Ultraconserved elements (UCEs), stretches of DNA that are identical between 
distantly related species, are enigmatic genomic features whose function is not 
well understood. First identified and characterized in mammals, UCEs have been 
proposed to play important roles in gene regulation, RNA processing, and 
maintaining genome integrity. However, because all of these functions can 
tolerate some sequence variation, their ultraconserved and ultraselected nature 
is not explained. We investigated whether there are highly conserved DNA 
elements without genic function in distantly related plant genomes. We compared 
the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged 
∼115 million years ago (Mya). We identified 36 highly conserved elements with at 
least 85% similarity that are longer than 55 bp. Interestingly, these elements 
exhibit properties similar to mammalian UCEs, such that we named them UCE-like 
elements (ULEs). ULEs are located in intergenic or intronic regions and are 
depleted from segmental duplications. Like UCEs, ULEs are under strong purifying 
selection, suggesting a functional role for these elements. As their mammalian 
counterparts, ULEs show a sharp drop of A+T content at their borders and are 
enriched close to genes encoding transcription factors and genes involved in 
development, the latter showing preferential expression in undifferentiated 
tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, 
species that diverged ∼50 Mya, we identified a different set of ULEs with 
similar properties in monocots. The identification of ULEs in plant genomes 
offers new opportunities to study their possible roles in genome function, 
integrity, and regulation.