학술논문
Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
Document Type
Academic Journal
Author
Source
Genome Biology (Online Edition). January 19, 2024, Vol. 25 Issue 1
Subject
Language
English
Abstract
Author(s): Rebecca Serra Mari[sup.1,2], Sven Schrinner[sup.3,2], Richard Finkers[sup.4,5], Freya Maria Rosemarie Ziegler[sup.6,7,8,9], Paul Arens[sup.5], Maximilian H.-W. Schmidt[sup.6,7], Björn Usadel[sup.6,7,8,9], Gunnar W. Klau[sup.3,6] and Tobias Marschall[sup.1,2] Background Polyploidy is common in [...]
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.
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.