Genome sequence analysis of a giant-rooted 'Sakurajima daikon' radish (Raphanus sativus)

Abstract

Daikon radish (Raphanus sativus) roots vary in size and shape between cultivars. This study reports the genome sequence assembly of a giant-rooted Sakurajima daikon radish variety, Okute-Sakurajima, which produces extremely large round roots. Radish genome assembly is hampered by the repetitive and complex nature of the genome. To address this, single-molecule real-time technology was used to obtain long-read sequences at 60x genome coverage. De novo assembly of the long reads generated 504.5 Mb contig sequences consisting of 1,437 sequences with contig N50 length of 1.2 Mb, including 94.1% of the core eukaryotic genes. Nine pseudomolecule sequences, comprising 69.3% of the assembled contig length, were generated with high-density SNP genetic maps. The chromosome-level sequences revealed structure variations and rearrangements among Brassicaceae genomes. In total, 89,915 genes were predicted in the Okute-Sakurajima genome, 30,033 of which were unique to the assembly in this study. The improved genome information generated in this study will not only form a new baseline resource for radish genomics, but will also provide insights into the molecular mechanisms underlying formation of giant radish roots.