Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
Rebecca Serra Mari | Sven Schrinner | Richard Finkers | Freya Maria Rosemarie Ziegler | Paul Arens | Maximilian H.-W. Schmidt | Björn Usadel | Gunnar W. Klau | Tobias Marschall
Abstract Potato is one of the world’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses a major computational challenge. 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 to achieve chromosomal clustering and haplotype phasing on the assembly graph. Our approach generates high-quality assemblies of individual chromosomes with haplotype-specific sequence resolution of whole chromosome arms and can be applied in common breeding scenarios where collections of offspring are available.
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