Zoantharia is an order among the Hexacorallia (Anthozoa: Cnidaria), and includes at least 300 species. Previously reported genomes from scleractinian corals and actiniarian sea anemones have illuminated part of the hexacorallian diversification. However, little is known about zoantharian genomes and the early evolution of hexacorals. To explore genome evolution in this group of hexacorals, here, we report de novo genome assemblies of the zoantharians Palythoa mizigama (Pmiz) and Palythoa umbrosa (Pumb), both of which are members of the family Sphenopidae, and uniquely live in comparatively dark coral reef caves without symbiotic Symbiodiniaceae dinoflagellates. Draft genomes generated from ultra-low input PacBio sequencing totaled 373 Mbp and 319 Mbp for Pmiz and Pumb, respectively. Protein-coding genes were predicted in each genome, totaling 30,394 in Pmiz and 24,800 in Pumb, with each set having ∼93% BUSCO completeness. Comparative genomic analyses identified 3,036 conserved gene families, which were found in all analyzed hexacoral genomes. Some of the genes related to toxins, chitin degradation, and prostaglandin biosynthesis were expanded in these two Palythoa genomes and many of which aligned tandemly. Extensive gene family loss was not detected in the Palythoa lineage and five of ten putatively lost gene families likely had neuronal function, suggesting biased gene loss in Palythoa. In conclusion, our comparative analyses demonstrate evolutionary conservation of gene families in the Palythoa lineage from the common ancestor of hexacorals. Restricted loss of gene families may imply that lost neuronal functions were effective for environmental adaptation in these two Palythoa species.

The association between two hydrozoans, Stylaster sp. and Millepora spp., has been described as a case of pseudo-auto-epizoism, and has only been reported from the Caribbean region of the Atlantic Ocean. Here, we report on the occurrence of this association in the Pacific Ocean on coral reefs around Iriomote-jima Island, Japan, suggesting the association to be more widespread than had previously been thought. Moreover, Stylaster sp. colonies were observed living healthily on bleached and dead branches of Millepora spp., indicating that this interaction is facultative. The interaction reported here differs from the relationship between the Caribbean Stylaster roseus and Millepora alcicornis by the connection points between the two partners, which is made evident by the whitening of the Millepora counterpart in Iriomote-jima Island, while being seamless in the Caribbean association. Further research is necessary to fully understand the nature of these relationships, comprehending under what conditions it occurs, and establishing which species are involved in the interactions.

Two zooxanthellate octocorals, Heliopora coerulea and Nanipora kamurai (family Helioporidae, order Scleralcyonacea, class Octocorallia), produce aragonite calcium carbonate skeletons similar to those of scleractinian hexacorals and contribute to the formation of complex coral reef ecosystems. H. coerulea is known to occur along the coasts of the Kerama Islands, Okinawa, Japan and N. kamurai was originally described from the Kerama Islands. An environmental DNA metabarcoding (eDNA-M) method has recently been introduced for comprehensive surveys of zooxanthellate scleractinian corals, supplementing conventional visual census by SCUBA diving or snorkeling. In particular, the Scl-eDNA-M system, which targets mitochondrial 12S rDNA for eDNA amplification, has proven to be an efficient tool for taxonomically identifying nearly all scleractinian genera reported in Japan. Moreover, our recent study showed that Heliopora can also be detected using the Scl-eDNA-M system. This study is the first to examine whether the Scl-eDNA-M is also applicable for the eDNA-based identification of Nanipora . Analyses of primer composition for PCR amplification and metabarcoding of eDNAs sampled from the Kerama Islands confirmed that Nanipora can be detected by this method. Importantly, the results of this study demonstrated that the overall distribution of Nanipora differs from that of Heliopora . Whereas Nanipora was distributed along the coasts of the inland sea of the Keramas, Heliopora occurred mainly along the exposed outer coasts, with only one site hosting both species. Although such differential distributions need to be confirmed by further visual census survey, this study highlights the efficiency of eDNA-M system for broad surveys of zooxanthellate octocorals.