Fig. 5: SV-based dendrograms.

a All dendrograms followed the same overall topology, with gaur (G) and Nellore (N) clearly differentiated while the taurine cattle displayed three possible arrangements, with either the Original Braunvieh (O), Piedmontese (P), or Brown Swiss (B) more distantly related. The colored boxes represent the three possible orderings of the taurine cattle. b Box plots of 20 randomly constructed pangenomes with either all hifiasm, all Shasta, or mixing hifiasm and Shasta assemblies, as well as the low coverage equivalents show good agreement on autosomes displaying a specific topology (color from panel a). The box plots represent the median (center line), first and third quartile (box bottom and top), and 1.5x the interquartile range (whiskers). Outliers beyond this range are marked by diamond markers. The SNP dendrogram, based on parental short reads, generally predicted different topologies. c Pangenomes including all 30 assemblies from hifiasm (h), Shasta (s), Peregrine (p), Flye (f), HiCanu (c), and Raven (r) predict the same overall topology without ONT or HiFi specific branches. d An UpSet plot of a taurine cattle pangenome (Piedmontese, Brown Swiss, and the paternal [O1] and maternal [O2] haplotypes of Original Braunvieh) reveals inter-breed variation (green) as well as intra-breed variation in the Original Braunvieh haplotypes (red & orange). We can also identify phasing error candidates in the Original Braunvieh Shasta assemblies, where SVs are common to both Shasta assemblies but not both hifiasm assemblies (light and dark blue).