Extended Data Fig. 4: T-DNA junctions support the involvement of TMEJ in T-DNA concatenation.

a, Multiple sequence alignments of junctions between two T-DNA sequences grouped by orientation of the two sequences (RB-LB, LB-LB or RB-RB). Reference sequences were constructed assuming T-DNA molecules began and ended immediately upstream of the endonuclease (VirD2) recognition sequence (5′-CAGGATATATT-3′)^63,64. Filler sequences are in red and sequences consistent with microhomology-associated deletions are underlined. If filler sequences have a similar sequence nearby, they (and the nearby sequence) are also underlined. Asterisks indicate identical junctions occurring in independent plants. b, Depiction of T-DNA junctions with another T-DNA or binary vector sequence not immediately internally adjacent to the LB or RB. c. Classification of RB-LB, LB-LB and RB-RB sequences for each T1 line following a procedure previously described⁶⁵. NHEJ (<4 bp deletions and <5 bp insertions), insertions (≥5 bp with any deletion), non-microhomology (Non-MH; ≥4 bp deletion or <5 bp insertions with microhomologies <2), and microhomology (MH; ≥4 bp deletion with microhomologies ≥2). The latter three are associated with DNA polymerase theta.