Radish Genome Database
Aokubi daikon
Photo courtecy of Prof. Yuki Mitsui, Tokyo Univ. of Agric.
This Genome Browser is customized and maintained by NODAI Genome Research Center (NGRC) at Tokyo University of Agriculture.
We have released a major update to the Aokubi Raphanus sativus L. doubled haploid line reference genome. Compared with the previous short-read assembly (Rsativus_build1.00; Mitsui et al., 2015), the new version (Rsativus_build2.00; RSaok_v1; Masuda et al., manuscript under review) integrates Oxford Nanopore long-read sequencing and Bionano optical genome mapping to deliver a chromosome-scale assembly resolved into nine chromosomes.
Aokubi daikon (Raphanus sativus L.)
Aokubi daikon (Raphanus sativus L. var. hortensis cv. Aokubi) is a long-rooted Japanese radish cultivar with roots approximately 30–40 cm in length and a distinctive green upper part of the root (the "neck"). Its name is derived from the Japanese words "ao" (blue/green) and "kubi" (neck). Aokubi is widely cultivated in East Asia and is the most widely grown daikon variety in Japan, used in traditional dishes such as simmered dishes (e.g., oden), pickles (e.g., takuan), and grated daikon (daikon oroshi). Radish is thought to have originated in the Mediterranean region and later spread to Asia, where it diversified into a wide range of morphotypes.
Assembly and annotation statistics
| Metric | Rsativus_build1.00 | RSaok_v1(Rsativus_build2.00) |
|---|---|---|
| Reference | Mitsui et al. (2015) Sci. Rep. 5:10835 | Masuda et al. (manuscript under review) |
| Cultivar / line | R. sativus L. var. hortensis cv. Aokubi doubled haploid line | R. sativus L. var. hortensis cv. Aokubi doubled haploid line |
| Sequencing platform | Illumina HiSeq 2000 (121.8× coverage) | Oxford Nanopore PromethION (71.0 Gb, read N50 41.2 kb, 123× cov.) + Bionano Saphyr optical mapping |
| Total assembled size | 383.3 Mb (≥500 bp scaffolds) | 476.1 Mb (82.9% of estimated size) |
| Number of scaffolds | 40,123 (≥500 bp); 8,686 (≥2 kb) | 92 (= 9 pseudochromosomes + 5 unplaced scaffolds + 76 unplaced contigs + mitochondrial genome (mt) +chloroplast genome (cp)) |
| Number of pseudochromosomes | 9 pseudomolecules (partial; 179.8 Mb / 47% of assembly anchored via 1,384 markers) | 9 pseudochromosomes (98.2% of assembly anchored) |
| Contig N50 | 7.12 kb | 32.3 Mb (~4,500× improvement) |
| Scaffold N50 | 138.17 kb (≥500 bp); 158.63 kb (≥2 kb) | 52.2 Mb (~380× improvement) |
| BUSCO completeness | not reported | 99.2% (brassicales_odb12; C: 99.2 [S: 60.6, D: 38.6]) |
| Telomere identification | not reported | 17 / 18 chromosome termini (TTTAGGG motif) |
| Centromere identification | not reported | Resolved on all 9 chromosomes |
| Organelle genomes | not included | mt 244 kb (45% GC) + cp 153 kb (36% GC), both circular |
| Repetitive content | 36.68% | 61.5% |
| Protein-coding gene loci | 64,657 gene models (AUGUSTUS, Arabidopsis params, ab initio; RNA-seq used post-prediction for validation only) | 40,973 gene loci (BRAKER3 + TSEBRA, RNA-seq integrated as prediction hints; 46,183 mRNA transcripts) |
Publication
- Yuki Mitsui, Michihiko Shimomura, Kenji Komatsu, Nobukazu Namiki, Mari Shibata-Hatta, Misaki Imai, Yuichi Katayose, Yoshiyuki Mukai, Hiroyuki Kanamori, Kanako Kurita, Tsutomu Kagami, Akihito Wakatsuki, Hajime Ohyanagi, Hiroshi Ikawa, Nobuhiro Minaka, Kunihiro Nakagawa, Yu Shiwa & Takuji Sasaki. The radish genome and comprehensive gene expression profile of tuberous root formation and development. Sci. Rep. 5, 10835 (2015).
- Goro Masuda, Akito Hosoi, Kenji Komatsu, Yuki Mitsui, Yuko Arai-Kichise, Asuka Kamio, Rahul Sk, Hiroto Sekitoh, Miho Ozeki, Takashi Matsumoto, Shunsuke Yajima, Tomomi Tadokoro Chromosome-scale reference genome assembly of an Aokubi Raphanus sativus L. doubled haploid line. (manuscript under review)
Links
Genome Browser
Cite us
Please contact us (nodaigc[at]nodai.ac.jp) if you use data or information from this website. When using these data in publications or online materials, please cite our paper:
Masuda et al. Chromosome-scale reference genome assembly of an Aokubi Raphanus sativus L. doubled haploid line. Manuscript under review
and include a reference to this website:
https://www.nodai-genome.org/RSaok.html?lang=en .
Contact information
E-mail : nodaigc[at]nodai.ac.jp