Fig. 6: Topology of a tandem duplication on BTA6.

a, b Example subgraphs of the promoter region of GC from (a) hifiasm- and (b) Shasta-based pangenomes respectively. Reference paths (including those in bubbles) are colored gray, while the tandem duplications are orange. Two insertions observed uniquely in Nellore and gaur haplotypes are blue, shown in circles 1 and 2. Complex bubbles generally have suboptimal topologies due to the lack of base-level alignment. For example, the 725 bp insertion is obvious in a), but appears as the difference between a 1400 bp and 667 bp path in (b). However, both subgraphs identify the approximately 200 bp (1) and 700 bp (2) insertions in Nellore and gaur, as well as the tandem duplication in Brown Swiss and Original Braunvieh. c The 12 Kb repeat structure (orange) is clearly identified by RepeatMasker across all assemblies, shown here for the ARS-UCD1.2 reference and Shasta assemblies for gaur, Nellore, Piedmontese, Brown Swiss, and Original Braunvieh. The two marked gaur/Nellore insertions (1&2) are consistent with the pangenomes in (a, b). One additional copy in Brown Swiss and Original Braunvieh is shown (yellow), while the tandem duplication eventually ends with a similar repeat (Bov-tA3, black) to the other assemblies. d The identified CNV region shows clear coverage increase in only Brown Swiss and Original Braunvieh, across both HiFi and ONT haplotype-resolved reads, although the HiFi reads suggest one less additional copy than ONT reads. e F1 short reads also show increased coverage for the NxB and OxO trios. The NxB coverage increase is consistent with only the Brown Swiss haplotype carrying additional copies.