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Homeobox genes belong to a phylogenetically widespread family of regulatory genes that play important roles in pattern formation and cell-fate specification in several model systems (e.g., Drosophila, mouse, and C. elegans). Although the evolution of many classes of homeobox genes predates the diversification of the Bilateria, comparatively little is known about homeobox genes in outgroups to the Bilateria, such as the Cnidaria. We used the polymerase chain reaction to recover 12 partial homeoboxes from 2 species of sea anemones, Metridium senile and Nematostella vectensis (phylum Cnidaria; class Anthozoa). These homeoboxes appear to represent 9 distinct, mutually paralogous homeobox genes, 5 of which belong to previously identified cnidarian homeobox classes, and 4 of which appear to represent previously unidentified classes. The evolutionary relationships between the homeodomains of sea anemones and of bilaterian animals were assessed through database searches and phylogenetic analyses. As many as 5 of the anemone homeoboxes may belong to the Hox class, which suggests that the Hox gene complement of cnidarians is larger than previously expected. Homologs of the even-skipped gene of Drosophila were also identified in both Metridium and Nematostella.

Homeoboxes in Sea Anemones (Cnidaria; Anthozoa): A PCR-Based Survey of Nematostella vectensis and Metridium senile