The single amphioxus Hox cluster contains 15 genes and may well resemble the 
ancestral chordate Hox cluster. We have sequenced the Hox genomic complement of 
the European amphioxus Branchiostoma lanceolatum and compared it to the American 
species, Branchiostoma floridae, by phylogenetic footprinting to gain insights 
into the evolution of Hox gene regulation in chordates. We found that Hox 
intergenic regions are largely conserved between the two amphioxus species, 
especially in the case of genes located at the 3' of the cluster, a trend 
previously observed in vertebrates. We further compared the amphioxus Hox 
cluster with the human HoxA, HoxB, HoxC, and HoxD clusters, finding several 
conserved noncoding regions, both in intergenic and intronic regions. This 
suggests that the regulation of Hox genes is highly conserved across chordates, 
consistent with the similar Hox expression patterns in vertebrates and 
amphioxus.