Homeodomain transcription factors are involved in many developmental processes [1] and have been intensely studied in a few model organisms, such as mouse, Drosophila and Caenorhabditis elegans. Homeobox genes fall into 10 classes (ANTP, PRD, POU, LIM, TALE, SIX, Cut, ZFH, HNF1, Prox) and 89 different families/groups, all of which are present in vertebrates. Additional groups may be uncovered by further genome annotation, particularly of complex vertebrate genomes. Eight of these groups have been found only in vertebrates, but not in the genome of the tunicate Ciona intestinalis. The other 81 groups of homeobox gene that have been detected in vertebrates so far probably appeared during the early evolution of bilaterians or earlier, as they are also present outside the chordates. How the homeobox genes evolved during and after the main radiation of the bilaterians remains poorly understood, as only a few animal genomes have been sequenced completely. However, drastic changes have occurred at least in the lineage of C. elegans[2], such as loss of several Hox genes and Hox cluster fragmentation [3]. Here we report considerable alterations of the homeobox gene complement in the tunicate lineage.
