Analysis of the central nervous system transcriptome of the eastern rock lobster Sagmariasus verreauxi reveals its putative neuropeptidome

Neuropeptidergic Signaling in the American Lobster Homarus americanus: New Insights from High-Throughput Nucleotide Sequencing

Peptides are the largest and most diverse class of molecules used for neurochemical communication, playing key roles in the control of essentially all aspects of physiology and behavior. The American lobster, Homarus americanus, is a crustacean of commercial and biomedical importance; lobster growth and reproduction are under neuropeptidergic control, and portions of the lobster nervous system serve as models for understanding the general principles underlying rhythmic motor behavior (including peptidergic neuromodulation). While a number of neuropeptides have been identified from H. americanus, and the effects of some have been investigated at the cellular/systems levels, little is currently known about the molecular components of neuropeptidergic signaling in the lobster. Here, a H. americanus neural transcriptome was generated and mined for sequences encoding putative peptide precursors and receptors; 35 precursor- and 41 receptor-encoding transcripts were identified. We predicted 194 distinct neuropeptides from the deduced precursor proteins, including members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin C, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone (CHH), CHH precursor-related peptide, diuretic hormone 31, diuretic hormone 44, eclosion hormone, FLRFamide, GSEFLamide, insulin-like peptide, intocin, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone, proctolin, pyrokinin, SIFamide, sulfakinin and tachykinin-related peptide families. While some of the predicted peptides are known H. americanus isoforms, most are novel identifications, more than doubling the extant lobster neuropeptidome. The deduced receptor proteins are the first descriptions of H. americanus neuropeptide receptors, and include ones for most of the peptide groups mentioned earlier, as well as those for ecdysis-triggering hormone, red pigment concentrating hormone and short neuropeptide F. Multiple receptors were identified for most peptide families. These data represent the most complete description of the molecular underpinnings of peptidergic signaling in H. americanus, and will serve as a foundation for future gene-based studies of neuropeptidergic control in the lobster.

Transcriptome analysis of the molting gland (Y-organ) from the blackback land crab, Gecarcinus lateralis

In decapod crustaceans, arthropod steroid hormones or ecdysteroids regulate molting. These hormones are synthesized and released from a pair of molting glands called the Y-organs (YO). Cyclic nucleotide, mTOR, and TGFβ/Smad signaling pathways mediate molt cycle-dependent phase transitions in the YO. To further identify the genes involved in the regulation of molting, a YO transcriptome was generated from three biological replicates of intermolt blackback land crab, Gecarcinus lateralis. Illumina sequencing of cDNA libraries generated 227,811,829 100-base pair (bp) paired-end reads; following trimming, 90% of the reads were used for further analyses. The trimmed reads were assembled de novo using Trinity software to generate 288,673 contigs with a mean length of 872 bp and a median length of 1842 bp. Redundancy among contig sequences was reduced by CD-HIT-EST, and the output constituted the baseline transcriptome database. Using Bowtie2, 92% to 93% of the reads were mapped back to the transcriptome. Individual contigs were annotated using BLAST, HMMER, TMHMM, SignalP, and Trinotate, resulting in assignments of 20% of the contigs. Functional and pathway annotations were carried out via gene ontology (GO) and KEGG orthology (KO) analyses; 58% and 44% of the contigs with BLASTx hits were assigned to GO and KO terms, respectively. The gene expression profile was similar to a crayfish YO transcriptome database, and the relative abundance of each contig was highly correlated among the three G. lateralis replicates. Signal transduction pathway orthologs were well represented, including those in the mTOR, TGFβ, cyclic nucleotide, MAP kinase, calcium, VEGF, phosphatidylinositol, ErbB, Wnt, Hedgehog, Jak-STAT, and Notch pathways.

