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

Patrick Driguez; Salim Bougouffa; Karen Carty; Alexander Putra; Kamel Jabbari; Muppala P. Reddy; Richard Willem Otto Soppe; Ming Sin Cheung; Yoshinori Fukasawa; Luca Ermini

doi:10.1186/s13059-021-02475-z

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

Patrick Driguez, Salim Bougouffa, Karen Carty, Alexander Putra, Kamel Jabbari, Muppala P. Reddy, Richard Willem Otto Soppe, Ming Sin Cheung, Yoshinori Fukasawa, Luca Ermini

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

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.

Original language	English (US)
Journal	Genome biology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1186/s13059-021-02475-z
State	Published - Sep 4 2021

ASJC Scopus subject areas

Genetics

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10.1186/s13059-021-02475-z

https://repository.kaust.edu.sa/bitstream/10754/670946/1/s13059-021-02475-z.pdf

Cite this

@article{ddb76f748e7d46c69ee8465b744e5a4a,

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

abstract = "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.",

author = "Patrick Driguez and Salim Bougouffa and Karen Carty and Alexander Putra and Kamel Jabbari and Reddy, {Muppala P.} and Soppe, {Richard Willem Otto} and Cheung, {Ming Sin} and Yoshinori Fukasawa and Luca Ermini",

note = "KAUST Repository Item: Exported on 2021-09-07 Acknowledgements: We thank Dr. Boubacar Kountche and Prof. Salim AlBabili for insightful discussions on the wet-lab work and their constructive support for BCL, and the KAUST Supercomputing Core Lab for providing support for the computing resources. We thank Dr. Dean Nicolle for the phenotypic identification of the two Eucalyptus species and the three anonymous reviewers for their constructive criticism. We thank the KAUST Core Labs management for supporting this study. In fond memory of our talented colleague Dr. Kamel Jabbari.",

year = "2021",

month = sep,

day = "4",

doi = "10.1186/s13059-021-02475-z",

language = "English (US)",

volume = "22",

journal = "Genome biology",

issn = "1474-7596",

publisher = "BioMed Central",

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T1 - LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology.

AU - Driguez, Patrick

AU - Bougouffa, Salim

AU - Carty, Karen

AU - Putra, Alexander

AU - Jabbari, Kamel

AU - Reddy, Muppala P.

AU - Soppe, Richard Willem Otto

AU - Cheung, Ming Sin

AU - Fukasawa, Yoshinori

AU - Ermini, Luca

N1 - KAUST Repository Item: Exported on 2021-09-07 Acknowledgements: We thank Dr. Boubacar Kountche and Prof. Salim AlBabili for insightful discussions on the wet-lab work and their constructive support for BCL, and the KAUST Supercomputing Core Lab for providing support for the computing resources. We thank Dr. Dean Nicolle for the phenotypic identification of the two Eucalyptus species and the three anonymous reviewers for their constructive criticism. We thank the KAUST Core Labs management for supporting this study. In fond memory of our talented colleague Dr. Kamel Jabbari.

PY - 2021/9/4

Y1 - 2021/9/4

N2 - 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.

AB - 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.

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UR - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02475-z

U2 - 10.1186/s13059-021-02475-z

DO - 10.1186/s13059-021-02475-z

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C2 - 34479618

SN - 1474-7596

VL - 22

JO - Genome biology

JF - Genome biology

IS - 1

ER -

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

Abstract

ASJC Scopus subject areas

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LeafGo - Eucalyptus and Peanut genome sequencing

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

Abstract

ASJC Scopus subject areas

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LeafGo - Eucalyptus and Peanut genome sequencing

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