Transcriptome

Genomics

Wireless

Evolutionary biology

Biology

Gene

Operating system

Genome editing

Gene expression

Genome

Throughput

Sequence assembly

Computer science

Human genetics

Genome Biology

Computational biology

Scaffold

Genetics

Database

Genome biology

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.

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