Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge).
Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge).
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DOI：
10.1186/s13742-015-0104-3
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发表时间：
2015
期刊：
影响因子：
9.2
通讯作者：
Chen W
中科院分区：
文献类型：
--
作者：
Zhang G;Tian Y;Zhang J;Shu L;Yang S;Wang W;Sheng J;Dong Y;Chen W
丹参（Salvia miltiorrhiza Bunge），又名中国丹参，为唇形科丹参属植物。它在中医学上很有价值，主要用于治疗心脑血管疾病。由于其药理潜力，正在进行的研究旨在确定丹参中的新生物活性化合物及其生物合成途径。到目前为止，只有这种草药植物的表达序列标签（EST）和RNA-seq数据可供公众使用。因此，我们建议，丹参参考基因组的构建将有助于阐明重要的次生代谢产物的生物合成途径，从而推进从这种植物的新药研究。我们使用Illumina技术在395 × raw read coverage的帮助下组装了高度杂合的丹参基因组，使用单分子测序技术在约10 × raw read coverage的帮助下组装了丹参基因组。最终的基因组草图约为641 Mb，重叠群N50大小为82.8 kb，支架N50大小为1.2 Mb。进一步分析预测丹参基因组中有34，598个蛋白质编码基因和1，644个独特的基因家族。丹参基因组草图将为研究这种中药中的新型生物活性化合物提供宝贵的资源。本文的在线版本（doi：10.1186/s13742-015-0104-3）包含补充材料，可供授权用户使用。
Danshen (Salvia miltiorrhiza Bunge), also known as Chinese red sage, is a member of Lamiaceae family. It is valued in traditional Chinese medicine, primarily for the treatment of cardiovascular and cerebrovascular diseases. Because of its pharmacological potential, ongoing research aims to identify novel bioactive compounds in danshen, and their biosynthetic pathways. To date, only expressed sequence tag (EST) and RNA-seq data for this herbal plant are available to the public. We therefore propose that the construction of a reference genome for danshen will help elucidate the biosynthetic pathways of important secondary metabolites, thereby advancing the investigation of novel drugs from this plant. We assembled the highly heterozygous danshen genome with the help of 395 × raw read coverage using Illumina technologies and about 10 × raw read coverage by using single molecular sequencing technology. The final draft genome is approximately 641 Mb, with a contig N50 size of 82.8 kb and a scaffold N50 size of 1.2 Mb. Further analyses predicted 34,598 protein-coding genes and 1,644 unique gene families in the danshen genome. The draft danshen genome will provide a valuable resource for the investigation of novel bioactive compounds in this Chinese herb. The online version of this article (doi:10.1186/s13742-015-0104-3) contains supplementary material, which is available to authorized users.