Building genomic resources to facilitate the study and use of Solanum microdontum, a wild relative of cultivated potato.

Solanum microdontum Bitter is a diploid wild Andean relative of potato that has shaped the domestication and adaptation of modern cultivated potato to diverse environments. S. microdontum has the potential to provide a wealth of untapped genetic material for use in addressing current challenges in potato breeding. Here, we report a high-quality 772 Mb reference genome sequence for S. microdontum that is anchored to 12 chromosomes. The resulting genome assembly has 99.0% complete benchmarking universal single copy orthologs and an N50 scaffold length of over 57 Mb, indicating a high level of completeness. Annotation of the assembly resulted in the identification of 37,324 protein-coding genes and 65% repetitive sequence. A total of 1,187 nucleotide-binding leucine-rich repeat genes were predicted from the assembly, of which, 93.1% overlapped an annotated high-confidence gene model. A k-mer-based kinship matrix derived from a 107-member S. microdontum diversity panel revealed an underlying population structure that corresponds to geographic proximity. The S. microdontum dataset enhances publicly available potato genome resources by providing breeders with genetic, molecular, and germplasm resources for newly developed diploid potato breeding programs.