Whole genome sequencing of a transformable and highly regenerable diploid potato

The heterozygous Solanum tuberosum Group Phureja clone 1S1 has a high regeneration rate, self-fertility, desirable tuber traits and is amenable to Agrobacterium-mediated transformation. To create a contiguous genome assembly, a homozygous doubled monoploid of 1S1 (DM1S1) was sequenced using 44 Gbp of long reads generated from Oxford Nanopore Technologies (ONT), yielding a 736 Mb assembly that encoded 31,145 protein-coding genes. We used trained gene finder and empirical transcript evidence from ONT cDNA to annotate genes in DM1S1. Variant analysis with Illumina reads from 1S1 was used to deduce its alternate haplotype. The final assembly for DM1S1 represents a nearly complete genic space, shown by the presence of 99.6% (C:99.5%[S:97.8%, D:1.7%],F:0.1%,M:0.4%,n:1614) of the Benchmarking Universal Single Copy Orthologs. These genetic and genomic resources provide a toolkit for applications of genome editing in both basic and applied research of potato.