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

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...

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Autores principales: Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B., Schatz, Michael C., Soyk, Sebastian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9753292/
https://www.ncbi.nlm.nih.gov/pubmed/36522651
http://dx.doi.org/10.1186/s13059-022-02823-7
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author Alonge, Michael
Lebeigle, Ludivine
Kirsche, Melanie
Jenike, Katie
Ou, Shujun
Aganezov, Sergey
Wang, Xingang
Lippman, Zachary B.
Schatz, Michael C.
Soyk, Sebastian
author_facet Alonge, Michael
Lebeigle, Ludivine
Kirsche, Melanie
Jenike, Katie
Ou, Shujun
Aganezov, Sergey
Wang, Xingang
Lippman, Zachary B.
Schatz, Michael C.
Soyk, Sebastian
author_sort Alonge, Michael
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02823-7.
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spelling pubmed-97532922022-12-16 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 Genome Biol Short Report 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02823-7. BioMed Central 2022-12-15 /pmc/articles/PMC9753292/ /pubmed/36522651 http://dx.doi.org/10.1186/s13059-022-02823-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Short Report
Alonge, Michael
Lebeigle, Ludivine
Kirsche, Melanie
Jenike, Katie
Ou, Shujun
Aganezov, Sergey
Wang, Xingang
Lippman, Zachary B.
Schatz, Michael C.
Soyk, Sebastian
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
title Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
title_full Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
title_fullStr Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
title_full_unstemmed Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
title_short Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
title_sort automated assembly scaffolding using ragtag elevates a new tomato system for high-throughput genome editing
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9753292/
https://www.ncbi.nlm.nih.gov/pubmed/36522651
http://dx.doi.org/10.1186/s13059-022-02823-7
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