Asymmetrical strand invasion polarity at intermediate mitochondrial repeats. (A) Relative changes from wild type in deep sequence coverage across each environment for repeat CC in msh1 first-generation (left) and advanced-generation (right) mutants were used to define strand invasion polarity. Polarity shown in the lower panel is based on depletion of region 1 relative to region 2 compared to wild type and on an increase in region 3 relative to region 4 compared to wild type. To quantify read depth of flanking regions, we considered all read pairs for which one end mapped to the repeat and the other mapped to the region flanking the repeat. Thus, the length of the flanking sequence is approximately 220 bp. (B) Graphical representation of strand invasion polarities across clusters of repeats in the Arabidopsis Col-0 mitochondrial genome. Polarities were defined by deep sequence analysis using the procedure shown in (A) and confirmed by DNA gel blot analysis. Polarity of strand invasion was established on the basis of which repeat-flanking region displayed an increase in sequence depth and, in the case of class I repeats, a concomitant decrease in sequence depth across the other repeat-flanking region.