A proposed model for the ARR TE-mediate deletion. A. Structure of the chromosome 3 (gray bar) of the original variety, CLE, showing the occurrence of CitMule (position 6785327; red track) with the transposon inverted repeats (TIRs, green and yellow arrows) and a putative recombination hotspot (position 7797540; blue star) formed by a GAA/TTC track. B. A triplex DNA structure is formed in ARR at the recombination hotspot generating a loop that eventually brings the upstream end of CitMule near to the vicinity of position 8686356. Two transposase monomers bind to the transposon inverted repeats. C. Looping of the transposon brings the two ends of the transposable element close together. Transposase monomers form a dimer generating a paired-end complex. The complex recruits other involved proteins such as topoisomerases (blue object) and translins (purple object) resulting in the formation of a synaptic complex. Other putative trans-factors are not represented. D. Transposase, first, cuts the CitMule away from the flanking donor DNA and after cleavage the transposase/complex is released. E. In normal insertions, it is expected that transposase encounters a unique target side for insertion, generating the same TSD sequence in each side of the insertion. In ARR, the transposase/complex recognized two different CitMule target sites separated by approximately 2 Mb. One of these was the target site at position 8686356 and the other one was at position 6785296. Note that this position and the original position of CitMule are separated by 35 bp. F. Transposase catalyzes the inverted insertion of the transposon between these 2 target sites provoking in this way the release of the fragment spanning from one target site to the other one. Therefore, these events resulted in both an inverted insertion of CitMule and a 2 MB deletion in chromosome 3 as observed in ARR.