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

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

doi:10.1186/s13059-021-02475-z

Patrick Driguez, Ming Sin Cheung + Show 8 more

Open Access

https://doi.org/10.1186/s13059-021-02475-z

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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.

Highlights

Plants represent the dominant kingdom of life in terms of Earth biomass [1], and through colonization of terrestrial and aquatic habitats, are responsible for maintaining ecological and atmospheric balance
For the Eucalyptus species, libraries were produced and sequenced with the GridION platform demonstrating the suitability of the laboratory component of LeafGo for ONT sequencing [34, 37, 38]
We compared continuous long read (CLR) and HiFi data using the latest tools for genome assembly and assembled the two Eucalyptus species and A. hypogaea into high-quality draft genomes

Summary

Introduction

Plants represent the dominant kingdom of life in terms of Earth biomass [1], and through colonization of terrestrial and aquatic habitats, are responsible for maintaining ecological and atmospheric balance. The main benefit of long-read sequencing technologies for genomics, compared to the more dominant short-read/Illumina sequencing, is the ability to assemble genomes relatively by linking reads that span across repetitive genomic regions. This property when combined with ultra-long reads, highly accurate sequencing, and complementary scaffolding technologies has thereby enabled highly accurate telomere to telomere assemblies [6,7,8]. The many benefits of long-read sequencing have driven demand for high-quality high molecular weight (HMW) DNA, and led to advances in sequencing technologies and genome assembly tools

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