Fig. 3

Organisation of transgene integration sites within the genome of N. benthamiana ΔXT/FT, as explored using chimeric sequencing reads spanning integration boundaries. a Expected model for the chimeric reads mapping, as exemplified by the insertion at scaffold Niben101Scf03674. Shown are chimeric reads mapping on the host genome with one side (dark red) and on the transgene promoter/terminator site with the other side (blue). The dashed lines connect the two sides, while the cyan vertical lines outline the boundary between the host genome and the transgene. Regions without read coverage are shown in gray, while covered regions are shown in black (host) or orange (transgene). b Transgene insertion site on scaffold Niben101Scf03823. A stretch of undetermined bases (~ 500 bp) within the Nb-1 assembly is indicated in green. The numbers over the cyan vertical lines indicate the junction positions on the Niben101Scf03823 scaffold. The proposed rearrangement of the region is shown in Additional file 1: Figure S4