Sequencing of the Radish Genome

Radish (Raphanus sativus L.) is an edible root vegetable crop cultivated worldwide. It is a close relative of Brassica crops such as Kimchi cabbage and cabbage that share mesopolyploidy before domestication. Despite of its importance in agriculture and evolutionary biology, little is known on the radish genome. Here we report the radish genome sequencing project to make a reference genome sequence of Korean radish, cv. WK10039 (2n=18). The genome size of WK10039 was estimated to be 510.8 Mb by K-mer analysis of NGS sequences. We sequenced the genome based on a whole genome shotgun sequencing strategy as follow: (1) We produced 54X raw sequences of single (1.5 kb) and mate-paired (3, 8, 20, and 30 kb) DNA sequence using Roche/454 GS-FLX Plus platform (average read length of ~600 bp) and then assembled them into contigs using Newbler assembler. (2) For homopolymer correction and additional assembly, we generated 188X pared-end short reads using Illumina/Solexa HiSeq1000 platform (read length of 100 bp in both ends). (3) We also included ~25,000 BAC-end sequences and 24X PacBio single molecule sequences to enlarge the sequence scaffolds of the genome. The current assembly covers approximately 353.5 Mb with contig N50 of 25 kb. The reference genome assembly will be a fundamental basis of radish biology as well as a genomic toolbox for breeding.