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

View ORCID ProfileMichael Alonge, Ludivine Lebeigle, View ORCID ProfileMelanie Kirsche, View ORCID ProfileSergey Aganezov, View ORCID ProfileXingang Wang, View ORCID ProfileZachary B. Lippman, View ORCID ProfileMichael C. Schatz, View ORCID ProfileSebastian Soyk
doi: https://doi.org/10.1101/2021.11.18.469135
Michael Alonge
1Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
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Ludivine Lebeigle
2Center for Integrative Genomics, University of Lausanne, Lausanne, CH-1015, Switzerland
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Melanie Kirsche
1Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
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Sergey Aganezov
1Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
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Xingang Wang
3Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Zachary B. Lippman
3Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
4Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Michael C. Schatz
1Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
3Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
5Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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  • For correspondence: mschatz@cs.jhu.edu sebastian.soyk@unil.ch
Sebastian Soyk
2Center for Integrative Genomics, University of Lausanne, Lausanne, CH-1015, Switzerland
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  • For correspondence: mschatz@cs.jhu.edu sebastian.soyk@unil.ch
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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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/malonge/RagTag

  • https://github.com/pan-sol/pan-sol-data

  • https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA779684

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted November 19, 2021.
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Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing
Michael Alonge, Ludivine Lebeigle, Melanie Kirsche, Sergey Aganezov, Xingang Wang, Zachary B. Lippman, Michael C. Schatz, Sebastian Soyk
bioRxiv 2021.11.18.469135; doi: https://doi.org/10.1101/2021.11.18.469135
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Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing
Michael Alonge, Ludivine Lebeigle, Melanie Kirsche, Sergey Aganezov, Xingang Wang, Zachary B. Lippman, Michael C. Schatz, Sebastian Soyk
bioRxiv 2021.11.18.469135; doi: https://doi.org/10.1101/2021.11.18.469135

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