Draft Sequences of the Radish (Raphanus sativus L.) Genome

Kitashiba Hiroyasu, Li Feng, Hirakawa Hideki, Kawanabe Takahiro, Zou Zhongwei, Hasegawa Yoichi, Tonosaki Kaoru, Shirasawa Sachiko, Fukushima Aki, Yokoi Shuji, Yoshihito Takahata, Kakizaki Tomohiro, Ishida Masahiko, Okamoto Shunsuke, Sakamoto Koji, Shirasawa Kenta, Tabata Satoshi, Takeshi Nishio

Research output: Contribution to journalArticle

94 Citations (Scopus)

Abstract

Radish (Raphanussativus L., n = 9) is one of the major vegetables in Asia. Since thegenomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) fora radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.

Original languageEnglish
Pages (from-to)481-490
Number of pages10
JournalDNA Research
Volume21
Issue number5
DOIs
Publication statusPublished - 2014

Keywords

  • Draft sequence
  • High-density genetic map
  • Radish

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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    Hiroyasu, K., Feng, L., Hideki, H., Takahiro, K., Zhongwei, Z., Yoichi, H., Kaoru, T., Sachiko, S., Aki, F., Shuji, Y., Takahata, Y., Tomohiro, K., Masahiko, I., Shunsuke, O., Koji, S., Kenta, S., Satoshi, T., & Nishio, T. (2014). Draft Sequences of the Radish (Raphanus sativus L.) Genome. DNA Research, 21(5), 481-490. https://doi.org/10.1093/dnares/dsu014