The genome of tropically adapted Brahman cattle (Bos taurus indicus) reveals novel genome variation in production animals

Recent advances in sequencing technology have revolutionised access to large scale genomic data that can be assembled into a platinum quality genome. Here we present a high quality genome assembly with less than 300 gaps of a Brahman cow (B. taurus indicus). The assembly was generated using 195GB of PacBio and 169GB of Oxford Nanopore Technologies sequence data. The high quality genome assembly allows us to identify substantial GC content variation that is positively associated with gene rich islands, and negatively associated with genetic variation in the form of structural variants. In addition, 92371 structural variants that are segregating in the brahman population were identified. Gene ontology analysis revealed that genes with varying copy numbers were enriched for gene ontology terms related to immune function. This analysis has revealed the complex structure of the mammalian genome of an outbred species, and identifies the ability of long read data from diploid species can be used to not only assemble a high quality genome, but also discover novel genetic variation within that genome.