FIGURE 1.

Special interest genomic regions (SIGRs) regulate ecologically important traits, but are difficult to analyse using classical genomic methods since suppressed recombination leads to high repeat densities. Haplotype divergence, represented as distinct blue and black SIGR boxes, further hampers the use of single reference genome assemblies. (a) For illustration purposes, example recombination frequencies in centimorgan (cM) per megabase pair (Mb) are shown along a chromosomal region including a SIGR. (b) The repeat density (in %) is shown for the same genomic region. Blue and orange colours indicate low and high densities of repetitive DNA sequences, respectively. In the close‐up of the SIGR, genes are shown as red arrows and repeats as orange boxes