It is now well established that there were four Hox gene clusters in the genome 
of the last common ancestor of extant gnathostomes. To better understand the 
evolution of the organization and expression of these genomic regions, we have 
studied the Hox gene clusters of a shark (Scyliorhinus canicula). We sequenced 
225,580 expressed sequence tags from several embryonic cDNA libraries. Blast 
searches identified corresponding transcripts to almost all the HoxA, HoxB, and 
HoxD cluster genes. No HoxC transcript was identified, suggesting that this 
cluster is absent or highly degenerate. Using Hox gene sequences as probes, we 
selected and sequenced seven clones from a bacterial artificial chromosome 
library covering the complete region of the three gene clusters. Mapping of 
cDNAs to these genomic sequences showed extensive alternative splicing and 
untranslated exon sharing between neighboring Hox genes. Homologous noncoding 
exons could not be identified in transcripts from other species using sequence 
similarity. However, by comparing conserved noncoding sequences upstream of 
these exons in different species, we were able to identify homology between some 
exons. Some alternative splicing variants are probably very ancient and were 
already coded for by the ancestral Hox gene cluster. We also identified several 
transcripts that do not code for Hox proteins, are probably not translated, and 
all but one are in the reverse orientation to the Hox genes. This survey of the 
transcriptome of the Hox gene clusters of a shark shows that the high complexity 
observed in mammals is a gnathostome ancestral feature.