Genes Genomics 2025 Oct 29; doi: 10.1007/s13258-025-01703-1.

Conservation and diversity of genes expressed in the spines of the sea urchin.

???displayArticle.abstract???
BACKGROUND: Echinoids, known as sea urchins, are a benthic family of marine invertebrates named for their spiny projections. Echinodermata translates from Greek to "Spiny Skin," yet in the laboratory setting, it is the embryos, not the spines, of these animals that are subjected to a wealth of molecular analyses. OBJECTIVE: In this study, we test the identity of genes expressed in the spines and identify conservation between four distant species. METHODS: We generated several transcriptomes de novo from four selected sea urchin species with a great diversity in size, color, and shape, representing 255 MYA of evolution (Strongylocentrotus purpuratus, Hemicentrotus pulcherrimus, Lytechinus variegatus, Eucidaris tribuloides). From de novo spine transcriptomes, we test for orthologous gene families, generating a wealth of orthogroups, as well as a species tree constructed from the available transcripts of only the spine. RESULTS: Core families of transcripts shared between all species, reveal that pathways involved in cell surface antigen-recognition, protein turnover, and cytoskeletal structure are each shared by diverse species of Echinoids. A basal branching species, Eucidaris tribuloides, contained a large number of unique transcripts, reflecting its unique spine morphology. When the spine transcriptome from Lytechinus variegatus was depleted of transcripts expressed elsewhere from the adult sea urchin, the resulting enriched spine transcriptomes were used for Orthofinder analysis, DEG analysis, and GO pathway analysis. CONCLUSION: Regardless of species, the spines are an organ with an abundance of gene expression for sensory, structural, and defense functions, well attuned to its habitat in the benthos.

???displayArticle.pubmedLink??? 41160353
???displayArticle.link??? Genes Genomics
???displayArticle.grants??? [+]