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

Abstract

Background: Nervous systems originated before the split of Proto- and Deuterostomia, more than 600 million years ago. Four animal phyla (Cnidaria, Placozoa, Ctenophora, Porifera) diverged before this split and studying these phyla could give us important information on the evolution of the nervous system. Here, we have annotated the neuropeptide preprohormone genes of twenty species belonging to the subclass Hexacorallia or Ceriantharia (Anthozoa: Cnidaria), using thirty-seven publicly accessible genome or transcriptome databases. Studying hexacorals is important, because they are versatile laboratory models for development (e.g., Nematostella vectensis) and symbiosis (e.g., Exaiptasia diaphana) and also are prominent reef-builders.

Results: We found that each hexacoral or ceriantharian species contains five to ten neuropeptide preprohormone genes. Many of these preprohormones contain multiple copies of immature neuropeptides, which can be up to 50 copies of identical or similar neuropeptide sequences. We also discovered preprohormones that only contained one neuropeptide sequence positioned directly after the signal sequence. Examples of them are neuropeptides that terminate with the sequence RWamide (the Antho-RWamides). Most neuropeptide sequences are N-terminally protected by pyroglutamyl (pQ) or one or more prolyl residues, while they are C-terminally protected by an amide group. Previously, we isolated and sequenced small neuropeptides from hexacorals that were N-terminally protected by an unusual L-3-phenyllactyl group. In our current analysis, we found that these N-phenyllactyl-peptides are derived from N-phenylalanyl-peptides located directly after the signal sequence of the preprohormone. The N-phenyllactyl- peptides appear to be confined to the hexacorallian order Actiniaria and do not occur in other cnidarians. On the other hand, (1) the neuropeptide Antho-RFamide (pQGRFamide); (2) peptides with the C-terminal sequence GLWamide; and (3) tetrapeptides with the X₁PRX₂amide consensus sequence (most frequently GPRGamide) are ubiquitous in Hexacorallia.

Conclusions: We found GRFamide, GLWamide, and X₁PRX₂amide peptides in all tested Hexacorallia. Previously, we discovered these three neuropeptide classes also in Cubozoa, Scyphozoa, and Staurozoa, indicating that these neuropeptides originated in the common cnidarian ancestor and are evolutionarily ancient. In addition to these ubiquitous neuropeptides, other neuropeptides appear to be confined to specific cnidarian orders or subclasses.

Keywords: Cnidaria; Coral; Functional genomics; Genome; Nervous system; Neuropeptide; Phylogenomics; Reef restoration; Sea anemone; Transcriptome.

Fig. 1

Schematic drawing showing the phylogenetic positions of the subclasses Ceriantharia, Hexacorallia and Octocorallia and the classes Hydrozoa, Cubozoa, Scyphozoa, and Staurozoa. Cnidaria are a sister group to Bilateria. The figure also shows that X₁PRX₂amide and GRFamide peptides are present in all testet Octocorallia, Cubozoa, Scyphozoa, and Staurozoa [34]. In the current paper, we are investigating these and other neuropeptides in Ceriantharia and Hexacorallia. Modified from [34]

Fig. 2

Phylogenetic relationships between the various Hexacorallia orders and the subclasses Ceriantharia and Octocorallia. All hexacoral orders were studied in this paper except for the Antipatharia, which has no species with a sequenced genome or transcriptome. This figure is based on data from [59, 60]

Fig. 3

Presence of the GLWamide (highlighted in blue), GRFamide (highlighted in yellow), and X₁PRX₂amide (where X₂ is either S, A, or G; highlighted in purple) peptides in the subclasses Ceriantharia, Hexacorallia, and Octocorallia and the classes Cubozoa, Scyphozoa, and Staurozoa. This figure has the same structure as Fig.1. It shows that the three peptide families are present in all mentioned classes and subclasses, except for the Octocorallia that lack the GLWamides. Nevertheless, it can be concluded that the three peptide families originated in the common cnidarian ancestor. The other neuropeptide families identified in this paper (Additional files 4, 5, 6, 7, 8, 9, and 10) are either class-, subclass-, or order-specific and are no good candidate for being primordial neuropeptides

Fig. 4

Alignment of GLWamide and GVWamide peptides from species belonging to the subclasses Hexacorallia and Ceriantharia, or orders Cubozoa, Scyphozoa, and Staurozoa. These alignments show that the GVWamides have four out of six residues in common with the canonical GLWamide peptide MMA. In addition, there are conserved L/V residues at position 5 of all peptides