Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.

ABSTRACT: Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive select

SUBMITTER: Low WY 

PROVIDER: S-EPMC7190621 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature