We screened plant genome sequences, primarily from rice and Arabidopsis 
thaliana, for CpG islands, and identified DNA segments rich in CpG dinucleotides 
within these sequences. These CpG-rich clusters appeared in the analysed 
sequences as discrete peaks and occurred at the frequencies of one per 4.7 kb in 
rice and one per 4.0 kb in A. thaliana. In rice and A. thaliana, most of the 
CpG-rich clusters were associated with genes, which suggests that these clusters 
are useful landmarks in genome sequences for identifying genes in plants with 
small genomes. In contrast, in plants with larger genomes, only a few of the 
clusters were associated with genes. These plant CpG-rich clusters satisfied the 
criteria used for identifying human CpG islands, which suggests that these CpG 
clusters may be regarded as plant CpG islands. The position of each island 
relative to the 5'-end of its associated gene varied considerably. Genes in the 
analysed sequences were grouped into five classes according to the position of 
the CpG islands within their associated genes. A large proportion of the genes 
belonged to one of two classes, in which a CpG island occurred near the 5'-end 
of the gene or covered the whole gene region. The position of a plant CpG island 
within its associated gene appeared to be related to the extent of 
tissue-specific expression of the gene; the CpG islands of most of the widely 
expressed rice genes occurred near the 5'-end of the genes.