Additional file 7: of Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

Sequence logos of CHD chromodomains. Note that the chromodomain sequences are highly divergent both between and within individual groups of chromoviruses. Three sites corresponding to the aromatic cage motif found in HP1-like chromodomains [50] are marked with triangles if the aromatic amino-acid residues (Y, F, W) are present in most sequences or with crosses if they are mostly absent. The proportion of the aromatic amino-acid residues at the three sites in different groups of chromoviruses is summarized in the table. (PDF 93 kb