LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology

Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and...

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Autores principales: Driguez, Patrick, Bougouffa, Salim, Carty, Karen, Putra, Alexander, Jabbari, Kamel, Reddy, Muppala, Soppe, Richard, Cheung, Ming Sin, Fukasawa, Yoshinori, Ermini, Luca
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8414726/
https://www.ncbi.nlm.nih.gov/pubmed/34479618
http://dx.doi.org/10.1186/s13059-021-02475-z
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author Driguez, Patrick
Bougouffa, Salim
Carty, Karen
Putra, Alexander
Jabbari, Kamel
Reddy, Muppala
Soppe, Richard
Cheung, Ming Sin
Fukasawa, Yoshinori
Ermini, Luca
author_facet Driguez, Patrick
Bougouffa, Salim
Carty, Karen
Putra, Alexander
Jabbari, Kamel
Reddy, Muppala
Soppe, Richard
Cheung, Ming Sin
Fukasawa, Yoshinori
Ermini, Luca
author_sort Driguez, Patrick
collection PubMed
description Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02475-z.
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spelling pubmed-84147262021-09-09 LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology Driguez, Patrick Bougouffa, Salim Carty, Karen Putra, Alexander Jabbari, Kamel Reddy, Muppala Soppe, Richard Cheung, Ming Sin Fukasawa, Yoshinori Ermini, Luca Genome Biol Method Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02475-z. BioMed Central 2021-09-03 /pmc/articles/PMC8414726/ /pubmed/34479618 http://dx.doi.org/10.1186/s13059-021-02475-z Text en © The Author(s) 2021 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 Method
Driguez, Patrick
Bougouffa, Salim
Carty, Karen
Putra, Alexander
Jabbari, Kamel
Reddy, Muppala
Soppe, Richard
Cheung, Ming Sin
Fukasawa, Yoshinori
Ermini, Luca
LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
title LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
title_full LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
title_fullStr LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
title_full_unstemmed LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
title_short LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
title_sort leafgo: leaf to genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8414726/
https://www.ncbi.nlm.nih.gov/pubmed/34479618
http://dx.doi.org/10.1186/s13059-021-02475-z
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