Table 1 Key findings summary of ONT-sequenced GABI-Kat T-DNA insertion lines

GK-038B07

2

0 (1)^b

4^c

3

FST-predicted insertion in Chr5 is part of a fusion of Chr3 and Chr5, 2 T-DNA arrays detected at translocation fusion points of which one contains in addition an inversion of ~ 2 Mbp fused with another T-DNA array, additional insertion of a complex T-DNA array in Chr1.

GK-089D12

1

1

2

1

Fusion of Chr3 and Chr5, FSTs are derived from the single DNA::genome junction that contains LB, both translocation fusions contain mostly canonical T-DNAs, failure to confirm 2nd T-DNA::genome junction explained by shortened T-DNA.

GK-430F05

1

1

3

2

Three T-DNA insertion sites, two complex T-DNA arrays with one containing more than 5 kbp BVB^d, the confirmed T-DNA insertion in Chr3 is complex, no theoretical explanation for failure of confirmation PCR at 2nd DNA::genome junction, one insertion in the pericentromeric region of (probably) Chr4 containing a rearranged RB region.

GK-654A12^d

1

1

2^c

1

Fusion of Chr1 and Chr4 with a complex T-DNA array that also contains BVB, Chr1-part of the fusion predicted by FST, the compensating fusion of Chr4 and Chr1 does not contain T-DNA at the translocation fusion point, translocation explains failure to confirm 2nd T-DNA::genome junction, additional insertion of a T-DNA array in Chr2 with a 162 bp duplicated inversion at the integration site.

GK-767D12

1

1

2

1

Large segmental duplication and inversion at the predicted insertion site, a long T-DNA array also containing BVB present at the southern end of the segmental duplication, inversion explains failure to confirm 2nd T-DNA::genome junction, the northern fusion point of the inverted segmental duplication does not contain T-DNA, another canonical T-DNA insertion in Chr2 but with 4 Mbp distance.

GK-909H04

1

1

3

2

The predicted T-DNA insertion contains an inverted duplication of 20 kbp at the integration site explains why the 2nd T-DNA::genome junction could not be confirmed, integration of 652 bp derived from the plastome at the northern fusion point of the duplication but no T-DNA, two additional canonical T-DNA insertions in Chr1 and Chr2.

GK-947B06

1

1

2

1

Complex T-DNA array insertion of 3 T-DNAs at the predicted insertion site in Chr1, no theoretical explanation for failure of the confirmation PCR at the 2nd DNA::genome junction, additional complex insertion containing 2 T-DNAs and BVB on Chr2.