The genomes of many higher plant species are the most highly methylated among 
eukaryotes. We report here that in spite of their heavy methylation, genomic 
DNAs from four plant species contain a fraction that is very rich in 
non-methylated sites. The fraction was characterized in maize where it 
represents about 2.5% of the total nuclear genome. In order to establish the 
genomic origin of the fraction, three maize genes containing clustered CpG were 
tested for methylation and were found to be non-methylated in the CpG-rich 
regions. By contrast, tested CpGs were methylated in a gene whose sequence 
showed no clustering of CpG. These observations suggest that the CpG-rich 
fraction of plants is at least partially derived from non-methylated regions 
that are associated with genes. A similar phenomenon has been described in 
vertebrate genomes. We discuss the evolution of CpG islands in both groups of 
organisms, and their possible uses in mapping and gene isolation in plants.