Extended Data Fig. 2: Sequence features for the breakpoints of the three Sb supergene inversions, In(16)1 [chr16:14,549,064-24,031,576], In(16)2 [chr16: 13,705,210-24,030,990], and In(16)3 [chr16: 12,612,565-13,683,100].

a, The red and blue blocks represent the 200nt segments adjacent to the In(16)1 proximal breakpoint (red arrow), and the magenta and gold blocks represent the 200nt segments adjacent to the distal breakpoint (black arrow) of this inversion. The blue and magenta blocks, and the segment between them, are inverted between SB and Sb, as indicated by the grey arrow. The Sb haplotype has a 9nt insertion at the proximal breakpoint and a 27,953nt insertion at the distal breakpoint (black blocks). Percentages are the sequence similarity (disregarding deletions) between SB and Sb for the 200nt segments immediately upstream and downstream of the breakpoints. b, The In(16)1 proximal breakpoint (red arrow) on the SB haplotype is located in exon 1 of the “F-box/WD repeat-containing protein 4-like” gene (NCBI Gene symbol: LOC105199310; green blocks depict exons; pale green represents the UTRs and dark green the coding sequence [CDS] regions). The red and blue lines under exon 1 indicate the segments that are upstream or downstream of the proximal breakpoint. c, The In(16)1 distal breakpoint (black arrow) on the SB haplotype is located in the 5′ UTR of the “Phosphoglycerate mutase 2” gene (NCBI Gene symbol: LOC105193833; green blocks depict exons; pale green represents the UTRs and dark green the CDS regions). The red and blue lines under exon 1 indicate the segments that are upstream or downstream of the distal breakpoint. d, The red and blue blocks represent the 200nt segments adjacent to the In(16)2 proximal breakpoint (red arrow), and the magenta and gold blocks the 200nt segments adjacent to the distal breakpoint (black arrow) of this inversion. The red block contains the 3′ end of a Jockey-like mobile element. The Sb haplotype has a 14nt insertion (black block) at the proximal breakpoint as well as a second Jockey-like mobile element gene (pink block) and a 10,310nt insertion (black block) just upstream of the distal breakpoint. e, The In(16)2 proximal breakpoint (red arrow) in the SB haplotype is located in the single exon (dark green) of a Jockey-like mobile element. f, The In(16)2 distal breakpoint (black arrow) in the SB haplotype is located in the 5′ UTR of the uncharacterized gene “LOC105193832” (containing 3 exons depicted as green blocks; pale green represents the UTR and dark green the CDS region). g, The red and blue blocks represent the 200nt segments adjacent to the In(16)3 proximal breakpoint (red arrow), and the magenta and gold blocks the 200nt segments adjacent to the distal breakpoint (black arrow) of this inversion. The SB haplotype has a 334nt insertion at the proximal breakpoint and a 3,100nt insertion at the distal breakpoint (black blocks); both are absent in the Sb haplotype, which instead has a 62,682nt insertion at the proximal breakpoint and a 142nt insertion at the distal breakpoint (black blocks). h, The In(16)3 proximal breakpoint (red arrow) in the SB haplotype is located just upstream of a region containing 24 dinucleotide (AT) repeats. i, The In(16)3 distal breakpoint (black arrow) in the SB haplotype is located within a region containing 21 dinucleotide (AT) repeats.