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

Alonge, Michael; Lebeigle, Ludivine; Kirsche, Melanie; Jenike, Katie; Ou, Shujun; Aganezov, Sergey; Wang, Xingang; Lippman, Zachary B.; Schatz, Michael C.; Soyk, Sebastian

doi:10.1186/s13059-022-02823-7

articleGenome biologyDec 15, 2022GOLD OA

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

MAMichael Alonge LLLudivine Lebeigle MKMelanie Kirsche KJKatie Jenike SOShujun Ou

Johns Hopkins University · University of Lausanne · +3 more institutions

PubMed

Indexed incrossrefdoajpubmed

Abstract

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.

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914

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FWCI: 70.42
Percentile: 100%
References: 63

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Authors

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Topics & keywords

Topics

Keywords

Biology
Genome editing
Scaffold
Genome
Computational biology
Throughput
Genome Biology
Sequence assembly

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