A Complete Nuclear Genome Sequence from the Extinct Eurasian Wild Aurochs (Bos primigenius)

The extinct wild Eurasian aurochs (Bos primigenius) was the progenitor of domestic taurine cattle (B. taurus). Although genetic and archaeological studies pinpoint the Near East as the centre of origin for Bos taurus, recent genetic evidence suggests that historical admixture may have occurred between domestic taurine cattle and wild aurochsen. Here, we present analyses of the first complete nuclear genome from an archaeologically-verified and exceptionally well-preserved aurochs humerus bone sample recovered from a cave site in Derbyshire, England and radiocarbon-dated to 6,738 ± 68 calibrated years before present (laboratory sample code: CPC98). Previous work in our laboratory has shown that this aurochs possessed a haplogroup P mitochondrial sequence, which predominates in Northern European aurochs samples examined to-date. For the present study, DNA extracts from the CPC98 humerus bone were prepared for Illumina^® short read, high-throughput DNA sequencing. A consensus CPC98 B. primigenius nuclear genome was assembled, using the complete B. taurus genome. A mean read depth of 6.2× was generated from 470 million reads aligned to unique locations in the template genome, yielding a genome coverage of 2.37 Gb. Phylogenetic analyses using Illumina^® BovineSNP50 BeadChip genotype data from modern B. taurus and B. indicus cattle place the CPC98 sample as an outgroup to all modern taurine cattle, consistent with common ancestry of taurine cattle from Near-Eastern aurochs. We have performed comparative analyses of coding sequences or candidate regulatory regions associated with genes using high-throughput DNA sequencing data from modern B. taurus and B. indicus cattle to identify over 300 genes in which CPC98 and indicine cattle share potentially functional SNP or indel alleles not seen in taurine cattle. Selection at these genes throughout the history of domestication and selective breeding may have played a key role in shaping the genome of modern taurine cattle.