The first chromosome-level cubozoan genome differentiates unique and common cnidarian features

Abstract Cnidarians are aquatic invertebrates that can be found in both freshwater and marine habitats, including the corals, sea anemones, hydroids, true jellyfish (scyphozoans), and box jellyfish (cubozoans). Despite most cnidarian groups already having representative genomic resources, a high-quality genome of the cubozoan remains lacking. Here, we obtained the first chromosomal-level genome of the box jellyfish Tripedalia maipoensis, having a genome assembly size of 637.8 Mb and a scaffold N50 of 47.1 Mb. By comparing the cubozoan genome to other cnidarian lineages, unique and common features of cnidarians, including cnidarian-specific opsins, toxins, neuropeptides, sesquiterpenoid hormones, and microRNAs were revealed. The high-quality genome of a cubozoan presented in this study reveals distinct cnidarian features and provides a crucial missing foundation for further understanding cnidarian evolution more broadly.