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

作者：Rebecca Serra Mari, Sven Schrinner, Richard Finkers, Freya Maria Rosemarie Ziegler, Paul Arens, Maximilian Schmidt, Björn Usadel, Gunnar W. Klau, Tobias Marschall · 发表于：Genome biology · 年份：2024 · DOI：10.1186/s13059-023-03160-z · 被引用次数：28 · 研究领域：Plant Disease Resistance and Genetics、Chromosomal and Genetic Variations、Plant Pathogens and Resistance

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.