Construction of a chromosome-scale long-read reference genome assembly for potato

Background: Worldwide, the cultivated potato, Solanum tuberosum L., is the number one vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at a minimal cost.

Findings: Here, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C) yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8 %) of the estimated 844 Mb genome, of which, 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length cDNA sequencing enabled annotation of 32,917 high-confidence pro...