Ultraconserved elements (UCEs) are DNA sequences that are 100% identical (no 
base substitutions, insertions, or deletions) and located in syntenic positions 
in at least two genomes. Although hundreds of UCEs have been found in animal 
genomes, little is known about the incidence of ultraconservation in plant 
genomes. Using an alignment-free information-retrieval approach, we have 
comprehensively identified all long identical multispecies elements (LIMEs), 
which include both syntenic and nonsyntenic regions, of at least 100 identical 
base pairs shared by at least two genomes. Among six animal genomes, we found 
the previously known syntenic UCEs as well as previously undescribed nonsyntenic 
elements. In contrast, among six plant genomes, we only found nonsyntenic LIMEs. 
LIMEs can also be classified as either simple (repetitive) or complex 
(nonrepetitive), they may occur in multiple copies in a genome, and they are 
often spread across multiple chromosomes. Although complex LIMEs were found in 
both animal and plant genomes, they differed significantly in their composition 
and copy number. Further analyses of plant LIMEs revealed their functional 
diversity, encompassing elements found near rRNA and enzyme-coding genes, as 
well as those found in transposons and noncoding DNA. We conclude that despite 
the common presence of LIMEs in both animal and plant lineages, the evolutionary 
processes involved in the creation and maintenance of these elements differ in 
the two groups and are likely attributable to several mechanisms, including 
transfer of genetic material from organellar to nuclear genomes, de novo 
sequence manufacturing, and purifying selection.