Teleost fishes have extra Hox gene clusters owing to shared or lineage-specific 
genome duplication events in rayfinned fish (actinopterygian) phylogeny. Hence, 
extrapolating between genome function of teleosts and human or even between 
different fish species is difficult. We have sequenced and analyzed Hox gene 
clusters of the Senegal bichir (Polypterus senegalus), an extant representative 
of the most basal actinopterygian lineage. Bichir possesses four Hox gene 
clusters (A, B, C, D); phylogenetic analysis supports their orthology to the 
four Hox gene clusters of the gnathostome ancestor. We have generated a 
comprehensive database of conserved Hox noncoding sequences that include 
cartilaginous, lobe-finned, and ray-finned fishes (bichir and teleosts). Our 
analysis identified putative and known Hox cis-regulatory sequences with 
differing depths of conservation in Gnathostoma. We found that although bichir 
possesses four Hox gene clusters, its pattern of conservation of noncoding 
sequences is mosaic between outgroups, such as human, coelacanth, and shark, 
with four Hox gene clusters and teleosts, such as zebrafish and pufferfish, with 
seven or eight Hox gene clusters. Notably, bichir Hox gene clusters have been 
invaded by DNA transposons and this trend is further exemplified in teleosts, 
suggesting an as yet unrecognized mechanism of genome evolution that may explain 
Hox cluster plasticity in actinopterygians. Taken together, our results suggest 
that actinopterygian Hox gene clusters experienced a reduction in selective 
constraints that surprisingly predates the teleost-specific genome duplication.