Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
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, hindering the use of genomic data in breeding strategies. Here, 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, which is available in many plant breeding settings, to achieve chromosomal clustering and haplotype phasing directly on the assembly graph. This involves a novel strategy for the analysis of k-mers unique to specific graph nodes. Our approach generates assemblies of individual chromosomes with phased haplotig N50 values of up to 13 Mb and haplotig lengths of up to 31 Mb. This major advance provides high-quality assemblies with haplotype-specific sequence resolution of whole chromosome arms and can be applied in common breeding scenarios where collections of offspring are available.
Serra Mari Rebecca、Finkers Richard、Usadel Bj?rn、Marschall Tobias、Schrinner Sven、Klau Gunnar W.、Schmidt Maximilian H.-W.、Arens Paul
Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine UniversityGennovation B.V.||Plant Breeding, Wageningen University & ResearchCluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University D¨1sseldorf||Forschungszentrum J¨1lich, Institute of Bio and Geosciences, Bioinformatics (IBG-4)||Bioeconomy Science Center, c/o Forschungszentrum J¨1lich||Biological Data Science, Heinrich Heine University D¨1sseldorfInstitute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine UniversityAlgorithmic Bioinformatics, Heinrich Heine University D¨1sseldorfAlgorithmic Bioinformatics, Heinrich Heine University D¨1sseldorf||Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University D¨1sseldorfCluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University D¨1sseldorf||Forschungszentrum J¨1lich, Institute of Bio and Geosciences, Bioinformatics (IBG-4)Plant Breeding, Wageningen University & Research
农业科学技术发展遗传学植物学
Serra Mari Rebecca,Finkers Richard,Usadel Bj?rn,Marschall Tobias,Schrinner Sven,Klau Gunnar W.,Schmidt Maximilian H.-W.,Arens Paul.Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/2022.05.10.491293.点此复制
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