Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing

被引：377

作者：

Alonge, Michael ^{[1
]}

Lebeigle, Ludivine ^{[2
]}

Kirsche, Melanie ^{[1
]}

Jenike, Katie ^{[1
]}

Ou, Shujun ^{[1
]}

Aganezov, Sergey ^{[1
]}

Wang, Xingang ^{[3
]}

Lippman, Zachary B. ^{[3
,4
]}

Schatz, Michael C. ^{[1
,3
,5
]}

Soyk, Sebastian ^{[2
]}

机构：

[1] Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD 21218 USA

[2] Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland

[3] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[4] Howard Hughes Med Inst, Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[5] Johns Hopkins Univ, Dept Biol, Baltimore, MD 21218 USA

来源：

GENOME BIOLOGY | 2022年 / 23卷 / 01期

基金：

美国国家卫生研究院; 瑞士国家科学基金会; 欧洲研究理事会; 美国国家科学基金会;

关键词：

Genome sequencing; Assembly scaffolding; Genome editing; Tomato; YIELD;

D O I：

10.1186/s13059-022-02823-7

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：

Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, and we establish chromosome-scale reference genomes for the widely used tomato genotype M82 along with Sweet-100, a new rapid-cycling genotype that we developed to accelerate functional genomics and genome editing in tomato. This work outlines strategies to rapidly expand genetic systems and genomic resources in other plant species.

引用

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