of the olfactory pathway

Crustacean olfaction is fundamental to most aspects of living and communicating in aquatic environments and more broadly, for individual- and population-level success. Accelerated ocean acidification from elevated CO2 threatens the ability of crabs to detect and respond to important olfactory-related cues. Here, we demonstrate that the ecologically and economically important Dungeness crab (Metacarcinus magister) exhibits reduced olfactory-related antennular flicking responses to a food cue when exposed to near-future CO2 levels, adding to the growing body of evidence of impaired crab behaviour. Underlying this altered behaviour, we find that crabs have lower olfactory nerve sensitivities (twofold reduction in antennular nerve activity) in response to a food cue when exposed to elevated CO2 . This suggests that near-future CO2 levels will impact the threshold of detection of food by crabs. We also show that lower olfactory nerve sensitivity in elevated CO2 is accompanied by a decrease in the olfactory sensory neuron (OSN) expression of a principal chemosensory receptor protein, ionotropic receptor 25a (IR25a) which is fundamental for odorant coding and olfactory signalling cascades. The OSNs also exhibit morphological changes in the form of decreased surface areas of their somata. This study provides the first evidence of the effects of high CO2 levels at multiple levels of biological organization in marine crabs, linking physiological and cellular changes with whole animal behavioural responses.

Humidity sensors that alert mosquitoes to nearby hosts and egg-laying sites

To reproduce and to transmit disease, female mosquitoes must obtain blood meals and locate appropriate sites for egg laying (oviposition). While distinct sensory cues drive each behavior, humidity contributes to both. Here, we identify the mosquito's humidity sensors (hygrosensors). Using generalizable approaches designed to simplify genetic analysis in non-traditional model organisms, we demonstrate that the ionotropic receptor Ir93a mediates mosquito hygrosensation as well as thermosensation. We further show that Ir93a-dependent sensors drive human host proximity detection and blood-feeding behavior, consistent with the overlapping short-range heat and humidity gradients these targets generate. After blood feeding, gravid females require Ir93a to seek high humidity associated with preferred egg-laying sites. Reliance on Ir93a-dependent sensors to promote blood feeding and locate potential oviposition sites is shared between the malaria vector Anopheles gambiae and arbovirus vector Aedes aegypti. These Ir93a-dependent systems represent potential targets for efforts to control these human disease vectors.

A cyclic lipopeptide produced by an antagonistic bacterium relies on its tail and transient receptor potential-type Ca2+ channels to immobilize a green alga

The antagonistic bacterium Pseudomonas protegens secretes the cyclic lipopeptide (CLiP) orfamide A, which triggers a Ca²⁺ signal causing rapid deflagellation of the microalga Chlamydomonas reinhardtii. We performed chemical synthesis of orfamide A derivatives and used an aequorin reporter line to measure their Ca²⁺ responses. Immobilization of algae was studied using a modulator and mutants of transient receptor potential (TRP)-type channels. By investigating targeted synthetic orfamide A derivatives, we found that N-terminal amino acids of the linear part and the terminal fatty acid region are important for the specificity of the Ca²⁺ -signal causing deflagellation. Molecular editing indicates that at least two distinct Ca²⁺ -signaling pathways are triggered. One is involved in deflagellation (Thr³ change, fatty acid tail shortened by 4C), whereas the other still causes an increase in cytosolic Ca²⁺ in the algal cells, but does not cause substantial deflagellation (Leu¹ change, fatty acid hydroxylation, fatty acid changes by 2C). Using mutants, we define four TRP-type channels that are involved in orfamide A signaling; only one (ADF1) responds additionally to low pH. These results suggest that the linear part of the CLiP plays one major role in Ca²⁺ signaling, and that orfamide A uses a network of algal TRP-type channels for deflagellation.

