Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

Benjamin Istace
ORCID logo ,
Caroline Belser
,
Cyril Falentin
,
Karine Labadie
,
Franz Boideau
ORCID logo ,
Gwenaëlle Deniot
,
Loeiz Maillet
,
Corinne Cruaud
,
Laurie Bertrand
,
Anne-Marie Chèvre
,
Patrick Wincker
,
Mathieu Rousseau-Gueutin
,
Jean-Marc Aury
* ORCID logo
Version 1 : Received: 9 July 2021 / Approved: 12 July 2021 / Online: 12 July 2021 (22:55:37 CEST)

A peer-reviewed article of this Preprint also exists.

Istace, B.; Belser, C.; Falentin, C.; Labadie, K.; Boideau, F.; Deniot, G.; Maillet, L.; Cruaud, C.; Bertrand, L.; Chèvre, A.-M.; Wincker, P.; Rousseau-Gueutin, M.; Aury, J.-M. Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case. Biology 2021, 10, 732. Istace, B.; Belser, C.; Falentin, C.; Labadie, K.; Boideau, F.; Deniot, G.; Maillet, L.; Cruaud, C.; Bertrand, L.; Chèvre, A.-M.; Wincker, P.; Rousseau-Gueutin, M.; Aury, J.-M. Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case. Biology 2021, 10, 732.

Abstract

With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Indeed, 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, and especially 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 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.

Keywords

Genome sequencing; de novo Assembly; Scaffolding; Chromosome-scale; Nanopore sequencing; Long reads; Optical maps; Bionano Genomics; Hi-C; Omni-C; Pore-C; Plant genomes

Subject

Biology and Life Sciences, Anatomy and Physiology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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