The SET domain, first identified within and named after proteins encoded by 
three Drosophila genes [Su(var)3-9, E(z), and Trithorax], is recognized as a 
signature motif for histone methyltransferases that are involved in epigenetic 
processes. The SUV39H family of SET domain proteins methylate specifically the 
residue lysine 9 of histone H3, creating a code for gene silencing. This family 
of proteins contain at their C termini a unique catalytic domain consisting of 
pre-SET, SET, and post-SET domains. Sequence homology-based searches identified 
15 Arabidopsis, 14 maize, and 12 rice proteins that can be assigned to the 
SUV39H family. These high numbers in plants are in marked contrast to the 
situation in animals, in which each species appears to contain only two to three 
proteins of this family. Our phylogenetic analyses revealed that plant proteins 
can be classified into seven orthology groups. Representative members of each 
group can be found in single plant species, suggesting that different group 
members are evolutionarily conserved to perform specific functions.