Comparative genomics of zooxanthellate and azooxanthellate Palythoa (Cnidaria: Zoantharia) provides insights into symbiosis evolution and the origin of palytoxin

Zoantharians (Cnidaria) are globally distributed from shallow reefs to the deep sea, yet their genomic resources remain scarce. Within the zoantharian genus Palythoa, most species harbor photosymbiotic dinoflagellates, whereas some have secondarily lost this symbiosis, allowing genomic changes associated with symbiotic status to be examined. Palythoa is also the original source of palytoxin, one of the most potent marine toxins known, but whether it is produced by the host or by associated microorganisms remains unresolved. Here we generated high-quality genome assemblies of two zooxanthellate Palythoa species and compared five Palythoa genomes spanning both symbiotic states with those of other anthozoans. Across anthozoans, genome size scaled with transposable element content, particularly retrotransposons. The azooxanthellate lineage carries substitutions in conserved domains of the symbiosis-related proteins LePin and NPC2 and shows rapid evolution of the lectin gene CLEC4A, whereas NF-{kappa}B and V-type H+-ATPase remain conserved. Palythoa genomes showed no lineage-specific expansion of polyketide synthase (PKS) genes; cnidarian PKS genes were restricted to P. caribaeorum and P. sp. sakurajimensis (clade III). In contrast, 27 bacterial PKS sequences were recovered from metatranscriptomes and a metagenome-assembled genome across species, including an azooxanthellate species, indicating that they derive from associated bacterial rather than Symbiodiniaceae. These genomes provide a comparative framework for zoantharians and reveal genomic changes associated with symbiotic status. We propose that palytoxin originates from associated bacteria rather than from the host, a hypothesis that can be tested by identifying the producing bacteria and their biosynthetic gene clusters.