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

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.

SUBMITTER: Serra Mari R

PROVIDER: S-EPMC10797741 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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

Serra Mari Rebecca R Schrinner Sven S Finkers Richard R Ziegler Freya Maria Rosemarie FMR Arens Paul P Schmidt Maximilian H-W MH Usadel Björn B Klau Gunnar W GW Marschall Tobias T

Genome biology 20240119 1

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-qual ...[more]

PMID: 38243222

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