Genome sequence and analysis of a Japanese radish (<i>Raphanus sativus</i>) cultivar named ‘Sakurajima Daikon’ possessing giant root

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Aim</jats:title> <jats:p>The complex genome of a Japanese radish (Raphanus sativus) cultivar named ‘Okute-Sakurajima’ with an extremely large edible round root was analysed to explore its genomic characteristics.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods and Results</jats:title> <jats:p>Single-molecule real-time technology was used to obtain long sequence reads to cover 60× of the genome. De novo assembly generated 504.5 Mb contigs consisting of 1,437 sequences with the N50 value of 1.2 Mb and included 94.1% of the core eukaryotic genes. Nine pseudomolecules, comprising 69.3% of the assembled contigs, were generated along with a high-density SNP genetic map. The sequence data thus established revealed the presence of structural variations and rearrangements in the Brassicaceae genomes.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion and perspective</jats:title> <jats:p>A total of 89,915 genes were identified in the ‘Okute-Sakurajima’ genome, 30,033 of which were newly found in this study. The genome information reported here will not only contribute to the establishment of a new resource for the radish genomics but also provide insights into the molecular mechanisms underlying formation of the giant root.</jats:p> </jats:sec>