Chemosensory-Related Genes in Marine Copepods

Living organisms deeply rely on the acquisition of chemical signals in any aspect of their life, from searching for food, mating and defending themselves from stressors. Copepods, the most abundant and ubiquitous metazoans on Earth, possess diversified and highly specified chemoreceptive structures along their body. The detection of chemical stimuli activates specific pathways, although this process has so far been analyzed only on a relatively limited number of species. Here, in silico mining of 18 publicly available transcriptomes is performed to delve into the copepod chemosensory genes, improving current knowledge on the diversity of this multigene family and on possible physiological mechanisms involved in the detection and analysis of chemical cues. Our study identifies the presence of ionotropic receptors, chemosensory proteins and gustatory receptors in copepods belonging to the Calanoida, Cyclopoida and Harpacticoida orders. We also confirm the absence in these copepods of odorant receptors and odorant-binding proteins agreeing with their insect specificity. Copepods have evolved several mechanisms to survive in the harsh marine environment such as producing proteins to respond to external stimulii. Overall, the results of our study open new possibilities for the use of the chemosensory genes as biomarkers in chemical ecology studies on copepods and possibly also in other marine holozooplankters.

The Effect of Feed Frequency on Growth, Survival and Behaviour of Juvenile Spiny Lobster (Panulirus ornatus)

Simple Summary

Sensory stimuli including olfactory, visual, acoustic and tactile input, are important aspects of feed exposure and optimisation of feeding schedules. These aspects were investigated in our study, with a focus on the effect of feed frequency (one, two, four, eight, sixteen and thirty-two feed supplies per day) on survival, growth and behaviour of juvenile P. ornatus. Increasing daily feed frequency from one to sixteen improved feed intake and growth.

Abstract

Spiny lobsters have a range of complex chemical communication pathways that contribute to feeding behaviour. Feed intake is modulated by feed availability and feed characteristics, such as attractiveness and palatability, with behavioural factors, such as social competition and circadian rhythm, providing an extra layer of complexity. In this study, we investigated the effect of feed frequency on survival and growth of early-stage (instar 2–6) juvenile Palunirus ornatus. In addition, we investigated the interactive effect of feed frequency and circadian rhythm on lobster feed response. Lobsters were fed a set ration at a frequency of either one, two, four, eight, sixteen or thirty-two times per day over 49 days. The effect of feed frequency on growth and survival was determined. Circadian feeding activity under these feeding treatments was assessed by time-lapse photography. Increased feed frequency from one to sixteen feeds daily improved growth by increasing apparent feed intake (AFI) and feed attraction, as confirmed by the increased presence of lobsters in the feeding area. The rapid leaching of feed attractant, particularly free amino acid, suggests a beneficial effect of multiple feeding frequencies on feed intake and growth. However, more than sixteen feeds per day resulted in decreased feed intake and a subsequent reduction in growth. The decrease in feed intake is thought to be associated with saturation of the culture environment with attractants, resulting in a reduced behavioural response to feed supplies. This may indicate the need for depletion of attractants to retrigger a feeding response. As lobsters were grown communally, faster growth at sixteen rations per day was also coupled with increased cannibalism, likely driven by increased vulnerability with the occurrence of more frequent ecdysis events. Whereas circadian rhythm indicated more activity at night, an interaction between daytime activity and feed frequency was not observed.

Becoming nose-blind-Climate change impacts on chemical communication

Chemical communication via infochemicals plays a pivotal role in ecological interactions, allowing organisms to sense their environment, locate predators, food, habitats, or mates. A growing number of studies suggest that climate change-associated stressors can modify these chemically mediated interactions, causing info-disruption that scales up to the ecosystem level. However, our understanding of the underlying mechanisms is scarce. Evidenced by a range of examples, we illustrate in this opinion piece that climate change affects different realms in similar patterns, from molecular to ecosystem-wide levels. We assess the importance of different stressors for terrestrial, freshwater, and marine ecosystems and propose a systematic approach to address highlighted knowledge gaps and cross-disciplinary research avenues.

Sequence and structural conservation reveal fingerprint residues in TRP channels

Transient receptor potential (TRP) proteins are a large family of cation-selective channels, surpassed in variety only by voltage-gated potassium channels. Detailed molecular mechanisms governing how membrane voltage, ligand binding, or temperature can induce conformational changes promoting the open state in TRP channels are still a matter of debate. Aiming to unveil distinctive structural features common to the transmembrane domains within the TRP family, we performed phylogenetic reconstruction, sequence statistics, and structural analysis over a large set of TRP channel genes. Here, we report an exceptionally conserved set of residues. This fingerprint is composed of twelve residues localized at equivalent three-dimensional positions in TRP channels from the different subtypes. Moreover, these amino acids are arranged in three groups, connected by a set of aromatics located at the core of the transmembrane structure. We hypothesize that differences in the connectivity between these different groups of residues harbor the apparent differences in coupling strategies used by TRP subgroups.

