Toward the Rs2.0: Upgrade of the Radish Genome Based on Long-Read Sequencing and Optical Genome Mapping

The radish genome assembly Rs1.0 serves as a valuable resource in radish biology and breeding. The total size of Rs1.0 is 426.2 Mb in size, 83.6% of the estimated genome size of Raphanus sativus cv. WK10039 (510 Mb), and has approximately 55 Mb gaps. To generate next version of assembly with improved quality, we have applied two independent approaches based on the recent advances in single molecule sequencing and optical genome mapping. We generated 18.5 Gb PacBio RS II data with N50 of 12.5 kb and assembled the reads into 514.6 Mb contigs with N50 of 115.4 kb using Canu assembler. For optical genome mapping, two rounds of optical mapping using Irys nanochannel generated 84X physical image data. Assembly of the image data generated 221 contig maps covering 45 Mb with N50 of 203 kb. Integration of these data into Rs1.0 will largely improve quality of the radish genome assembly.