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Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing.
Alonge, Michael; Lebeigle, Ludivine; Kirsche, Melanie; Jenike, Katie; Ou, Shujun; Aganezov, Sergey; Wang, Xingang; Lippman, Zachary B; Schatz, Michael C; Soyk, Sebastian.
Affiliation
  • Alonge M; Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Lebeigle L; Center for Integrative Genomics, University of Lausanne, CH-1015, Lausanne, Switzerland.
  • Kirsche M; Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Jenike K; Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Ou S; Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Aganezov S; Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
  • Wang X; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
  • Lippman ZB; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
  • Schatz MC; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
  • Soyk S; Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA. mschatz@cs.jhu.edu.
Genome Biol ; 23(1): 258, 2022 12 15.
Article in En | MEDLINE | ID: mdl-36522651
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Solanum lycopersicum Language: En Journal: Genome Biol Journal subject: BIOLOGIA MOLECULAR / GENETICA Year: 2022 Type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Solanum lycopersicum Language: En Journal: Genome Biol Journal subject: BIOLOGIA MOLECULAR / GENETICA Year: 2022 Type: Article Affiliation country: United States