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

Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary, Schatz, Michael, Soyk, Sebastian (November 2021) Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing. bioRxiv. (Unpublished)

[thumbnail of 2021.Alonge.tomato_genome_editing.pdf] PDF
2021.Alonge.tomato_genome_editing.pdf
Available under License Creative Commons Attribution Non-commercial No Derivatives.

Download (10MB)

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 rapid-cycling genotype that we developed to accelerate functional genomics and genome editing. This work outlines strategies to rapidly expand genetic systems and genomic resources in other plant species.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant > tomato
CSHL Authors:
Communities: CSHL labs > Lippman lab
CSHL labs > Schatz lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 19 November 2021
Date Deposited: 07 Dec 2021 19:59
Last Modified: 16 May 2024 14:30
URI: https://repository.cshl.edu/id/eprint/40446

Actions (login required)

Administrator's edit/view item Administrator's edit/view item