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

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

2024

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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