Nervous System Development and Neuropeptides Characterization in Embryo and Larva: Insights from a Non-Chordate Deuterostome, the Sea Cucumber Apostichopus japonicus

The neuropeptidomes of the sea cucumbers Stichopus cf. horrens and Holothuria scabra

The Philippines is a renowned marine biodiversity hotspot, home to several sea cucumber species with unusual biological traits. Among these, Stichopus cf. horrens is notable for its ability to undergo rapid body wall liquefaction when stressed, coupled with remarkable regenerative abilities. In contrast, Holothuria scabra has one of the most robust body walls in sea cucumbers and thrives in many regimes in the tropics. Despite their intriguing traits, the neurobiology and chemical diversity of these species remain underexplored. Neuropeptides are important components of an animal's neurobiological toolkit that underlie various physiological and behavioral processes. Thus, the discovery of neuropeptides is a crucial step for understanding the molecular underpinnings of unique traits in sea cucumbers. Leveraging the throughput and sensitivity of tandem mass spectrometry, we obtained an unbiased view of the endogenous peptidomes of radial nerve cord tissues of non-model sea cucumber species, H. scabra and S. cf. horrens. In this work, we sequenced 60 mature peptides from S. cf. horrens that were derived from 22 precursor proteins, and 43 peptides originating from 25 precursor proteins in H. scabra nervous tissues. A total of seven previously unannotated and uncharacterized neuropeptide precursors were identified, thereby expanding the known animal neuropeptide repertoire. Furthermore, we discovered consistent structural features in mature neuropeptides based on the type of post-translational modifications while pushing forward potentially novel proteolytic processing sites during peptide maturation based on the enriched flanking amino acid residues. Collectively, our results provide preliminary data that expand our understanding of echinoderm neurobiology through neuropeptide discovery, potentially paving the way for innovative solutions to address the global demand for echinoderms.

Functional evolution of thyrotropin-releasing hormone neuropeptides: Insights from an echinoderm

Feeding behavior is regulated by a complex network of endogenous neuropeptides. In chordates, this role is suggested to be under the control of diverse factors including thyrotropin-releasing hormone (TRH). However, whether this regulatory activity of TRH is functionally conserved in non-chordate metazoans, and to what extent this process is underpinned by interactions of TRH with other neuropeptides such as cholecystokinin (CCK, known as a satiety signal), remain unclear. This study investigated the TRH signaling system in the echinoderm Apostichopus japonicus. Bioinformatic analyses and ligand-binding assays identified a functional TRH receptor (AjTRHR) that activated signaling via the MAPK/ERK1/2 pathways. Experimental administration of TRH significantly reduced feeding activity, while up-regulating CCK expression. RNA interference (RNAi) experiments confirmed that both CCK and TRH are essential components of satiety signaling, working synergistically to mediate feeding inhibition. Evolutionary analysis of TRH-type peptides revealed greater conservation of the short isoform of TRH compared to the long isoform, probably driven by strong selection acting on the functional redundancy. These findings provide compelling evidence of a TRH-mediated signaling system in non-chordate deuterostomes, expanding our understanding of neuropeptide-regulated feeding mechanisms in marine invertebrates.

Neuronal cell populations in circumoral nerve ring of sea cucumber Apostichopus japonicus: Ultrastructure and transcriptional profile

The echinoderm nervous system has been studied as a model for understanding the evolution of the chordate nervous system. Neuronal cells are essential groups that release a 'cocktail' of messenger molecules providing a spectrum of biological actions in the nervous system. Among echinoderms, most evidence on neuronal cell types has been obtained from starfish and sea urchin. In sea cucumbers, most research has focused on the location of neuronal cells, whereas their transcriptional features have rarely been investigated. Here, we observed the ultrastructure of neuronal cells in the sea cucumber, Apostichopus japonicus. The transcriptional profile of neuronal cells from the circumoral nerve ring (CNR) was investigated using single-cell RNA sequencing (scRNA-seq), and a total of six neuronal cell types were identified. 26 neuropeptide precursor genes (NPPs) and 28 G-protein-coupled receptors (GPCR) were expressed in the six neuronal cell types, comprising five NPP/NP-GPCR pairs. Unsupervised pseudotime analysis of neuronal cells showed their different differentiation status. We also located the neuronal cells in the CNR by immunofluorescence (IF) and identified the potential hub genes of key cell populations. This broad resource serves as a valuable support in the development of cell-specific markers for accurate cell-type identification in sea cucumbers. It also contributes to facilitating comparison across species, providing a deeper understanding of the evolutionary processes of neuronal cells.

Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific that can cause severe bioerosion on the reef community. However, the lack of genomic information has hindered the study of its ecology and evolution. Here, we report the chromosomal-level genome (885.8 Mb) of the long-spined sea urchin D. setosum using a combination of PacBio long-read sequencing and Omni-C scaffolding technology. The assembled genome contains a scaffold N50 length of 38.3 Mb, 98.1% of complete BUSCO (Geno, metazoa_odb10) genes (the single copy score is 97.8% and the duplication score is 0.3%), and 98.6% of the sequences are anchored to 22 pseudo-molecules/chromosomes. A total of 27,478 gene models have were annotated, reaching a total of 28,414 transcripts, including 5,384 tRNA and 23,030 protein-coding genes. The high-quality genome of D. setosum presented here is a valuable resource for the ecological and evolutionary studies of this coral reef-associated sea urchin.

Sea cucumbers: an emerging system in evo-devo

A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.