Figure 1

LINE superfamilies. Relationships between LINE superfamilies/groups and assignment of clades to superfamilies/groups based on reverse transcriptase (RT) phylogeny [7, 9, 10]. LINE clades were first assigned to five groups (R2, L1, RTE, I and Jockey) by Eickbush and Malik [8]. Groups are called superfamilies in the TE classification paper by Wicker et al. [7]. The ORF1 is not present in some RTE clades (shown with a dashed outline). In this paper, all Jockey superfamily/group full-length sequences from the Repbase database were assigned to three lineages based on an APE-RT phylogeny (see Figure 3). Subgroups were identified within the three lineages and ORF1 structures (see Figure 2) mapped onto the phylogeny (see Figures 4, 5 and 6).