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Open Access Highly Accessed Research article

The evolution of ultraconserved elements with different phylogenetic origins

Taewoo Ryu12*, Loqmane Seridi12 and Timothy Ravasi12*

Author Affiliations

1 Integrative Systems Biology Lab., Division of Biological and Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia

2 Department of Medicine, Division of Medical Genetics, University of California, San Diego, 9500 Gilman Drive La Jolla, CA, 92093-0688, USA

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BMC Evolutionary Biology 2012, 12:236  doi:10.1186/1471-2148-12-236

Published: 5 December 2012



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.


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.


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.

Ultraconserved elements; Developmental enhancers; Transcriptional regulatory networks; Genome evolution; Marine biology