Prediction of the neuropeptidomes of members of the Astacidea (Crustacea, Decapoda) using publicly accessible transcriptome shotgun assembly (TSA) sequence data

The decapod infraorder Astacidea is comprised of clawed lobsters and freshwater crayfish. Due to their economic importance and their use as models for investigating neurochemical signaling, much work has focused on elucidating their neurochemistry, particularly their peptidergic systems. Interestingly, no astacidean has been the subject of large-scale peptidomic analysis via in silico transcriptome mining, this despite growing transcriptomic resources for members of this taxon. Here, the publicly accessible astacidean transcriptome shotgun assembly data were mined for putative peptide-encoding transcripts; these sequences were used to predict the structures of mature neuropeptides. One hundred seventy-six distinct peptides were predicted for Procambarus clarkii, including isoforms of adipokinetic hormone-corazonin-like peptide (ACP), allatostatin A (AST-A), allatostatin B, allatostatin C (AST-C) bursicon α, bursicon β, CCHamide, crustacean hyperglycemic hormone (CHH)/ion transport peptide (ITP), diuretic hormone 31 (DH31), eclosion hormone (EH), FMRFamide-like peptide, GSEFLamide, intocin, leucokinin, neuroparsin, neuropeptide F, pigment dispersing hormone, pyrokinin, RYamide, short neuropeptide F (sNPF), SIFamide, sulfakinin and tachykinin-related peptide (TRP). Forty-six distinct peptides, including isoforms of AST-A, AST-C, bursicon α, CCHamide, CHH/ITP, DH31, EH, intocin, myosuppressin, neuroparsin, red pigment concentrating hormone, sNPF and TRP, were predicted for Pontastacus leptodactylus, with a bursicon β and a neuroparsin predicted for Cherax quadricarinatus. The identification of ACP is the first from a decapod, while the predictions of CCHamide, EH, GSEFLamide, intocin, neuroparsin and RYamide are firsts for the Astacidea. Collectively, these data greatly expand the catalog of known astacidean neuropeptides and provide a foundation for functional studies of peptidergic signaling in members of this decapod infraorder.

Neuropeptides in the cerebral ganglia of the mud crab, Scylla paramamosain: transcriptomic analysis and expression profiles during vitellogenesis

Neuropeptides play a critical role in regulating animal reproduction. In vertebrates, GnRH, GnIH and kisspeptin are the key neuropeptide hormones of the reproductive axis, however, the reproductive axis for invertebrates is vague. Knowledge on ovarian development of the mud crab, Scylla paramamosain, is critical for aquaculture and resources management of the commercially important species. This study employed Illumina sequencing, reverse transcription-polymerase chain reaction and quantitative real-time PCR techniques to identify neuropeptides that may be involved in ovarian development of S. paramamosain. A total of 32 neuropeptide transcripts from two dozen neuropeptide families, 100 distinct mature peptides were predicted from the transcriptome data of female S. paramamosain cerebral ganglia. Among them, two families, i.e. GSEFLamide and WXXXRamide, were first identified from the cerebral ganglia of crustaceans. Of these neuropeptides, 21 transcripts of interest were selected for further confirmation and all of them were detected in the cerebral ganglia, as well as in other nervous tissues and the ovary. Most of them also had differential expression in the cerebral ganglia during various vitellogenic stages, suggesting their likely involvement in regulating vitellogenesis and ovarian maturation. Overall, these findings provide an important basis for subsequent studies on peptide function in reproduction of S. paramamosain.

Neuropeptide discovery in Symphylella vulgaris (Myriapoda, Symphyla): In silico prediction of the first myriapod peptidome

Arthropods have contributed greatly to our understanding of peptidergic control of physiology and behavior, and being the largest and most diverse animal phylum, represent a model for investigating peptide hormone evolution. Surprisingly, one arthropod subphylum, the Myriapoda, is uninvestigated in terms of its peptide hormones. The public deposition of a transcriptome for Symphylella vulgaris, a pseudocentipede, provides a means for peptide discovery in myriapods. Here, in silico transcriptome mining was used to identify 47 S. vulgaris neuropeptide-encoding transcripts within this dataset. The identified transcripts allowed for the deduction of 31 unique pre/preprohormone sequences, with 97 distinct mature peptides predicted from the deduced proteins. The predicted S. vulgaris peptidome includes members of the adipokinetic hormone/red pigment concentrating hormone, adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin C (AST-C), allatotropin, CCHamide, crustacean cardioactive peptide, GSEFLamide, insulin-like peptide, intocin, proctolin, pyrokinin, short neuropeptide F, SIFamide and sulfakinin families. This is the first, and thus far only, peptidome predicted for a myriapod. Of particular note were a modified AST-C, TYWKQCAFNAVSRFamide, that lacks one of two cysteine residues (i.e. one at position 13) stereotypically present in members of this peptide family (and hence is missing the disulfide bridge that spans these residues) and a SIFamide, PPFNGSIFamide, that is truncated due to a lysine for arginine substitution in the dibasic residue pair commonly located at positions 3 and 4 of stereotypical full-length isoforms (e.g. the crustacean peptide GYRKPPFNGSIFamide). The peptides predicted here represent the only extant resource for initiating investigations of native peptidergic signaling in the Myriapoda.

