Fig. 2: Alignment of single PacBio reads to the inversion breakpoints on chromosomes 6, 12, 17, and 23.
From: The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring
The reference haplotype represents the sequence from the reference assembly, while the assembly of the alternate haplotype is shown below. Blue arrows represent the orientation of sequences in the two haplotypes. The breakpoints are indicated as vertical black lines. Alignments of single PacBio HiFi reads to the reference and alternate haplotypes are indicated with thick red arrows. Genes near the breakpoints are indicated above the reference sequence and described in Supplementary Data 1. a Chromosome 6 (modified from ref. 31). A part of the HiFi read maps to unplaced_scaffold (un_sc) 699 (indicated by red dotted lines) as the reference assembly is not scaffolded at this region. b Chromosome 12. c Chromosome 17 (modified from ref. 31). d Chromosome 23. A part of the HiFi read maps to un_sc 1537 (indicated by red dotted lines) as the reference assembly is not scaffolded at this region. The dot plots below the read alignments for chromosomes 12 and 17 compare inverted duplications flanking the breakpoints, which are also indicated as yellow boxes on the inversion haplotypes. The length of the inverted duplications on chromosomes 12 and 17 are 8 kb and 3 kb, respectively.
