title: Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis.
abstract: BACKGROUND
  Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone Nematostella vectensis challenge recent claims that the Hox code is a bilaterian invention and that no "true" Hox genes exist in the phylum Cnidaria.
  
  
  RESULTS
  Phylogenetic analyses of 18 Hox-related genes from Nematostella identify putative Hox1, Hox2, and Hox9+ genes. Statistical comparisons among competing hypotheses bolster these findings, including an explicit consideration of the gene losses implied by alternate topologies. In situ hybridization studies of 20 Hox-related genes reveal that multiple Hox genes are expressed in distinct regions along the primary body axis, supporting the existence of a pre-bilaterian Hox code. Additionally, several Hox genes are expressed in nested domains along the secondary body axis, suggesting a role in "dorsoventral" patterning.
  
  
  CONCLUSIONS
  A cluster of anterior and posterior Hox genes, as well as ParaHox cluster of genes evolved prior to the cnidarian-bilaterian split. There is evidence to suggest that these clusters were formed from a series of tandem gene duplication events and played a role in patterning both the primary and secondary body axes in a bilaterally symmetrical common ancestor. Cnidarians and bilaterians shared a common ancestor some 570 to 700 million years ago, and as such, are derived from a common body plan. Our work reveals several conserved genetic components that are found in both of these diverse lineages. This finding is consistent with the hypothesis that a set of developmental rules established in the common ancestor of cnidarians and bilaterians is still at work today.
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Ryan
authors.forename: Maureen E
authors.initials: ME
authors.lastname: Mazza
authors.forename: Kevin
authors.initials: K
authors.lastname: Pang
authors.forename: David Q
authors.initials: DQ
authors.lastname: Matus
authors.forename: Andreas D
authors.initials: AD
authors.lastname: Baxevanis
authors.forename: Mark Q
authors.initials: MQ
authors.lastname: Martindale
authors.forename: John R
authors.initials: JR
authors.lastname: Finnerty
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D005075:Biological Evolution; D019521:Body Patterning; D018507:Gene Expression Regulation, Developmental; D005801:Genes, Homeobox; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D012615:Sea Anemones / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid