An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation

Solanum verrucosum is a wild diploid potato species notable for carrying the uncharacterized Rpi-ver1 gene conferring resistance to Phytophthora infestans, possessing unusually structured centromeres, and exhibiting the rare trait of self-compatibility, the genetic basis of which remains unknown. Here, we present a high-quality genome assembly and annotation of S. verrucosum accession CPC54. A comprehensive inventory of resistance genes is provided, and candidate genes for Rpi-ver1 are identified through remapping approaches. The sequence and epigenetic landscape of centromeres are resolved, revealing a mosaic of repeatless and repetitive domains. These centromeres consist of tandem arrays of kilobase-sized repeats, some of which show signatures of transposable element origin. Specific subfamilies of CRM and Tekay elements appear to have adapted to centromeric regions. The basis of self-compatibility in S. verrucosum is investigated with respect to the S-RNase gene, which is found to be present and intact but expressed at very low levels. Notably, upstream insertions of transposable elements are present that may interfere with its expression.