Sequencing and chromosome-scale assembly of plant genomes, brassica rapa as a use case

Abstract

With the rise of long-read sequencers and long-range technologies, delivering high-qual-ity plant genome assemblies is no longer reserved to large consortia. Not only sequencing tech-niques, 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 yel-low sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assem-bled 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 capa-bility of each technology.