Identification and Expression Profile of Chemosensory Receptor Genes in Aromia bungii (Faldermann) Antennal Transcriptome

The red-necked longicorn beetle, Aromia bungii (Faldermann) (Coleoptera: Cerambycidae), is a major destructive, wood-boring pest, which is widespread throughout the world. The sex pheromone of A. bungii was reported earlier; however, the chemosensory mechanism of the beetle remains almost unknown. In this study, 45 AbunORs, 6 AbunGRs and 2 AbunIRs were identified among 42,197 unigenes derived from the antennal transcriptome bioinformatic analysis of A. bungii adults. The sequence of putative Orco (AbunOR25) found in this study is highly conserved with the known Orcos from other Coleoptera species, and these Orco genes might be potentially used as target genes for the future development of novel and effective control strategies. Tissue expression analysis showed that 29 AbunOR genes were highly expressed in antennae, especially in the antennae of females, which was consistent with the idea that females might express more pheromone receptors for sensing pheromones, especially the sex pheromones produced by males. AbunOR5, 29, 31 and 37 were clustered with the pheromone receptors of the cerambycid Megacyllene caryae, suggesting that they might be putative pheromone receptors of A. bungii. All six AbunGRs were highly expressed in the mouthparts, indicating that these GRs may be involved in the taste perception process. Both AbunIRs were shown to be female-mouthparts-biased, suggesting that they might also be related to the tasting processes. Our study provides some basic information towards a deeper understanding of the chemosensing mechanism of A. bungii at a molecular level.

Genealogical relationships of mushroom bodies, hemiellipsoid bodies, and their afferent pathways in the brains of Pancrustacea: Recent progress and open questions

According to all latest phylogenetic analyses, the taxon Pancrustacea embraces the crustaceans in the traditional sense and the hexapods. Members of the Pancrustacea for a long time have been known to display distinct similarities in the architecture of their brains. Here, we review recent progress and open questions concerning structural and functional communalities of selected higher integrative neuropils in the lateral protocerebrum of pancrustaceans, the mushroom bodies and hemiellipsoid bodies. We also discuss the projection neuron pathway which provides a distinct input channel to both mushroom and hemiellipsoid bodies from the primary chemosensory centers in the deutocerebrum. Neuronal characters are mapped on a current pancrustacean phylogeny in order to extract those characters that are part of the pancrustacean ground pattern. Furthermore, we summarize recent insights into the evolutionary transformation of mushroom body morphology across the Pancrustacea.

Acoel Single-Cell Transcriptomics: Cell Type Analysis of a Deep Branching Bilaterian

Bilaterian animals display a wide variety of cell types, organized into defined anatomical structures and organ systems, which are mostly absent in prebilaterian animals. Xenacoelomorpha are an early-branching bilaterian phylum displaying an apparently relatively simple anatomical organization that have greatly diverged from other bilaterian clades. In this study, we use whole-body single-cell transcriptomics on the acoel Isodiametra pulchra to identify and characterize different cell types. Our analysis identifies the existence of ten major cell type categories in acoels all contributing to main biological functions of the organism: metabolism, locomotion and movements, behavior, defense, and development. Interestingly, although most cell clusters express core fate markers shared with other animal clades, we also describe a surprisingly large number of clade-specific marker genes, suggesting the emergence of clade-specific common molecular machineries functioning in distinct cell types. Together, these results provide novel insight into the evolution of bilaterian cell types and open the door to a better understanding of the origins of the bilaterian body plan and their constitutive cell types.

G protein-coupled receptors as candidates for modulation and activation of the chemical senses in decapod crustaceans

