Fig. 1

Organization of the nuclear genome of GK-038B07 with a focus on translocations, inversions and T-DNA structures. A: Ideograms of the chromosomes display the reciprocal fusion of Chr3 and Chr5 as well as a 2 Mbp inversion between two T-DNA arrays at the fusion sites; numbers indicate end points of pseudochromosome fragments according to TAIR9. Chromosomes depicted in grey match the Col0 sequence. The insert displays the color codes used for all five chromosomes; N, northern end of chromosome; S, southern end of chromosome. B-E: Visualization of the four T-DNA insertion loci of GK-038B07 resolved by local assembly. LB and RB, T-DNA left and right border; dark red, bona fide T-DNA sequences located between the borders; light red, sequence parts from the binary vector backbone (BVB); numbers above the red bar indicate nucleotide positions with position 1 placed at the left end of LB in the binary vector which makes position 4 the start of the transferred DNA [13]; numbers below the colored bars indicate pseudochromosome positions according to TAIR9