Journal
GENOME BIOLOGY
Volume 23, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-022-02823-7
Keywords
Genome sequencing; Assembly scaffolding; Genome editing; Tomato
Funding
- US National Institutes of Health
- National Science Foundation (NSF) [S10OD028632-01]
- NSF PGRP grant [DBI-1350041]
- Human Frontiers Scientific Program (HFSP) award [IOS-1732253, IOS-1543901, IOS-1758800]
- Howard Hughes Medical Institutes [RGP0025/2021]
- European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (ERC Starting Grant EPICROP)
- Swiss National Science Foundation (SNSF) Eccellenza Professorial Fellowship [802008]
- [PCEFP3_181238]
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This study introduces RagTag, a toolset for automating assembly scaffolding and patching, and establishes chromosome-scale reference genomes for tomato genotypes M82 and Sweet-100. This provides convenience for functional genomics and genome editing in tomato.
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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