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Members of the Emx homeobox gene class are expressed during embryogenesis in 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 Emx genes, with two conserved intron sites. The Drosophila homolog empty spiracles (ems) has just one intron, which may be shared with chordates; the other has been secondarily lost in this Drosophila gene and in a cnidarian Emx-related gene. We identify a highly conserved peptide motif close to the amino terminus of Emx proteins, demonstrate its similarity to a sequence found in a variety of transcription factors, and argue that it arose through convergent evolution in homeobox and forkhead genes. Finally, our molecular phylogenetic analysis strongly supports the presence of a single Emx gene in the ancestor of chordates and gene duplication along the vertebrate lineage.

Original publication




Journal article


Mol Biol Evol

Publication Date





1520 - 1528


Amino Acid Motifs, Amino Acid Sequence, Animals, Base Sequence, Chordata, Nonvertebrate, Conserved Sequence, Evolution, Molecular, Gene Duplication, Gene Library, Genes, Homeobox, Homeodomain Proteins, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Sequence Homology, Amino Acid, Transcription Factors, Vertebrates