Many studies have characterized class A GPCRs in crustaceans; however, their expression in crustacean chemosensory organs has yet to be detailed. Class A GPCRs comprise several subclasses mediating diverse functions. In this study, using sequence homology, we classified all putative class A GPCRs in two chemosensory organs (antennular lateral flagellum [LF] and walking leg dactyls) and brain of four species of decapod crustaceans (Caribbean spiny lobster Panulirus argus, American lobster Homarus americanus, red-swamp crayfish Procambarus clarkii, and blue crab Callinectes sapidus). We identified 333 putative class A GPCRs– 83 from P. argus, 81 from H. americanus, 102 from P. clarkii, and 67 from C. sapidus–which belong to five distinct subclasses. The numbers of sequences for each subclass in the four decapod species are (in parentheses): opsins (19), small-molecule receptors including biogenic amine receptors (83), neuropeptide receptors (90), leucine-rich repeat-containing GPCRs (LGRs) (24), orphan receptors (117). Most class A GPCRs are predominately expressed in the brain; however, we identified multiple transcripts enriched in the LF and several in the dactyl. In total, we found 55 sequences with higher expression in the chemosensory organs relative to the brain across three decapod species. We also identified novel transcripts enriched in the LF including a metabotropic histamine receptor and numerous orphan receptors. Our work establishes expression patterns for class A GPCRs in the chemosensory organs of crustaceans, providing insight into molecular mechanisms mediating neurotransmission, neuromodulation, and possibly chemoreception.

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

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

A chromosome-level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean

Mud crabs, found throughout the Indo-Pacific region, are coastal species that are important fisheries resources in many tropical and subtropical Asian countries. Here, we present a chromosome-level genome assembly of a mud crab (Scylla paramamosain). The genome is 1.55 Gb (contig N50 191 kb) in length and encodes 17,821 proteins. The heterozygosity of the assembled genome was estimated to be 0.47%. Effective population size analysis suggested that an initial large population size of this species was maintained until 200 thousand years ago. The contraction of cuticle protein and opsin genes compared with Litopenaeus vannamei is assumed to be correlated with shell hardness and light perception ability, respectively. Furthermore, the analysis of three chemoreceptor gene families, the odorant receptor (OR), gustatory receptor (GR) and ionotropic receptor (IR) families, suggested that the mud crab has no OR genes and shows a contraction of GR genes and expansion of IR genes. The numbers of the three gene families were similar to those in three other decapods but different from those in two nondecapods and insects. In addition, IRs were more diversified in decapods than in nondecapod crustaceans, and most of the expanded IRs in the mud crab genome were clustered with the antennal IR clades. These findings suggested that IRs might exhibit more diverse functions in decapods than in nondecapods, which may compensate for the smaller number of GR genes. Decoding the S. paramamosain genome not only provides insight into the genetic changes underpinning ecological traits but also provides valuable information for improving the breeding and aquaculture of this species.

The Structure and Function of Ionotropic Receptors in Drosophila

Ionotropic receptors (IRs) are a highly divergent subfamily of ionotropic glutamate receptors (iGluR) and are conserved across Protostomia, a major branch of the animal kingdom that encompasses both Ecdysozoa and Lophothrochozoa. They are broadly expressed in peripheral sensory systems, concentrated in sensory dendrites, and function in chemosensation, thermosensation, and hygrosensation. As iGluRs, four IR subunits form a functional ion channel to detect environmental stimuli. Most IR receptors comprise individual stimulus-specific tuning receptors and one or two broadly expressed coreceptors. This review summarizes the discoveries of the structure of IR complexes and the expression and function of each IR, as well as discusses the future direction for IR studies.

Oxygen sensing in crustaceans: functions and mechanisms

Animals that live in changing environments need to adjust their metabolism to maintain body functions, and sensing these changing conditions is essential for mediating the short- and long-term physiological and behavioral responses that make these adjustments. Previous research on nematodes and insects facing changing oxygen levels has shown that these animals rapidly respond using atypical soluble guanylyl cyclases (sGCs) as oxygen sensors connected to downstream cGMP pathways, and they respond more slowly using hypoxia-inducible transcription factors (HIFs) that are further modulated by oxygen-sensing prolyl hydroxylases (PHs). Crustaceans are known to respond in different ways to hypoxia, but the mechanisms responsible for sensing oxygen levels are more poorly understood than in nematodes and insects. Our paper reviews the functions of and mechanisms underlying oxygen sensing in crustaceans. Furthermore, using the oxygen sensing abilities of nematodes and insects as guides in analyzing available crustacean transcriptomes, we identified orthologues of atypical sGCs, HIFs, and PHs in crustaceans, including in their chemosensory organs and neurons. These molecules include atypical sGCs activated by hypoxia (Gyc-88E/GCY-31 and Gyc-89D/GCY-33) but not those activated by hyperoxia (GCY-35, GCY-36), as well as orthologues of HIF-α, HIF-β, and PH. We offer possible directions for future research on oxygen sensing by crustaceans.

