Fig. 4

Phylogeny of non-LTR elements based on their RT domains. The phylogeny is based on the alignment shown in (Additional file 1: Figure S3) of the ~ 250 aa catalytic RT domains of the elements listed in (Additional file 2: Table S5). The phylogeny is a 50% maximum likelihood tree, rooted with the CRE clade. The numbers at nodes represent the percentage of bootstrap values for 100 replicates. Clade names are prefixed to the element names for the 11 major non-LTR clades. The ciliate non-LTR form a new clade. The names of the elements for the 5 Paramecium groups are colored: blue, Group 1; green, Group 2; magenta, Group 3; red, Group 4; pink, Group 5. The amino acid divergence scale is indicated. Schematic diagrams of ORF structure of representative Paramecium elements from each group and representatives of the 11 major clades identified in [18] are shown next to the phylogeny. The representatives are the same as in [18]; however for Tad, Tad1 from N. crassa is shown; for R1, TRAS1 from B. mori is shown; and for I, the element from D. melanogaster is shown. The domains are RT, reverse transcriptase; APE, apurinic/apyrimidinic endonuclease; REL-ENDO, restriction enzyme-like endonuclease; RNH, RNase H domain. Vertical bars represent zinc-finger domains. The two ORFs are shown as offset whether or not they are in the same frame. For Group 1 and Group 2, there is a +1 frameshift. For Group 3, the two ORFs are in the same frame