Echinoderms are highly regenerative animals that share a common ancestor with chordates, including humans. While the two phyla share a common ancestor, echinoderms defeat humans when it comes to regeneration. Regeneration is the replacement of damaged cells or regrowth of damaged tissues or organs naturally. Despite the significant differences in the body plan of echinoderms and humans, the similarities in their genome structure, the genes these two groups share, the phylogenetic relationship they have, and the simplicity of experimentation make echinoderms a valuable group to study regeneration. We expect that understanding tissue regeneration in echinoderms can set a stage for improved treatments and provide insights for developing therapeutic approaches to treat human injuries in the future.
Even within such a highly regenerative phylum as echinoderms, some species regenerate more readily than others. Holothurians, commonly known as sea cucumbers, occupy a special place in this regard, as they can fully and rapidly regenerate their body parts and major organs, including: the viscera, central nervous system, body wall, and muscles. However, the available genomic resources are very limited to implement holothuroids as animal models to study regeneration. Moreover, the available genomic resources do not represent diversity within the phylum. Hence, to fill this gap, I have updated an easy-to-use web-based application, EchinoDB, a database resource that includes the genomic and transcriptomic data on 42 unique echinoderm species, spanning the deepest divergences within the five extant classes of the phylum in addition to the 2 new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus.
Among sea cucumbers, the vast majority of molecular studies have been done on a single species, Holothuria glaberrima which do not represent the diversity of various regenerative events, including: regeneration of the gut luminal epithelium (mesodermal to endodermal) and regeneration of the pharyngeal bulb. However, other sea cucumber species, especially, those of the order Dendrochirotida are capable of such exceptional regeneration events. Therefore, I sequenced and annotated the draft genome of a dendrochirotid Sclerodactyla briareus to gain a deeper understanding of the regulatory molecular mechanisms controlling regeneration and genomic aspects behind the diversity of regeneration, seen in echinoderms.
To illustrate the practical utility of the dendrochirotid genome for regeneration studies, key components of the Notch and Wnt signaling pathways were selected and identified in the genome of hairy sea cucumber S. briareus. This is a biologically relevant example as these pathways are crucial for tissue regeneration in echinoderms. They are highly conserved across all multi-cellular animals and are known to coordinate many cellular events, including: cell proliferation, de-differentiation, cell division, and apoptosis. Therefore, I aimed to retrieve 29 selected genes of the Notch pathway and 25 selected genes of the canonical Wnt signaling pathway. Except for Mesp2 (a Notch pathway gene), all other genes were identified in the newly assembled draft genome of S. briareus.
I also studied S. briareus for primordial host-viral interactions and to learn about the evolution of their immune system by looking at the recombination activating genes (RAG) in relation to Strongylocentrotus purpuratus and other echinoderms. The objective was to discover and characterize novel viral sequences within S. briareus alongside the evolution of immune genes (RAG-Like) in marine environment. However, because of the gaps in the assembly, I was unable to find any evidence of viral markers in the genome of S. briareus. The paucity of full-length contigs in the genome assembly also resulted into only 3 protein sequences that may potentially share a sequence homology with RAG1-Like gene, but further investigation is needed. The lack of results require improvements in the genome assembly and the availability of increased data for RAG-Like genes on echinoderms. Nevertheless, this work is still useful for regeneration studies on echinoderms.