Potato wild relatives (Solanum section Petota) are a source of genetic diversity for climate-smart improvement of modern cultivars (S. tuberosum). Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. The allotetraploid S. acaule Bitter. has been used to introgress cold tolerance into potato cultivars. The current study presents the subgenomes of S. acaule.  The genome assembly is 1.34 Gb in 24 chromosomes with an N50 of 56.2 Mb, making the theoretical tetraploid S. acaule genome 2.68 Gb. The dataset contains annotations for the S. acaule genome assembly. All sequence data in this study is deposited in NCBI and available under BioProject PRJNA779368, PRJNA1023364 and PRJNA1023365.