More than one way to smell ashore - Evolution of the olfactory pathway in terrestrial malacostracan crustaceans

Crustaceans provide a fascinating opportunity for studying adaptations to a terrestrial lifestyle because within this group, the conquest of land has occurred at least ten times convergently. The evolutionary transition from water to land demands various morphological and physiological adaptations of tissues and organs including the sensory and nervous system. In this review, we aim to compare the brain architecture between selected terrestrial and closely related marine representatives of the crustacean taxa Amphipoda, Isopoda, Brachyura, and Anomala with an emphasis on the elements of the olfactory pathway including receptor molecules. Our comparison of neuroanatomical structures between terrestrial members and their close aquatic relatives suggests that during the convergent evolution of terrestrial life-styles, the elements of the olfactory pathway were subject to different morphological transformations. In terrestrial anomalans (Coenobitidae), the elements of the primary olfactory pathway (antennules and olfactory lobes) are in general considerably enlarged whereas they are smaller in terrestrial brachyurans compared to their aquatic relatives. Studies on the repertoire of receptor molecules in Coenobitidae do not point to specific terrestrial adaptations but suggest that perireceptor events - processes in the receptor environment before the stimuli bind - may play an important role for aerial olfaction in this group. In terrestrial members of amphipods (Amphipoda: Talitridae) as well as of isopods (Isopoda: Oniscidea), however, the antennules and olfactory sensilla (aesthetascs) are largely reduced and miniaturized. Consequently, their primary olfactory processing centers are suggested to have been lost during the evolution of a life on land. Nevertheless, in terrestrial Peracarida, the (second) antennae as well as their associated tritocerebral processing structures are presumed to compensate for this loss or rather considerable reduction of the (deutocerebral) primary olfactory pathway. We conclude that after the evolutionary transition from water to land, it is not trivial for arthropods to establish aerial olfaction. If we consider insects as an ingroup of Crustacea, then the Coenobitidae and Insecta may be seen as the most successful crustacean representatives in this respect.

Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery

BACKGROUND

Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region.

METHODS

This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus.

RESULTS

Using a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5' ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3' ETS (287 bp). A total of 1,281 SSRs were identified.

Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus

Background

Whole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ‘primer walking’ or ‘long PCR’ followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a ‘gold’ standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobster Panulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region.

Results

LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not ‘perfect’, phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other related species in the same genus, family, and superorder.

Conclusions

This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.

Single cell transcriptomes reveal expression patterns of chemoreceptor genes in olfactory sensory neurons of the Caribbean spiny lobster, Panulirus argus

BACKGROUND

Crustaceans express several classes of receptor genes in their antennules, which house olfactory sensory neurons (OSNs) and non-olfactory chemosensory neurons. Transcriptomics studies reveal that candidate chemoreceptor proteins include variant Ionotropic Receptors (IRs) including both co-receptor IRs and tuning IRs, Transient Receptor Potential (TRP) channels, Gustatory Receptors, epithelial sodium channels, and class A G-protein coupled receptors (GPCRs). The Caribbean spiny lobster, Panulirus argus, expresses in its antennules nearly 600 IRs, 17 TRP channels, 1 Gustatory Receptor, 7 epithelial sodium channels, 81 GPCRs, 6 G proteins, and dozens of enzymes in signaling pathways. However, the specific combinatorial expression patterns of these proteins in single sensory neurons are not known for any crustacean, limiting our understanding of how their chemosensory systems encode chemical quality.

RESULTS

The goal of this study was to use transcriptomics to describe expression patterns of chemoreceptor genes in OSNs of P. argus. We generated and analyzed transcriptomes from 7 single OSNs, some of which were shown to respond to a food odor, as well as an additional 7 multicell transcriptomes from preparations containing few (2-4), several (ca. 15), or many (ca. 400) OSNs. We found that each OSN expressed the same 2 co-receptor IRs (IR25a, IR93a) but not the other 2 antennular coIRs (IR8a, IR76b), 9-53 tuning IRs but only one to a few in high abundance, the same 5 TRP channels plus up to 5 additional TRPs, 12-17 GPCRs including the same 5 expressed in every single cell transcriptome, the same 3 G proteins plus others, many enzymes in the signaling pathways, but no Gustatory Receptors or epithelial sodium channels. The greatest difference in receptor expression among the OSNs was the identity of the tuning IRs.

