Fig. 3: Structural variations in two single male flies.

a Counts of various types of SVs in ISO1-1/2. VNTR indicates the variable number of tandem repeats. b The proportion of shared or individual-specific SVs in terms of homozygosity and occurrence in fly families. c The distribution of transposons in ISO1-1/2. For DNA and LINE transposons, individual element names are directly displayed, as only one element was identified. In the case of LTR retrotransposons, names of superfamilies are provided, as multiple elements were identified. d Two complex transposition examples: hobo insertion associated with a short triplication involving TSD on one side and a duplication of obst-B (top); and Jockey insertion associated with a deletion (bottom). Arrows indicate sequence arrangement order. In the top example, a one-bp microhomology (“T”) is marked in red, while the TSD or hobo recognition motif appears in yellow. For obst-B, the green box includes the sequences duplicated from the obst-B locus, larger orange boxes represent coding exons, smaller ones denote UTRs, and connecting lines indicate introns. Triplication is error-prone when “GA” is missing and an extra “A” is inserted. In the bottom example, the deletion is marked in grey. e A list of nine complex transpositions. f Distribution of non-B DNA motif counts on TE insertion sites (up- and downstream 200-bp window) and random 400-bp windows. Complex transposition represents TE insertion with extra duplications and/or deletions. The bar indicates the interquartile range, the whiskers indicate minima and maximums, and the thick line indicates the median. g A schematic model to explain the formation of complex transpositions through error-prone DNA repair.