Evolutionary History of LTR Retrotransposon Chromodomains in Plants

Figure 3

Multiple alignment of chromodomains. The following were used in the alignment: the “classical” and “shadow” chromo-like motifs of functional proteins from diverse animal species and Arabidopsis (At_CMT1); group I and group II chromodomains from diverse plant LTR retrotransposons belonged to Tcn1, Galadriel, Reina, and Tekay clades as well as unclassified (Other); CHD_I from Tcn1 LTR retrotransposons of fungi Cryptococcus neoformans. The GenBank accession numbers are indicated for each sequence. The most conservative domains for each of the groups are shown on the top. The chromo-box is indicated on the very top, which also shows the secondary structure elements (arrows indicate β-strands; rectangle α-helix) and conserved residues that form the complementary surface that is responsible for H3 peptide recognition (green boxes) [3–7]. Three aminoacids that have been shown to be under positive selection are highlighted in yellow.