CONCLUSIONS

Our results provide an initial view of the combinatorial expression patterns of receptor molecules in single OSNs in one species of decapod crustacean, including receptors directly involved in olfactory transduction and others likely involved in modulation. Our results also suggest differences in receptor expression in OSNs vs. other chemosensory neurons.

Transient receptor potential channels: current perspectives on evolution, structure, function and nomenclature

The transient receptor potential superfamily of ion channels (TRP channels) is widely recognized for the roles its members play in sensory nervous systems. However, the incredible diversity within the TRP superfamily, and the wide range of sensory capacities found therein, has also allowed TRP channels to function beyond sensing an organism's external environment, and TRP channels have thus become broadly critical to (at least) animal life. TRP channels were originally discovered in Drosophila and have since been broadly studied in animals; however, thanks to a boom in genomic and transcriptomic data, we now know that TRP channels are present in the genomes of a variety of creatures, including green algae, fungi, choanoflagellates and a number of other eukaryotes. As a result, the organization of the TRP superfamily has changed radically from its original description. Moreover, modern comprehensive phylogenetic analyses have brought to light the vertebrate-centricity of much of the TRP literature; much of the nomenclature has been grounded in vertebrate TRP subfamilies, resulting in a glossing over of TRP channels in other taxa. Here, we provide a comprehensive review of the function, structure and evolutionary history of TRP channels, and put forth a more complete set of non-vertebrate-centric TRP family, subfamily and other subgroup nomenclature.

Pulse magnetization elicits differential gene expression in the central nervous system of the Caribbean spiny lobster, Panulirus argus

Diverse animals use Earth's magnetic field to guide their movements, but the neural and molecular mechanisms underlying the magnetic sense remain enigmatic. One hypothesis is that particles of the mineral magnetite (Fe₃O₄) provide the basis of magnetoreception. Here we examined gene expression in the central nervous system of a magnetically sensitive invertebrate, the Caribbean spiny lobster (Panulirus argus), after applying a magnetic pulse known to alter magnetic orientation behavior. Numerous genes were differentially expressed in response to the pulse, including 647 in the brain, 1256 in the subesophageal ganglion, and 712 in the thoracic ganglia. Many such genes encode proteins linked to iron regulation, oxidative stress, and immune response, consistent with possible impacts of a magnetic pulse on magnetite-based magnetoreceptors. Additionally, however, altered expression also occurred for numerous genes with no apparent link to magnetoreception, including genes encoding proteins linked to photoreception, carbohydrate and hormone metabolism, and other physiological processes. Overall, the results are consistent with the magnetite hypothesis of magnetoreception, yet also reveal that in spiny lobsters, a strong pulse altered expression of > 10% of all expressed genes, including many seemingly unrelated to sensory processes. Thus, caution is required when interpreting the effects of magnetic pulses on animal behavior.

Phylogenetics Identifies Two Eumetazoan TRPM Clades and an Eighth TRP Family, TRP Soromelastatin (TRPS)

Transient receptor potential melastatins (TRPMs) are most well known as cold and menthol sensors, but are in fact broadly critical for life, from ion homeostasis to reproduction. Yet, the evolutionary relationship between TRPM channels remains largely unresolved, particularly with respect to the placement of several highly divergent members. To characterize the evolution of TRPM and like channels, we performed a large-scale phylogenetic analysis of >1,300 TRPM-like sequences from 14 phyla (Annelida, Arthropoda, Brachiopoda, Chordata, Cnidaria, Echinodermata, Hemichordata, Mollusca, Nematoda, Nemertea, Phoronida, Priapulida, Tardigrada, and Xenacoelomorpha), including sequences from a variety of recently sequenced genomes that fill what would otherwise be substantial taxonomic gaps. These findings suggest: 1) the previously recognized TRPM family is in fact two distinct families, including canonical TRPM channels and an eighth major previously undescribed family of animal TRP channel, TRP soromelastatin; 2) two TRPM clades predate the last bilaterian-cnidarian ancestor; and 3) the vertebrate-centric trend of categorizing TRPM channels as 1-8 is inappropriate for most phyla, including other chordates.

