A comprehensive overview of mitochondrial DNA insertions in the nuclear genome of the pig

The integration of nuclear mitochondrial DNA into the mammalian genomes is an ongoing but rare evolutionary process that produces nuclear sequences of mitochondrial origin (NUMTs). In this study we identified and analysed NUMTs of the porcine genome. We first constructed a comparative distribution map of NUMTs in the Sscrofa11.1 reference genome and in other 14 assembled and drafted pig genomes (of Asian and European origin). Then, a total of 581 whole genome sequencing datasets, from 35 different breeds or populations, were analysed for the discovery of recently integrated and polymorphic NUMT positions. Overall, we built a comprehensive catalogue of more than 500 NUMTs, some of which were not included in the assemble genomes. Breed-specific NUMTs as well as segregating NUMTs were also identified. This work lays the base for in-depth studies on the phylogeny of Sus scrofa populations.