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

TLDR

The cultivated potato is a major vegetable crop, and its genome was first sequenced in 2011 using short‑read shotgun sequencing. The study aims to produce an updated, chromosome‑scale reference genome for the DM1‑3 516 R44 potato clone using Oxford Nanopore long reads and Hi‑C scaffolding. The authors generated the assembly with Oxford Nanopore long reads and Hi‑C scaffolding, and annotated 32,917 protein‑coding genes using full‑length cDNA sequencing. The v6.1 assembly spans 741.6 Mb (87.8 % of the estimated 844 Mb genome), has a 595‑fold increase in N50 contig size, 99 % fewer contigs, a 44‑fold increase in scaffold N50, an LTR‑AI score of 13.56, and includes 32,917 high‑confidence genes and annotated centromeres, achieving reference‑quality genome and annotation.

Abstract

Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 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 minimal cost.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 complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes.Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.