Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Hequan Sun,Manish Goel,Kat Folz-Donahue,Bruno Huettel,Kristin Krause,Korbinian Schneeberger,Wen-Biao Jiao,Christian Kukat,José A Campoy

doi:10.1038/s41588-022-01015-0

Abstract

Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.

Highlights

Potato (Solanum tuberosum) is an important tuber crop and is among the five most produced crops in the world
The reference sequence for potato was generated from a double haploid plant, DM1-3 516 R44 (DM) and was initially published in 20114 and continuously improved over the past years including a recent update based on long read sequencing[5,6]
We generated an assembly of the autotetraploid genome of S. tuberosum ‘Otava’ using high-quality long PacBio HiFi reads (30× per haplotype) using hifiasm[19] (Fig. 1, Supplementary Table 1 and Extended Data Fig. 1; Methods)

Summary

Introduction

Potato (Solanum tuberosum) is an important tuber crop and is among the five most produced crops in the world. The reference sequence for potato was generated from a double haploid plant, DM1-3 516 R44 (DM) and was initially published in 20114 and continuously improved over the past years including a recent update based on long read sequencing[5,6]. Another major advancement in potato genomics was the recent assembly of a heterozygous diploid potato, RH89-039-16 (RH)[7]. This haplotype-resolved genome was generated from a variety of different sequencing technologies and phase information from a genetic map derived from selfed progeny. Even though straightforward in its application, chromosome conformation capture sequencing can lead to haplotype switch errors and requires additional efforts such as genetic maps for correction[7,9,18]

Methods

Results

Conclusion