Fig. 1: Overview of bovine trios.

a–c Representative animals for the parents of the three bovine trios and the respective F1s (OxO, NxB, and GxP) examined in this study. The OxO and GxP were female, while the NxB was male. d The three respective F1s were sequenced to 32-, 52-, and 51- fold HiFi coverage, with read N50 of 20, 21, and 14 Kb. ONT sequencing was performed to 36-, 103-, and 152-fold coverage respectively, with read N50 of 65, 45, and 49 Kb. Coverage is determined with respect to an assumed genome size of 2.7 Gb. F1 short reads (SR) were collected to 31-, 23-, and 37-fold coverage. e Separating F1 reads into parental haplotype bins improved with increasing heterozygosity for HiFi, but F1 reads were nearly 100% separable for ONT even at low heterozygosity (color from panel d). f HiFi reads were assembled with hifiasm, HiCanu, and Peregrine, while ONT reads were assembled with Shasta, Flye, and Raven. Green font indicates the tools used to produce the assemblies that are discussed in detail. Assemblies were assessed individually for quality metrics (blue lines) as well as integrated together into pangenome analyses (red lines).