Draft sequences of the radish (Raphanus sativus L.) genome.
Draft sequences of the radish (Raphanus sativus L.) genome.
复制标题
DOI：
10.1093/dnares/dsu014
复制
发表时间：
2014-10
期刊：
影响因子：
--
通讯作者：
Nishio T
中科院分区：
文献类型：
--
作者：
Kitashiba H;Li F;Hirakawa H;Kawanabe T;Zou Z;Hasegawa Y;Tonosaki K;Shirasawa S;Fukushima A;Yokoi S;Takahata Y;Kakizaki T;Ishida M;Okamoto S;Sakamoto K;Shirasawa K;Tabata S;Nishio T
萝卜（Raphanus sativus L.，n = 9）是亚洲主要的蔬菜之一。由于芸苔属及萝卜等近缘物种的基因组发生了基因组重排，因此基于已报道的芸苔属基因组序列进行功能分析是相当困难的。因此，我们进行了萝卜的基因组测序。通过下一代测序（NGS）获得了191.1 Gb的萝卜自交系基因组序列的短读段，并与细菌人工染色体末端序列一起构建了沿着76，592个≥300 bp的支架。最后，获得了402 Mb的完整基因组序列草案，跨越估计基因组大小的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标记与我们以前的研究中产生的746个标记一起用于构建连锁图。将该图谱与另一个主要用表达序列标签-简单重复序列标记构建的萝卜连锁图谱进一步组合成一个1, 166 cM、2,553个DNA标记的高密度整合图谱。共有1，345个支架被分配到连锁图谱，跨越116.0 Mb。对2,880对引物扩增的PCR产物进行NGS测序，鉴定出8个自交系的SNPs。
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.
登录
查看更多内容
DOI：
10.1093/dnares/dsr027
发表时间：
2011-10
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Li F;Hasegawa Y;Saito M;Shirasawa S;Fukushima A;Ito T;Fujii H;Kishitani S;Kitashiba H;Nishio T
通讯作者：
Nishio T
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
作者：
Mulder NJ;Apweiler R;Attwood TK;Bairoch A;Bateman A;Binns D;Bork P;Buillard V;Cerutti L;Copley R;Courcelle E;Das U;Daugherty L;Dibley M;Finn R;Fleischmann W;Gough J;Haft D;Hulo N;Hunter S;Kahn D;Kanapin A;Kejariwal A;Labarga A;Langendijk-Genevaux PS;Lonsdale D;Lopez R;Letunic I;Madera M;Maslen J;McAnulla C;McDowall J;Mistry J;Mitchell A;Nikolskaya AN;Orchard S;Orengo C;Petryszak R;Selengut JD;Sigrist CJ;Thomas PD;Valentin F;Wilson D;Wu CH;Yeats C
通讯作者：
Yeats C
影响因子：
5.8
作者：
Kofler, Robert;Schloetterer, Christian;Lelley, Tamas
通讯作者：
Lelley, Tamas
影响因子：
5.8
作者：
Stanke, Mario;Waack, Stephan
通讯作者：
Waack, Stephan