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. 2019 Jan 18;15(1):e1007819. doi: 10.1371/journal.pgen.1007819

Fig 2. T-DNA integration induced large scale rearrangements in the SAIL_232 genome.

Fig 2

Two T-DNA induced translocations occurred on chromosomes 3 (light blue) and 5 (lime green). (a) Inverted translocation of a 1.1 Mb segment split at a T-DNA insertion site (blue bar) was moved to a distal part of the same chromosome arm. The other chromosome arm was swapped with chromosome 5 (d). (b) The ONT assembly identified the underlying T-DNA inserts (boxed arrows) including a breakpoint (red line). (c) The chromosome swap joint site contains four pCSA110 vector fragments (boxed arrows) interspersed with breakpoints. These insertions change the GC signature in the respective region, and are confirmed by BNG alignment. (e) BNG maps (blue), aligned to Arabidopsis reference TAIR10 (green), are able to phase the WT (top) and T-DNA haplotypes (T-DNA; bottom) for this particular insertion site. Black lines indicate Nt.BspQI nicking sites.