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

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

doi:10.1186/s13059-022-02823-7

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

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

Whiting School of Engineering

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Article number	258
Journal	Genome biology
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s13059-022-02823-7
State	Published - Dec 2022

Keywords

Assembly scaffolding
Genome editing
Genome sequencing
Tomato

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/s13059-022-02823-7

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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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AU - Alonge, Michael

AU - Lebeigle, Ludivine

AU - Kirsche, Melanie

AU - Jenike, Katie

AU - Ou, Shujun

AU - Aganezov, Sergey

AU - Wang, Xingang

AU - Lippman, Zachary B.

AU - Schatz, Michael C.

AU - Soyk, Sebastian

PY - 2022/12

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N2 - 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.

AB - 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.

KW - Assembly scaffolding

KW - Genome editing

KW - Genome sequencing

KW - Tomato

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

Abstract

Keywords

ASJC Scopus subject areas

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