Figure 1.

Structure and organization of plant transposable element superfamilies (adapted from [16]). Schemes are not to scale. Protein coding domains: APE = apurinic endonuclease, CHR = chromodomain, EN = endonuclease, GAG = capsid protein, HEL = helicase, INT = integrase, PROT = proteinase, RH = RNAse H, RPA = replication protein A, RT = reverse transcriptase. eORF = extra open reading frame (unknown function), Tpase = transposase (* with DDE motif), YR = tyrosine recombinase, Y2 = YR with YY motif, ◊ = different possible locations of an additional cellular-like ribonuclease H (aRH) specific of the Tat lineages (see Table 1). Optional protein-coding domains only present in some superfamily lineages are indicated in brackets. Some structural features are also represented. Terminal repeats in the same or reverse orientation are indicated by black arrows, and purple rectangles refer to diagnostic sequences present in non-coding sequences. Specific base termination of some TEs are also indicated. PBS = primer binding site, PPT = poly purine tract. Interrupted line in Helitron representation means that the region may contain one or more additional ORFs.