Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data

Abstract

Potato is one of the worlds major staple crops and like many important crop plants it has a polyploid genome. Polyploid haplotype assembly poses a major computational challenge, hindering the use of genomic data in breeding strategies. Here, we introduce a novel strategy for the assembly of polyploid genomes and present an assembly of the autotetraploid potato cultivar Altus. Our method uses low-depth sequencing data from an offspring population, which is available in many plant breeding settings, to achieve chromosomal clustering and haplotype phasing directly on the assembly graph. This involves a novel strategy for the analysis of k-mers unique to specific graph nodes. Our approach generates assemblies of individual chromosomes with phased haplotig N50 values of up to 13 Mb and haplotig lengths of up to 31 Mb. This major advance provides high-quality assemblies with haplotype-specific sequence resolution of whole chromosome arms and can be applied in common breeding scenarios where collections of offspring are available.