cpDNAs with large deletions accumulate in cptk1 mutants. cpDNAs with large deletions accumulate in cptk1 mutants. A, Amplification of recombined cpDNA sequences by PCR using primers mapping far apart in the genome. B, Truncated cpDNA sequences specifically amplified from cptk1 resulting from microhomology-mediated repair processes. The cpDNA region analyzed is represented above, with the IRs (IRA and IRB), SSC, and part of the LSC regions. Scale bar (10 kb) is shown. Primers used for amplification in different combinations are indicated by the black arrowheads. The regions deleted in each sequence are represented, with the small repeats found at the junction borders. Coordinates on the genome are indicated on the left. (C) Coverage of reads mapped to the cpDNA following deep-sequencing of total DNA from wild-type (WT) and cptk1 leaves. The range is indicated on the upper left of the plots. D, Reads identified as corresponding to rearranged cpDNA molecules and their distribution among different genomic regions. Monique Le Ret et al. Plant Physiol. 2018;178:1643-1656 ©2018 by American Society of Plant Biologists