Building the Sequence Map of the Sheep and Goat Pan-Genome

Sheep and goats are regarded as the first domesticated livestock species. The understanding of Caprinae speciation and domestication will be of great value in understanding the subsequent domestication of the full repertoire of Euroasian livestock species. At present, huge amounts of re-sequencing data from sheep and goats are available on public database, waiting for integrated evaluation and use. We have generated the de novo genome assemblies of four wild Caprinae species, including Pseudois nayaur, Ammotragus lervia, Capra Ibex and Ovis ammon. Together with the other six independently available assemblies (ARS1 and CHIR_2.0 of goats, Oar4.0 of sheep, CapAeg1.0 and Caeg1 of wild goats, Ooril of wild sheep), a well merged Caprinae pan-genome was constructed, which will have great advantage over a single sheep or goat reference assembly in exploring genomic variations, especially for deleted copy number variations. This pan-genome is comprised of 2.76 Gb core sequences and ~782 Mb dispensable sequences. Based on our pan-genome and over a thousand re-sequencing data from wild/domestic goat and sheep samples, we have identified abundant gain/loss events in Caprinae species, a considerable proportion of which are specific to goat or sheep. Some of the goat or sheep specific gain sequences are accompanied with the acquirement of adaptive/agronomic genes. Meanwhile, many ruminant conserved genes are found to be lost in certain species. Notably, ~683 retrogenes were also identified. We speculate that these gain/loss events and retrogenes could have shaped the adaptation or domestication of goats and sheep. In summary, our findings have revealed the distribution of presence/absence variations across subfamily Caprinae, and summarized the general pattern of their origin and diffusion in domestication history, which also demonstrated that pan-genome could promote our understanding of livestock domestication and help identifying candidate causal mutations.