Chromodomains are thought to mediate protein-protein interactions between 
chromatin components. We have detected a chromodomain embedded within the 
catalytic region of a predicted Arabidopsis DNA methyltransferase that is 
diverged from other eukaryotic enzymes. The 791 residue "chromomethylase" (CMT1) 
is encoded by a floral transcript that is spliced from 20 exons and is present 
at only approximately 1/10(-7) of total mRNA. Genomic sequencing reveals an 
ancient haplotype split at CMT1 between Col-0 + Metz and the other ecotypes 
examined. In the Col-0 + Metz haplotype, alternative mRNA processing at intron 
13 truncates the coding region. In Ler, RLD, and No-0, similar truncation is 
caused by insertion of an intact retrotransposon, Evelknievel, which is present 
as a single copy in Ler and RLD and is currently methylated and inactive. 
Evelknievel is found at this site on a single branch that connects the Ler, RLD, 
and No-0 ecotypes but is absent from the genomes of all other ecotypes examined. 
A stop codon within exon 6 of the Metz ecotype confirms that CMT1 is 
nonessential. Nevertheless, comparison to CMT1 of Cardaminopsis arenosa, an 
outcrossing relative, indicates conservation for DNA methyltransferase function. 
We discuss how allelic diversity of CMT1 may reflect loosened selective 
constraints in a self-fertilizing species such as Arabidopsis thaliana.