Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case.

Anne-Marie Chèvre,Jean-Marc Aury,Karine Labadie,Loeiz Maillet,Laurie Bertrand,Franz Boideau,Gwenaëlle Deniot,Patrick Wincker,Mathieu Rousseau-Gueutin,Caroline Belser,Corinne Cruaud,Benjamin Istace,Cyril Falentin

doi:10.3390/biology10080732

Abstract

Simple SummaryReconstructing plant genomes is a difficult task due to their often large sizes, unusual ploidy, and large numbers of repeated elements. However, the field of sequencing is changing very rapidly, with new and improved methods released every year. The ultimate goal of this study is to provide readers with insights into techniques that currently exist for obtaining high-quality and chromosome-scale assemblies of plant genomes. In this work, we presented the advanced techniques already existing in the field and illustrated their application to reconstruct the genome of the yellow sarson, Brassica rapa cv. Z1.With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology.

Highlights

Assembling plant genomes has always been one of the most complex tasks in bioinformatics applied to genomics
That, at the moment of writing, we could not test the Q20+ kit and, could not validate the results shown by Oxford Nanopore
DNA was isolated from one gram of plant leaves previously placed in the dark following the protocol provided by Oxford Nanopore Technologies (Oxford, UK), “High molecular weight gDNA extraction from plant leaves” downloaded from the Oxford Nanopore Technologies’ (ONT) Community in March, 2019

Summary

Introduction

Assembling plant genomes has always been one of the most complex tasks in bioinformatics applied to genomics. They often contain many repeated elements, such as satellites or transposable elements. This leads to an increase in the size of the genome, which can reach tens of gigabases, for example the loblolly pine genome, which is 22 Gb in size [1]. The difficulty is further increased due to the high levels of heterozygosity and highly variable ploidy [2]. All these characteristics make reconstruction of such genomes almost impossible without the help of a large consortium. The resulting assemblies remained highly fragmented, and most repeats were not resolved

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