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

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...

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Bibliographic Details
Published in:Genome Biology Vol. 23; no. 1; p. 258
Main Authors: Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B., Schatz, Michael C., Soyk, Sebastian
Format: Journal Article
Language:English
Published: London BioMed Central 15.12.2022
Springer Nature B.V
BMC
Subjects:
Animal Genetics and Genomics
Assembly scaffolding
Automation
Bias
Bioinformatics
Biomedical and Life Sciences
Chromosomes
Cultivars
Evolutionary Biology
Experiments
Food quality
Fruits
Gene Editing
Genetics
Genome
Genome editing
Genome sequencing
Genomes
Genomics
Genotype
Genotypes
Human Genetics
Life Sciences
Microbial Genetics and Genomics
Mutation
Plant Genetics and Genomics
Short Report
Solanum lycopersicum - genetics
species
Tomato
tomatoes
Assembly scaffolding
Genome editing
Genome sequencing
Tomato
ISSN:1474-760X, 1474-7596, 1474-760X
Online Access:Get full text
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Summary: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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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02823-7