Kitashiba Hiroyasu, Li Feng, Hirakawa Hideki, Kawanabe Takahiro, Zou Zhongwei, Hasegawa Yoichi, Tonosaki Kaoru, Shirasawa Sachiko, Fukushima Aki, Yokoi Shuji, Takahata Yoshihito, Kakizaki Tomohiro, Ishida Masahiko, Okamoto Shunsuke, Sakamoto Koji, Shirasawa Kenta, Tabata Satoshi, Nishio Takeshi
Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan.
Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
DNA Res. 2014 Oct;21(5):481-90. doi: 10.1093/dnares/dsu014. Epub 2014 May 16.
Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes 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) for a 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.
萝卜（Raphanus sativus L.，n = 9）是亚洲主要蔬菜之一。由于包括萝卜在内的芸苔属及其相关物种的基因组发生了重排，基于已报道的白菜基因组序列进行功能分析非常困难。因此，我们对萝卜进行了基因组测序。通过下一代测序（NGS）获得了一个萝卜自交系基因组序列的191.1 Gb短读长，并构建了76,592个长度≥300 bp的支架以及细菌人工染色体末端序列。最终，获得了402 Mb的全基因组草图序列，覆盖了估计基因组大小的75.9%，包含61,572个预测基因。随后，221个单核苷酸多态性标记和768个PCR-RFLP标记与我们之前研究中产生的746个标记一起用于构建连锁图谱。该图谱进一步与另一个主要由表达序列标签-简单序列重复标记构建的萝卜连锁图谱合并，形成了一个1,166 cM的高密度整合图谱，包含2,553个DNA标记。共有1,345个支架被定位到连锁图谱上，覆盖116.0 Mb。通过NGS对2,880对引物扩增的混合PCR产物进行测序，并鉴定了8个自交系中的单核苷酸多态性。
