Supporting data for "Boxed, stalked and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa)"

Anthozoa, Endocnidozoa, and Medusozoa comprise the three major clades of Cnidaria. Medusozoa is further divided into four clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoathe latter three lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa, but there are currently no published genomes within Staurozoa and Cubozoa. Here we present three new draft genomes of <i>Calvadosia cruxmelitensis</i> (Staurozoa), <i>Alatina alata</i> (Cubozoa), and <i>Cassiopea xamachana</i> (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.