Figure 1: A neighbor-joining (NJ) phylogenetic tree based on multiple alignment of reverse transcriptase aminoacid sequences of LTR retrotransposons, including newly identified chromodomain-containing LTR retrotransposons from Selaginella moellendorffii (a) and the structural organization of novel retroelements from Selaginella (b). Statistical support was evaluated by bootstrapping (1000 replications); nodes with bootstrap values over 50% are shown. The plant-specific clades: Reina, CRM, Galadriel, and Tekay, as well as the Tcn1 clade, are indicated. The name of the host species and the accession number is indicated for the LTR elements that were taken from GenBank. Abbreviations: ORF: open reading frame, PR: aspartyl protease, RT: reverse transcriptase, RNH: ribonuclease H, INT: integrase, CHD_I and CHD_II: chromodomain group I and group II, CCHC: Zn-finger motif, TSD: target site duplications, and 5′ and 3′LTRs: 5′ and 3′ long terminal repeats. The positions of stop-codons (SM-Cranky) are marked by asterisks.