Jianli Wang*, Alison P. Lee*, Rimantas Kodzius, Sydney Brenner and B. Venkatesh.
Published in: Mol. Biol. Evol. (2009) 26: 487-490.
Human and other vertebrate genomes contain thousands of ultraconserved elements (UCEs) which are functional elements that are under evolutionary selection. The identification of UCEs is a powerful approach for discovering cis-regulatory elements in human and other vertebrate genomes. Although the origin and evolution of UCEs are not well understood, previous studies have suggested that a massive expansion of UCEs occurred during tetrapod evolution and the substitution rate in UCEs showed a significant decline in tetrapods compared to teleost fishes such as fugu and zebrafish (Stephen et al., Mol. Biol. Evol. 2008). Evidence for fewer UCEs in teleost fishes further supported the hypothesis that a large number of UCEs were de novo recruited in tetrapods and exapted to perform important functions. We have investigated UCEs in a cartilaginous fish, the elephant shark and show that nearly half the UCEs present in placental mammals existed in the common ancestor of jawed vertebrates (gnathostomes). Interestingly, UCEs have experienced a higher substitution rate in teleost fishes than in elephant shark and as a result, approximately one-third of ancient UCEs have diverged beyond recognition in teleost fishes. Our study also shows that protein-coding sequences are evolving at a slower rate in elephant shark than in other vertebrates. This finding underscores the importance of elephant shark as a model genome for understanding the evolution of vertebrate genomes. The higher substitution rate of UCEs in teleost fishes may have implications for the vast diversity of teleost fishes.