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

SIMPLE SUMMARY: Reconstructing 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. 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. 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.