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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Detalles Bibliográficos
Autores principales: Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B., Schatz, Michael C., Soyk, Sebastian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9753292/
https://www.ncbi.nlm.nih.gov/pubmed/36522651
http://dx.doi.org/10.1186/s13059-022-02823-7
Descripción
Sumario: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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02823-7.

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