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 protein-coding genes encoding 44,851 gene models that had
a significantly improved representation of conserved orthologs compared to
the previous annotation. The new assembly has improved
 contiguity with a 595-fold increase in N50 contig size, 99%
reduction in the numbersof 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. Conclusions: 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.