Generating a sequence map of the pig pan-genome

Abstract Pigs (Sus scrofa) exhibit diverse phenotypes in different breeds shaped by the combined effects of virous local adaptation and artificial selection. To comprehensively characterize the genetic diversity of pigs, we constructed a pig pan-genome by comparing 11 representative pig breeds of genome assemblies with the reference genome. Approximately 72.5 Mb non-redundant sequences were identified as “pan-sequences”. On average, 41.7 kb of spurious heterozygous SNPs per individual were removed and 12.9 kb novel SNPs per individual were recovered using pan-genome, thereby providing enhanced resolution for genetic diversity of different pig populations. Analysis using Hi-C, RNA-seq data and homolog annotation indicates that these pan-sequences contain protein-coding exons and regulatory elements. Our supplied pan-sequences can further improve the interpretation of local 3D genomes. This pan-genome as well as the accompanied web-based repository will serve as a primary resource for genetic diversity exploration to promote agricultural production and biomedical research.