Fig. 1

Input assemblies considered for the pangenome analyses. a Autosomal length of the Bos taurus taurus reference sequence (HER, ARS-UCD1.2) and 19 haplotype resolved assemblies considered during pangenome construction and downstream analyses. Three pangenomes were created with ARS-UCD1.2 [HER] and eleven input assemblies (Brown Swiss [BSW], Piedmontese [PIE], Highland [HIG], Angus [ANG], Original Braunvieh [OBV], Simmental [SIM], Brahman [BRA], Nellore [NEL], gaur [GAU], bison [BIS], yak [YAK]), whereas eight additional Original Braunvieh or Brown Swiss assemblies indicated with red text (OD1, OD2, OS1, OS2, B11, B12, B21, B22) were only considered for downstream analyses. The colour of the bars indicates the primary sequencing technology used to construct the assemblies. The black dashed line indicates the length of ARS-UCD1.2. b Centromeric and c telomeric completeness is generally higher in the HiFi- and ONT- than CLR-based input assemblies. The marker is the sum over the autosomes and error bars indicate the 95% confidence interval. d A tree constructed with mash from the assemblies reveals the expected separation between taurine, indicine and non-cattle. The asterisk indicates the backbone genome used by minigraph