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

Author:

Serra Mari RebeccaORCID,Schrinner SvenORCID,Finkers Richard,Ziegler Freya Maria Rosemarie,Arens Paul,Schmidt Maximilian H.-W.,Usadel BjörnORCID,Klau Gunnar W.ORCID,Marschall TobiasORCID

Abstract

AbstractPotato 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.

Funder

Universitätsklinikum Düsseldorf. Anstalt öffentlichen Rechts

Publisher

Springer Science and Business Media LLC

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