De novo assembly and functional annotation of the heart + hemolymph transcriptome in the Caribbean spiny lobster Panulirus argus

The spiny lobster, Panulirus argus, is an ecologically relevant species in shallow water coral reefs and a target of the most lucrative fishery in the greater Caribbean region. This study reports, for the first time, the heart + hemolymph transcriptome of the Caribbean spiny lobster Panulirus argus assembled from short Illumina 150bp PE raw reads. A total of 80,152,094 raw reads were assembled using the Oyster River Protocol pipeline. The assembly resulted in a total of 254,773 transcripts. Functional gene annotation was conducted using the software package 'dammit'. Lastly, gene enrichment analyses were conducted using the Gene Ontology (GO) and KEGG pathway (Kaas) databases. This resource will be of utmost importance in future research aiming at exploring the effect of local and regional anthropogenic disturbances, as well as global climate change on the molecular physiology of this overexploited species.

Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins

Crustaceans express genes for at least three classes of putative chemosensory proteins. These are: Ionotropic Receptors (IRs), derived from the heterotetrameric ionotropic glutamate receptors (iGluRs); Transient Receptor Potential (TRP) channels, a diverse set of sensor-channels that include several families of chemoreceptor channels; and Gustatory Receptor Like receptors (GRLs), ionotropic receptors that are homologues of Gustatory Receptors (GRs) of insects and are expressed sparingly in most crustaceans so far studied. IRs are typically numerically the most dominant of these receptor proteins in crustaceans and include two classes: co-receptor IRs, which are necessary for making a functional receptor-channel; and tuning IRs, whose specific combination in the IR subunits in the heterotetramer confers chemical specificity. Previous work showed that the transcriptomes from two major chemosensory organs-the lateral flagellum of the antennule (LF) and the tips of the legs (dactyls)-of the Caribbean spiny lobster Panulirus argus express four co-receptor IRs and over 100 tuning IRs. In this paper, we examined and compared the transcriptomes from the LF and dactyls of P. argus and three other decapod crustaceans-the clawed lobster Homarus americanus, red swamp crayfish Procambarus clarkii, and the blue crab Callinectes sapidus. Each species has at least ca. 100 to 250 IRs, 1 to 4 GRLs, and ca. 15 TRP channels including those shown to be involved in chemoreception in other species. The IRs show different degrees of phylogenetic conservation: some are arthropod-conserved, others are pancrustacean-conserved, others appear to be crustacean-conserved, and some appear to be species-specific. Many IRs appear to be more highly expressed in the LF than dactyl. Our results show that decapod crustaceans express an abundance of genes for chemoreceptor proteins of different types, phylogenetic conservation, and expression patterns. An understanding of their functional roles awaits determining their expression patterns in individual chemosensory neurons and the central projections of those neurons.

Mushroom body evolution demonstrates homology and divergence across Pancrustacea

Descriptions of crustacean brains have focused mainly on three highly derived lineages of malacostracans: the reptantian infraorders represented by spiny lobsters, lobsters, and crayfish. Those descriptions advocate the view that dome- or cap-like neuropils, referred to as 'hemiellipsoid bodies,' are the ground pattern organization of centers that are comparable to insect mushroom bodies in processing olfactory information. Here we challenge the doctrine that hemiellipsoid bodies are a derived trait of crustaceans, whereas mushroom bodies are a derived trait of hexapods. We demonstrate that mushroom bodies typify lineages that arose before Reptantia and exist in Reptantia thereby indicating that the mushroom body, not the hemiellipsoid body, provides the ground pattern for both crustaceans and hexapods. We show that evolved variations of the mushroom body ground pattern are, in some lineages, defined by extreme diminution or loss and, in others, by the incorporation of mushroom body circuits into lobeless centers. Such transformations are ascribed to modifications of the columnar organization of mushroom body lobes that, as shown in Drosophila and other hexapods, contain networks essential for learning and memory.