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

The molecular understanding of crustacean metamorphosis is hindered by small sized individuals and inability to accurately define molt stages. We used the spiny lobster Sagmariasus verreauxi where the large, transparent larvae enable accurate tracing of the transition from a leaf-shaped phyllosoma to an intermediate larval-juvenile phase (puerulus). Transcriptomic analysis of larvae at well-defined stages prior to, during, and following this transition show that the phyllosoma-puerulus metamorphic transition is accompanied by vast transcriptomic changes exceeding 25% of the transcriptome. Notably, genes previously identified as regulating metamorphosis in other crustaceans do not fluctuate during this transition but in the later, morphologically-subtle puerulus-juvenile transition, indicating that the dramatic phyllosoma-puerulus morphological shift relies on a different, yet to be identified metamorphic mechanism. We examined the change in expression of domains and gene families, with focus on several key genes. Our research implies that the separation in molecular triggering systems between the phyllosoma-puerulus and puerulus-juvenile transitions might have enabled the extension of the oceanic phase in spiny lobsters. Study of similar transitions, where metamorphosis is uncoupled from the transition into the benthic juvenile form, in other commercially important crustacean groups might show common features to point on the evolutionary advantage of this two staged regulation.

In silico Neuropeptidome of Female Macrobrachium rosenbergii Based on Transcriptome and Peptide Mining of Eyestalk, Central Nervous System and Ovary

Macrobrachium rosenbergii is the most economically important of the cultured freshwater crustacean species, yet there is currently a deficiency in genomic and transcriptomic information for research requirements. In this study, we present an in silico analysis of neuropeptide genes within the female M. rosenbergii eyestalk, central nervous system, and ovary. We could confidently predict 37 preproneuropeptide transcripts, including those that encode bursicons, crustacean cardioactive peptide, crustacean hyperglycemic hormones, eclosion hormone, pigment-dispersing hormones, diuretic hormones, neuropeptide F, neuroparsins, SIFamide, and sulfakinin. These transcripts are most prominent within the eyestalk and central nervous system. Transcript tissue distribution as determined by reverse transcription-polymerase chain reaction revealed the presence of selected neuropeptide genes of interest mainly in the nervous tissues while others were additionally present in the non-nervous tissues. Liquid chromatography-mass spectrometry analysis of eyestalk peptides confirmed the presence of the crustacean hyperglycemic hormone precursor. This data set provides a strong foundation for further studies into the functional roles of neuropeptides in M. rosenbergii, and will be especially helpful for developing methods to improve crustacean aquaculture.

Discovery of a novel insulin-like peptide and insulin binding proteins in the Eastern rock lobster Sagmariasus verreauxi

This study reports, for the first time in any of the commercially important decapod species, the identification of an insulin-like peptide (ILP), distinct from the androgenic gland hormone. Bioinformatics analysis of the de novo assembled spiny lobster, (Sagmariasus verreauxi) transcriptome, allowed identification of Sv-ILP1 as well as eight binding proteins. Binding proteins were termed as Sv-IGFBP, due to homology with the vertebrate insulin-like growth-factor binding protein and Sv-SIBD1-7, single insulin-binding domain protein (SIBD), similar to those identified in other invertebrate species. Sv-ILP1 was found to be expressed in the eyestalk, gonads and antennal gland of both sexes and to a lesser extent in male muscle, androgenic gland and hepatopancreas. The expression profiles of each binding protein were found to vary across tissues, with Sv-SIBD5, 6 and 7 showing higher expression in the gonad, demonstrated by PCR and digital gene expression. Further spatial investigations, using in-situ hybridisation, found Sv-ILP1 to be expressed in the neurosecretory cells of the thoracic ganglia, in keeping with the tissue expression of Drosophila ILP7 (DILP7). This correlative tissue expression, considered with the phylogenetic clustering of Sv-ILP1 and DILP7, suggests Sv-ILP1 to be a DILP7 orthologue. The broad expression of Sv-ILP1 strongly suggests that ILPs have a role beyond that of masculinisation in decapods. The function of these novel peptides may have application in enhancing aquaculture practices in the commercially important decapod species.

