Fig. 3

Disentangling complex variation at the K locus with the pangenome graph. A A one-dimensional view of the pangenome subgraph for the K locus, with nodes colored by path coverage (i.e., the number of times a haplotype path passes through them) and the locations of the genes PRLR and SPEF2 denoted. Huxu shows double path coverage of part of the locus, as well as an insertion. Alignment verified that this insertion contains the sequence of the avian leukosis virus ev21. B A two-dimensional view of the same graph, showing both the tandem duplication and the ev21 insertion. C At the junction where the paths containing the tandem duplication deviate from the paths that do not, all paths begin by traversing edge e1 and moving through most of the sequence of the K locus. However, at the e2/e3 fork, a path can either traverse e2 to leave the K locus, or traverse e3 and e4 to include a tandem duplication of parts of PRLR and SPEF2. D A more detailed view of the ev21 insertion, showing the two possible paths at this juncture: a path can traverse edge e5 to skip the insertion, or it can traverse edge e6, then the ev21 sequence, then e7, to include the insertion. E Linear untangled view of the locus, confirming previous studies of the structure of the locus, with a tandem duplication of parts of both genes and an insertion of the ev21 sequence