An amphioxus Emx homeobox gene reveals duplication during vertebrate evolution

Members of the Emx homeobox gene class are expressed during embryogenesis i n the brain and/or other head structures of phylogenetically diverse phyla. Here, we describe sequence, genomic structure, and molecular phylogenetic analysis of a cephalochordate (amphioxus) Emx class gene termed AmphiEmxA. The genomic structure of AmphiEmxA is very similar to that of vertebrate Em x genes, with two conserved intron sites. The Drosophila homolog empty spir acles (ems) has just one intron, which may be shared with chordates; the ot her has been secondarily lost in this Drosophila gene and in a cnidarian Em s-related gene. We identify a highly conserved peptide motif close to the a mino terminus of Emx proteins, demonstrate its similarity to a sequence fou nd in a variety of transcription factors, and argue that it arose through c onvergent evolution in homeobox and forkhead genes. Finally, our molecular phylogenetic analysis strongly supports the presence of a single Emx gene i n the ancestor of chordates and gene duplication along the vertebrate linea ge.