Figure 3.

Alignments of deduced (A) LINE-like RTase, (B) gypsy-like RTase, and (C) mariner-like transposase amino acid sequences with similarity to previously identified clades (6–8); newly designated LINE-like clades Gia, Aca and Pla; or known mariner subfamilies (3). Except for primer sequences, which are not included, the regions of RTases and transposases depicted correspond to the filled bars in Fig. 1. Rotifer species are underlined, with bdelloids in red and other rotifers in green. All other RTase or transposase sequences we determined are in blue. Three LINE-like sequences and nine gypsy-like sequences contained stop codons and/or frame shifts (*, stop codon; #, frameshift). LINE-like sequences are shown in two separate groups, corresponding to their difference in the B-C distance. Clones within parentheses have identical nucleotide sequences. Dendrograms obtained by neighbor-joining illustrate sequence similarity. For comparison, sequences of two or three known members of each clade are included in black. (Scale bar: 10% amino acid difference.)