Figure 4. mtDNA excision cascades, quantification of colony structural diversity, and contingency in subsequent excisions.
(a) Example locations of alignments from mapped reads (linear alignments here are bounded by breakpoints) observed in long reads within Petite sample 1b. Endpoints of arrows are the mean breakpoint location for the cluster of breakpoint signals that punctuate alignments in repeats. The first panel shows a primary alignment which has the longest span on the genome and exists in long repeats. The second panel shows smaller alternate alignments that exist within detected repeated structures at a lower frequency. Also included in gray is a sequencing coverage map of this sample. (b) Excision cascade in Petite sample 1b. This plot shows the same primary repeat unit in the first panel, and its contribution to total mitochondrial content as a percentage. The second panel shows the forms of alternate structures present in the same sample which were derived from the primary alignment, alongside their mitochondrial contribution as a percentage. (c) A schematic of the multiplicity of excision events that generate alternate repeat units. The primary concatemer is the red structure, where arrows indicate the alignments (contiguous regions of the reference) that make up the repeating units. The primary breakpoint between these alignments is denoted as a red arc. Colored rectangles above the alignments with the same colors indicate regions of homology in the primary structure that can interact to produce an excision. Dotted rectangles indicate excision sites that produce the alignments shown below them. In the lower half of the figure, five distinct excision events that can generate different repeat units are shown. These are grouped into three excision classes in the data: Type I, where excision occurs within primary alignments, Type II, where excisions span the existing primary breakpoint, and Type III, where excisions share one edge of the primary breakpoint. (d) The frequency of each class of excision across 35 alternate structures detected in the data. (e) A plot of the distance between alternate alignment edges and their closest primary alignment edge across all three classes, normalized by primary alignment length.