BACKGROUND: The modern coelacanth (Latimeria) is the extant taxon of a basal 
sarcopterygian lineage and sister group to tetrapods. Apart from certain 
apomorphic traits, its morphology is characterized by a high degree of retention 
of ancestral vertebrate structures and little morphological change. An insight 
into the molecular evolution that may explain the unchanged character of 
Latimeria morphology requires the analysis of the expression patterns of 
developmental regulator genes and their cis-regulatory modules (CRMs).
RESULTS: We describe the comparative and functional analysis of the sonic 
hedgehog (shh) genomic region of Latimeria menadoensis. Several putative 
enhancers in the Latimeria shh locus have been identified by comparisons to 
sarcopterygian and actinopterygian extant species. Specific sequence 
conservation with all known actinopterygian enhancer elements has been detected. 
However, these elements are selectively missing in more recently diverged 
actinopterygian and sarcopterygian species. The functionality of the putative 
Latimeria enhancers was confirmed by reporter gene expression analysis in 
transient transgenic zebrafish and chick embryos.
CONCLUSIONS: Latimeria shh CRMs represent the ancestral set of enhancers that 
have emerged before the split of lobe-finned and ray-finned fishes. In contrast 
to lineage-specific losses and differentiations in more derived lineages, 
Latimeria shh enhancers reveal low levels of sequence diversification. High 
overall sequence conservation of shh conserved noncoding elements (CNE) is 
consistent with the general trend of high levels of conservation of noncoding 
DNA in the slowly evolving Latimeria genome.