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

Author:

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

Abstract

AbstractAdvancing 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.

Funder

European Research Council

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung

National Institutes of Health

National Science Foundation

Howard Hughes Medical Institute

Human Frontier Science Program

Publisher

Springer Science and Business Media LLC

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