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 (December 2022) Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology, 23 (1). p. 258. ISSN 1474-7596

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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.

Item Type:	Paper
Subjects:	Investigative techniques and equipment Investigative techniques and equipment > assays bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes organism description > plant organism description > plant > tomato Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:	Wang, Xingang Lippman, Zachary B. Schatz, Michael C.
Communities:	CSHL labs > Lippman lab CSHL labs > Schatz lab CSHL Cancer Center Program CSHL Cancer Center Shared Resources > Sequencing Technology & Analysis Service
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	15 December 2022
Date Deposited:	04 Jan 2023 15:17
Last Modified:	09 Feb 2024 16:38
PMCID:	PMC9753292
URI:	https://repository.cshl.edu/id/eprint/40778

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