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

Area of Science:

• Plant genomics
• Bioinformatics
• Molecular biology

Background:

• High-quality genome assemblies are crucial for advancing crop genomics.
• Existing genetic systems can be limiting for functional genomics and genome editing.

Purpose of the Study:

• To introduce RagTag, a toolset for automating genome assembly scaffolding and patching.
• To establish chromosome-scale reference genomes for tomato genotypes M82 and Sweet-100.
• To outline strategies for expanding genetic systems in other plant species.

Main Methods:

• Development and application of the RagTag toolset for genome assembly.
• Generation of chromosome-scale reference genomes using RagTag.
• Characterization of a new rapid-cycling tomato genotype (Sweet-100).

Main Results:

• RagTag successfully automates assembly scaffolding and patching.
• Chromosome-scale reference genomes for tomato M82 and Sweet-100 were established.
• Sweet-100 provides a valuable resource for accelerated functional genomics in tomato.

Conclusions:

• RagTag is an effective tool for improving genome assemblies.
• The new tomato reference genomes will facilitate crop improvement.
• The presented strategies can accelerate genomic resource development in diverse plant species.