Evolution, developmental expression and function of odorant receptors in insects

Animals rely on their chemosensory system to discriminate among a very large number of attractive or repulsive chemical cues in the environment, which is essential to respond with proper action. The olfactory sensory systems in insects share significant similarities with those of vertebrates, although they also exhibit dramatic differences, such as the molecular nature of the odorant receptors (ORs): insect ORs function as heteromeric ion channels with a common Orco subunit, unlike the G-protein-coupled olfactory receptors found in vertebrates. Remarkable progress has recently been made in understanding the evolution, development and function of insect odorant receptor neurons (ORNs). These studies have uncovered the diversity of olfactory sensory systems among insect species, including in eusocial insects that rely extensively on olfactory sensing of pheromones for social communication. However, further studies, notably functional analyses, are needed to improve our understanding of the origins of the Orco-OR system, the mechanisms of ORN fate determination, and the extraordinary diversity of behavioral responses to chemical cues.

Drosophila menthol sensitivity and the Precambrian origins of transient receptor potential-dependent chemosensation

Transient receptor potential (TRP) cation channels are highly conserved, polymodal sensors which respond to a wide variety of stimuli. Perhaps most notably, TRP channels serve critical functions in nociception and pain. A growing body of evidence suggests that transient receptor potential melastatin (TRPM) and transient receptor potential ankyrin (TRPA) thermal and electrophile sensitivities predate the protostome-deuterostome split (greater than 550 Ma). However, TRPM and TRPA channels are also thought to detect modified terpenes (e.g. menthol). Although terpenoids like menthol are thought to be aversive and/or harmful to insects, mechanistic sensitivity studies have been largely restricted to chordates. Furthermore, it is unknown if TRP-menthol sensing is as ancient as thermal and/or electrophile sensitivity. Combining genetic, optical, electrophysiological, behavioural and phylogenetic approaches, we tested the hypothesis that insect TRP channels play a conserved role in menthol sensing. We found that topical application of menthol to Drosophila melanogaster larvae elicits a Trpm- and TrpA1-dependent nocifensive rolling behaviour, which requires activation of Class IV nociceptor neurons. Further, in characterizing the evolution of TRP channels, we put forth the hypotheses that three previously undescribed TRPM channel clades (basal, αTRPM and βTRPM), as well as TRPs with residues critical for menthol sensing, were present in ancestral bilaterians. This article is part of the Theo Murphy meeting issue 'Evolution of mechanisms and behaviour important for pain'.

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus

Barnacle settlement involves sensing of a variety of exogenous cues. A pair of antennules is the main sensory organ that the cyprid larva uses to explore the surface. Antennules are equipped with a number of setae that have both chemo- and mechanosensing function. The current study explores the repertoire of sensory receptors in Balanus improvisus cyprid antennules with the goal to better understand sensory systems involved in the settling behavior of this species. We carried out transcriptome sequencing of dissected B. improvisus cyprid antennules. The generated transcriptome assembly was used to search for sensory receptors using HMM models. Among potential chemosensory genes, we identified the ionotropic receptors IR25a, IR8a and IR93a, and several divergent IR candidates to be expressed in the cyprid antennules. We found one gustatory-like receptor but no odorant receptors, chemosensory or odorant-binding proteins. Apart from chemosensory receptors, we also identified 13 potential mechanosensory genes represented by several transient receptor potential channels (TRP) subfamilies. Furthermore, we analyzed changes in expression profiles of IRs and TRPs during the B. improvisus settling process. Several of the sensory genes were differentially expressed during the course of larval settlement. This study gives expanded knowledge about the sensory systems present in barnacles, a taxonomic group for which only limited information about receptors is currently available. It furthermore serves as a starting point for more in depth studies of how sensory signaling affects settling behavior in barnacles with implications for preventing biofouling.

Mushroom bodies in crustaceans: Insect-like organization in the caridid shrimp Lebbeus groenlandicus

Paired centers in the forebrain of insects, called the mushroom bodies, have become the most investigated brain region of any invertebrate due to novel genetic strategies that relate unique morphological attributes of these centers to their functional roles in learning and memory. Mushroom bodies possessing all the morphological attributes of those in dicondylic insects have been identified in mantis shrimps, basal hoplocarid crustaceans that are sister to Eumalacostraca, the most species-rich group of Crustacea. However, unless other examples of mushroom bodies can be identified in Eumalacostraca, the possibility is that mushroom body-like centers may have undergone convergent evolution in Hoplocarida and are unique to this crustacean lineage. Here, we provide evidence that speaks against convergent evolution, describing in detail the paired mushroom bodies in the lateral protocerebrum of a decapod crustacean, Lebbeus groenlandicus, a species belonging to the infraorder Caridea, an ancient lineage of Eumalacostraca.