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

被引：4

作者：

Mari, Rebecca Serra ^{[1
,2
]}

Schrinner, Sven ^{[3
,4
]}

Finkers, Richard ^{[5
,6
]}

Ziegler, Freya Maria Rosemarie ^{[7
,8
,9
,10
]}

Arens, Paul ^{[6
]}

Schmidt, Maximilian H. -W. ^{[7
,8
]}

Usadel, Bjoern ^{[7
,8
,9
,10
]}

Klau, Gunnar W. ^{[4
,7
]}

Marschall, Tobias ^{[1
,2
,3
]}

机构：

[1] Heinrich Heine Univ Dusseldorf, Inst Med Biometry & Bioinformat, Med Fac, Dusseldorf, Germany

[2] Heinrich Heine Univ Dusseldorf, Univ Hosp Dusseldorf, Dusseldorf, Germany

[3] Heinrich Heine Univ Dusseldorf, Ctr Digital Med, Dusseldorf, Germany

[4] Heinrich Heine Univ Dusseldorf, Fac Math & Nat Sci, Algorithm Bioinformat, Dusseldorf, Germany

[5] Gennovat BV, Agro Business Pk 10,PW, NL-6708 Wageningen, Netherlands

[6] Wageningen Univ & Res, Plant Breeding, Wageningen, Netherlands

[7] Heinrich Heine Univ Dusseldorf, Cluster Excellence Plant Sci CEPLAS, Dusseldorf, Germany

[8] Forschungszentrum Julich, Inst Bio & Geosci, Bioinformat IBG 4, Julich, Germany

[9] Bioecon Sci Ctr, c-o Forschungszentrum Julich, Julich, Germany

[10] Heinrich Heine Univ Dusseldorf, Fac Math & Nat Sci, Biol Data Sci, Dusseldorf, Germany

来源：

GENOME BIOLOGY | 2024年 / 25卷 / 01期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1186/s13059-023-03160-z

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：19

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