Neuropeptide discovery in the Araneae (Arthropoda, Chelicerata, Arachnida): elucidation of true spider peptidomes using that of the Western black widow as a reference

The public deposition of large transcriptome shotgun assembly (TSA) datasets for the Araneae (true spiders) provides a resource for determining the structures of the native neuropeptides present in members of this chelicerate order. Here, the Araneae TSA data were mined for putative peptide-encoding transcripts using the recently deduced neuropeptide precursors from the Western black widow Latrodectus hesperus as query templates. Neuropeptide-encoding transcripts from five spiders, Latrodectus tredecimguttatus, Stegodyphus mimosarum, Stegodyphus lineatus, Stegodyphus tentoriicola and Acanthoscurria geniculata, were identified, including ones encoding members of the allatostatin A, allatostatin B, allatostatin C, allatotropin, CAPA/periviscerokinin/pyrokinin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/ion transport peptide, diuretic hormone 31, diuretic hormone 44, eclosion hormone, FMRFamide-like peptide (FLP), GSEFLamide, insulin-like peptide, orcokinin, proctolin, short neuropeptide F, SIFamide, sulfakinin and tachykinin-related peptide (TRP) families. A total of 156 distinct peptides were predicted from the precursor proteins deduced from the S. mimosarum transcripts, with 65, 26, 21 and 12 peptides predicted from those deduced from the A. geniculata, L. tredecimguttatus, S. lineatus and S. tentoriicola sequences, respectively. Among the peptides identified were variant isoforms of FLP, orcokinin and TRP, peptides whose structures are similar to ones previously identified from L. hesperus. The prediction of these atypical peptides from multiple spiders suggests that they may be broadly conserved within the Araneae rather than being species-specific variants. Taken collectively, the data described here greatly expand the number of known Araneae neuropeptides, providing a foundation for future functional studies of peptidergic signaling in this important Chelicerate order.

In silico characterization of the neuropeptidome of the Western black widow spider Latrodectus hesperus

Technological advancements in high-throughput sequencing have resulted in the production/public deposition of an ever-growing number of arthropod transcriptomes. While most sequencing projects have focused on hexapods, transcriptomes have also been generated for members of the Chelicerata. One chelicerate for which a large transcriptome has recently been released is the Western black widow Latrodectus hesperus, a member of the Araneae (true spiders). Here, a neuropeptidome for L. hesperus was predicted using this resource. Thirty-eight peptide-encoding transcripts were mined from the L. hesperus transcriptome, with 216 distinct peptides predicted from the deduced pre/preprohormones. The identified peptides included members of the allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon α, bursicon β, CAPA/periviscerokinin/pyrokinin, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/ion transport peptide, diuretic hormone 31, diuretic hormone 44, FMRFamide-like peptide (FLP), GSEFLamide, insulin-like peptide, neuropeptide F (NPF), orcokinin, proctolin, short neuropeptide F, SIFamide, sulfakinin and tachykinin-related peptide (TRP) families. Of particular note were the identifications of a carboxyl (C)-terminally extended corazonin, FLPs possessing -IMRFamide, -MMYFamide, and -MIHFamide C-termini, a NPF and a sulfakinin each ending in -RYamide rather than -RFamide, a precursor whose orcokinins include C-terminally amidated isoforms, and a collection of TRPs possessing -FXPXLamide rather than the stereotypical -FXGXLamide C-termini. The L. hesperus peptidome is by far the largest thus far published for any member of the Chelicerata. Taken collectively, these data serve as a reference for future neuropeptide discovery in the Araneae and provide a foundation for future studies of peptidergic control in L. hesperus and other spiders.