BACKGROUND: Ultraconserved elements of DNA have been identified in vertebrate 
and invertebrate genomes. These elements have been found to have diverse 
functions, including enhancer activities in developmental processes. The 
evolutionary origins and functional roles of these elements in cellular systems, 
however, have not yet been determined.
RESULTS: Here, we identified a wide range of ultraconserved elements common to 
distant species, from primitive aquatic organisms to terrestrial species with 
complicated body systems, including some novel elements conserved in fruit fly 
and human. In addition to a well-known association with developmental genes, 
these DNA elements have a strong association with genes implicated in essential 
cell functions, such as epigenetic regulation, apoptosis, detoxification, innate 
immunity, and sensory reception. Interestingly, we observed that ultraconserved 
elements clustered by sequence similarity. Furthermore, species composition and 
flanking genes of clusters showed lineage-specific patterns. Ultraconserved 
elements are highly enriched with binding sites to developmental transcription 
factors regardless of how they cluster.
CONCLUSION: We identified large numbers of ultraconserved elements across 
distant species. Specific classes of these conserved elements seem to have been 
generated before the divergence of taxa and fixed during the process of 
evolution. Our findings indicate that these ultraconserved elements are not the 
exclusive property of higher modern eukaryotes, but rather transmitted from 
their metazoan ancestors.