In vertebrates, conserved noncoding elements (CNEs) are functionally constrained 
sequences that can show striking conservation over >400 million years of 
evolutionary distance and frequently are located megabases away from target 
developmental genes. Conserved noncoding sequences (CNSs) in plants are much 
shorter, and it has been difficult to detect conservation among distantly 
related genomes. In this article, we show not only that CNS sequences can be 
detected throughout the eudicot clade of flowering plants, but also that a 
subset of 37 CNSs can be found in all flowering plants (diverging ∼170 million 
years ago). These CNSs are functionally similar to vertebrate CNEs, being highly 
associated with transcription factor and development genes and enriched in 
transcription factor binding sites. Some of the most highly conserved sequences 
occur in genes encoding RNA binding proteins, particularly the RNA 
splicing-associated SR genes. Differences in sequence conservation between 
plants and animals are likely to reflect differences in the biology of the 
organisms, with plants being much more able to tolerate genomic deletions and 
whole-genome duplication events due, in part, to their far greater fecundity 
compared with vertebrates.