Genome sequence and analysis of a Japanese radish (Raphanus sativus) cultivar named 'Sakurajima Daikon' possessing giant root

• Published in: DNA research Vol. 27; no. 2
• Main Authors: Shirasawa, Kenta, Hirakawa, Hideki, Fukino, Nobuko, Kitashiba, Hiroyasu, Isobe, Sachiko
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-04-2020
• Subjects: Chromosomes, Plant - genetics; Genome, Plant; Genomes Explored; Molecular Sequence Annotation; Plant Roots - genetics; Plant Roots - growth & development; Polymorphism, Single Nucleotide; Raphanus - genetics; Raphanus - growth & development; chromosome-scale pseudomolecule sequences; genome sequence; radish; long-read sequence technology
• ISSN: 1340-2838; 1756-1663
• DOI: 10.1093/dnares/dsaa010

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.
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.
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.