Genome Biol. auth.: group Soyk

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Genome Biol. 2022 Dec 15;23(1):258. doi: 10.1186/s13059-022-02823-7.

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

Michael Alonge 1, Ludivine Lebeigle 2, Melanie Kirsche 1, Katie Jenike 1, Shujun Ou 1, Sergey Aganezov 1, Xingang Wang 3, Zachary B Lippman 3 4, Michael C Schatz 5 6 7, Sebastian Soyk 8

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.

Keywords: Assembly scaffolding; Genome editing; Genome sequencing; Tomato.