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

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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 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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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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Basic local alignment search tool.

Stephen F Altschul, Warren Gish, Webb Miller … (1990)

A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

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Minimap2: pairwise alignment for nucleotide sequences

Heng Li (2018)

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.

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Author and article information

Contributors

Michael C. Schatz: mschatz@cs.jhu.edu

Sebastian Soyk:

ORCID: http://orcid.org/0000-0003-0325-4404

sebastian.soyk@unil.ch

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1474-7596

ISSN (Electronic): 1474-760X

Publication date (Electronic): 15 December 2022

Publication date PMC-release: 15 December 2022

Publication date Collection: 2022

Volume: 23

Electronic Location Identifier: 258

Affiliations

[1 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Computer Science, , Johns Hopkins University, ; Baltimore, MD 21218 USA

[2 ]GRID grid.9851.5, ISNI 0000 0001 2165 4204, Center for Integrative Genomics, , University of Lausanne, ; CH-1015 Lausanne, Switzerland

[3 ]GRID grid.225279.9, ISNI 0000 0004 0387 3667, Cold Spring Harbor Laboratory, ; Cold Spring Harbor, NY 11724 USA

[4 ]GRID grid.225279.9, ISNI 0000 0004 0387 3667, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, ; Cold Spring Harbor, NY 11724 USA

[5 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Biology, , Johns Hopkins University, ; Baltimore, MD 21218 USA

Author information

Sebastian Soyk http://orcid.org/0000-0003-0325-4404

Article

Publisher ID: 2823

DOI: 10.1186/s13059-022-02823-7

PMC ID: 9753292

PubMed ID: 36522651

SO-VID: cee10de7-5405-4f30-872a-a68aaa47f43c

License:

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/. The Creative Commons Public Domain Dedication waiver ( http://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.

History

Date received : 8 December 2021

Date accepted : 28 November 2022

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: 802008

Award Recipient : Sebastian Soyk

Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung;

Award ID: PCEFP3_181238

Award Recipient : Sebastian Soyk

Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;

Award ID: S10OD028632-01

Award Recipient : Michael C. Schatz

Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;

Award ID: DBI-1350041

Award ID: IOS-1732253

Award ID: IOS-1543901

Award ID: IOS-1758800

Award Recipient : Zachary B. Lippman Michael C. Schatz

Funded by: FundRef http://dx.doi.org/10.13039/100000011, Howard Hughes Medical Institute;

Funded by: FundRef http://dx.doi.org/10.13039/100004412, Human Frontier Science Program;

Award ID: RGP0025/2021

Award Recipient : Michael C. Schatz

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: genome sequencing,assembly scaffolding,genome editing,tomato

Data availability:

ScienceOpen disciplines: Genetics

Keywords: genome sequencing, assembly scaffolding, genome editing, tomato

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

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Supplementary Information

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Arabidopsis genomics

Most cited references 49

The Sequence Alignment/Map format and SAMtools

Basic local alignment search tool.

Minimap2: pairwise alignment for nucleotide sequences

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