Bioluminescence serves important ecological functions in prey capture, predator avoidance, and mate attraction. To investigate the genomic basis of bioluminescence evolution in marine cnidarians, we focused on the order Scleralcyonacea, which possesses a bioluminescent system involving the core gene families LBP, LUC, and GFP. We generated a chromosome-level genome assembly for the sea pen (Cavernularia habereri). Phylogenomic analyses identified three independent bioluminescent lineages within Scleralcyonacea, including one ancestral origin in sea pens and two independent origins in deep-sea lineages. Among the three core gene families, only LBP copy number expansion was strongly associated with bioluminescence phenotype and showed elevated expression in luminous species. Furthermore, LBP expansions generated phylogenetically distinct clusters or tandem duplicates under positive selection, suggesting potential neofunctionalization. These findings suggested that lineage-specific LBP expansion likely contributed to the evolution of bioluminescence in Scleralcyonacea, providing broader insights into the evolution of bioluminescence in marine organisms.
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