Figure 6

ORF1 types mapped onto the CR1 lineage apurinic endonuclease ( APE)-reverse transcriptase (RT) phylogeny. The phylogenies are sub-trees of the Jockey superfamily APE-RT (ORF2) phylogeny (see Figure 3). Subgroups were identified based on phylogenetic clustering and the ORF1 type. These are delineated by alternate light and dark grey shading using FigTree [21] and numbered. Subgroup numbers are shown within white circle in the phylogeny and next to the ORF1 structure schematic. Subgroups were assigned to clades using the RTclass1 tool [9]. The ORF1 type/subtype (see Figure 2) and phylum in which elements were identified are shown above the schematic. The phylum is not shown if only a single sequence was identified. ORF1 domains were identified by multiple alignment of all sequences within the subgroup and an HMM-HMM comparision [22]. Coiled-coil domains were identified using Pcoils [23]. The ORF1 structure schematic shows domains 5’ to the endonuclease. The ORF1 structure is drawn to scale, domain lengths are the minimum identified. We have used the term ‘ORF1’ for simplicity’s sake, although in some cases domains are shown that are probably at the 5’ end of the ORF2 (L2 subgroup 5 and CR1 subgroup 4) or at the 5’ end of a single ORF (L2 subgroup 4 and CR1 subgroup 6). Domains are color-coded, details are shown in the key. CCHC, gag-like Cys₂HisCys zinc-knuckle; CTD, C terminal domain; PHD, plant homeodomain; RRM, RNA recognition motif; zf/lz, zinc finger/leucine zipper. Transposase 22 refers to the RCSB Protein Data Bank entry 2yko_A and Pfam entry PF02994, the L1ORF1 protein composed of a coiled-coil, RRM and CTD domain [24]. Red asterisks indicate single sequences within a subgroup from a different phylum. In Figure 4 (L2 lineage) these are a single Branchiostoma floridae (Chordata) sequence in subgroup 6 and a single Capitella species (Annelida) sequence in subgroup 3. In Figure 5 (Jockey lineage) this is a single Drosophila sequence in subgroup 2.