Ultraconserved elements, sequences with 100% identity with no insertions or deletions between genomes, have been found in both vertebrate and invertebrate genomes; whether plant genomes contain ultraconserved elements, however, is unknown. We consequently compared the genomes of Arabidopsis thaliana and rice, which diverged about 200 million years ago, and identified 25 ultraconserved elements that are longer than 100 bp. Similar to those previously found, ultraconserved elements in plants tend to occur in clusters and locate at noncoding regions; nevertheless, they have many distinct features. For instance, the longest ultraconserved element between the 2 plant genomes is 1491 bp, much longer than the longest one (779 bp) between the human and rodent genomes. Some biological implications are discussed, but the functions of these plant ultraconserved elements and the reasons why they are practically frozen during the evolution of millions of years remain a mystery.

Key words: Ultraconserved element; Genome; Arabidopsis thaliana; and Rice.