Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400？MYA and most probably was associated with the evolution of chromatin organization. 1. Introduction A chromodomain (CHD) is a protein domain involved in chromatin remodeling and the regulation of gene expression in eukaryotes (e.g., [1–3]). CHDs perform a wide range of functions, including chromatin targeting and interactions between different proteins, RNA and DNA [3]. There are two major groups of CHDs that are found in eukaryotic chromodomain-containing proteins. The so-called “classical” CHDs carry the characteristic chromo-box motif (Y/f)-(L/F/Y)-(L/I/V)-K-(W/y)-(k/r)-g (single-letter code, capital letters standing for the most prominent aminoacid) [4]. The “classical” CHDs are highly conserved among eukaryotes and are represented in a large number of proteins in many genomes. They are believed to have a similar three-dimensional structure, which consists of an N-terminal three-stranded β-barrel capped by a C-terminal helix [5]. Three conserved residues, Y24, W45, and Y48, are essential for aromatic pocket formation [6, 7]. The second group of CHDs, “shadow” chromodomains, is more variable and includes chromo-related domains, which are well conserved in their central region, but they deviate significantly in other regions. The majority of the “shadow” CHDs contain the conserved residue W45 and lack Y24 and Y48 [3, 4]. In comparison with the “classical” CHDs, the shadow chromodomains contain one helix at the N-terminus and another inserted before the C-terminal helix [8]. The best-known protein with
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