De novo transcriptome assembly of the cubomedusa Tripedalia cystophora, including the analysis of a set of genes involved in peptidergic neurotransmission

Abstract

Background The phyla Cnidaria, Placozoa, Ctenophora, and Porifera emerged before the split of proto- and deuterostome animals, about 600 million years ago. These early metazoans are interesting, because they can give us important information on the evolution of various tissues and organs, such as eyes and the nervous system. Generally, cnidarians have simple nervous systems, which use neuropeptides for their neurotransmission, but some cnidarian medusae belonging to the class Cubozoa (box jellyfishes) have advanced image-forming eyes, probably associated with a complex innervation. Here, we describe a new transcriptome database from the cubomedusa Tripedalia cystophora. Results Based on the combined use of the Illumina and PacBio sequencing technologies, we produced a highly contiguous transcriptome database from T. cystophora. We then developed a software program to discover neuropeptide preprohormones in this database. This script enabled us to annotate seven novel T. cystophora neuropeptide preprohormone cDNAs: One coding for 19 copies of a peptide with the structure pQWLRGRFamide; one coding for six copies of a different RFamide peptide; one coding for six copies of pQPPGVWamide; one coding for eight different neuropeptide copies with the C-terminal LWamide sequence; one coding for thirteen copies of a peptide with the RPRAamide C-terminus; one coding for four copies of a peptide with the C-terminal GRYamide sequence; and one coding for seven copies of a cyclic peptide, of which the most frequent one has the sequence CTGQMCWFRamide. We could also identify orthologs of these seven preprohormones in the cubozoans Alatina alata, Carybdea xaymacana, Chironex fleckeri, and Chiropsalmus quadrumanus. Furthermore, using TBLASTN screening, we could annotate four bursicon-like glycoprotein hormone subunits, five opsins, and 52 other family-A G protein-coupled receptors (GPCRs), which also included two leucine-rich repeats containing G protein-coupled receptors (LGRs) in T. cystophora . The two LGRs are potential receptors for the glycoprotein hormones, while the other GPCRs are candidate receptors for the above-mentioned neuropeptides. Conclusions By combining Illumina and PacBio sequencing technologies, we have produced a new high-quality de novo transcriptome assembly from T. cystophora that should be a valuable resource for identifying the neuronal components that are involved in vision and other behaviors in cubomedusae. Electronic supplementary material The online version of this article (10.1186/s12864-019-5514-7) contains supplementary material, which is available to authorized users.

A comparative genomics study of neuropeptide genes in the cnidarian subclasses Hexacorallia and Ceriantharia

“…Our analyses showed that all investigated cnidarians possessed a GRFamide neuropeptide: pQGRFamide in Octocorallia; pQWLRGRFamide in Cubozoa and Scyphozoa; and pQFLRGRFamide in Staurozoa. Furthermore, we found that all investigated species produced RPRSamide or a related neuropeptide sequence (consensus sequence X 1 PRX 2 amide, where X 2 was S, A, or G) [34,37]. Because the Cubozoa, Scyphozoa, Staurozoa, and Octocorallia have their closest evolutionary root in the common ancestral cnidarian (Fig.…”

“…This question, however, can now be solved, because the genomes from many cnidarians have been sequenced and numerous cnidarian transcriptomes are also available [37][38][39][40][41][42][43][44][45][46][47][48][49][50][51]. Last year, we developed a bioinformatics tool that could analyze cnidarian genomes and transcriptomes for the presence of neuropeptide preprohormones genes [37]. Using this script, we analyzed all available genome and transcriptome databases from Cubozoa, Scyphozoa, Staurozoa (belonging to the subphylum Medusozoa) and Octocorallia (belonging to the class Anthozoa) for the presence of neuropeptide preprohormones [34,37].…”

“…Last year, we developed a bioinformatics tool that could analyze cnidarian genomes and transcriptomes for the presence of neuropeptide preprohormones genes [37]. Using this script, we analyzed all available genome and transcriptome databases from Cubozoa, Scyphozoa, Staurozoa (belonging to the subphylum Medusozoa) and Octocorallia (belonging to the class Anthozoa) for the presence of neuropeptide preprohormones [34,37]. Our analyses showed that all investigated cnidarians possessed a GRFamide neuropeptide: pQGRFamide in Octocorallia; pQWLRGRFamide in Cubozoa and Scyphozoa; and pQFLRGRFamide in Staurozoa.…”

“…Table 1 gives the accession numbers of the genome and transcriptome databases that we used for the analyses of the various members of Hexacorallia and Ceriantharia. These analyses were carried out, using a script described in [37] that was based on the presence of two or more similar neuropeptide copies on a neuropeptide preprohormone (see also Methods). However, to avoid the exclusion of single copy neuropeptide preprohormones, we also applied TBLASTN and a related software program named Regex (Regular expression).…”

A G-protein-coupled receptor mediates neuropeptide-induced oocyte maturation in the jellyfish Clytia

“…Given our imperfect knowledge of pro-peptide processing in cnidarians, some of the synthetic peptides may not correspond to endogenous peptides [29,30]. Only one of the 16 GPCRs was activated by this peptide mixture.…”