A chromosome-level genome assembly of Solanum brevicaule (PI 473011) Y1-5, a wild potato relative with robust resistance to potato cyst nematodes

Potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are globally recognized quarantine pests that can cause severe yield losses in potatoes if left uncontrolled. Deploying host resistance remains the most effective, economical, and environmentally sustainable strategy for PCN control. The U.S. Potato Genebank (USPG) maintains a rich collection of wild potato species, providing a valuable resource for discovering novel resistance to PCN. In this study, we identified a Solanum brevicaule clone (PI 473011; designated Y1-5) from the USPG that exhibits robust resistance to both PCN species. We sequenced the whole genome of Y1-5 using PacBio high-fidelity (HiFi) sequencing technology and generated a haplotype-resolved assembly, with genome sizes of 763.49 Mb and 764.93 Mb for haplotypes 1 and 2, respectively. Repeat elements accounted for approximately 65% of the genome, while gene prediction identified 80,021 protein-coding genes, over 96% of which were functionally annotated. A comprehensive set of genes encoding nucleotide-binding and leucine-rich repeat (NLR) proteins‒intracellular receptors that mediate disease resistance‒was identified in the annotated genome. NLR genes were particularly enriched on chromosomes 4, 6, and 11. Importantly, Y1-5 was found to encode more coiled-coil-type NLRs (CNLs) than several previously sequenced wild Solanum clones. These findings suggest that Y1-5 may serve as a promising new source of resistance to potato diseases. Development of this genomic resource is valuable for understanding the mechanisms of PCN resistance and for supporting potato breeding efforts to develop varieties with durable nematode resistance.