Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)

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	Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)
	Zhang GH 1; Tian Y 2,3; Zhang J 4; Shu LP 5; Yang SC 1; Wang W 6; Sheng J 2; Dong Y5,7; Chen W2,7; loyalyang@163.com ; wchenntr@gmail.com
	2015
发表期刊	GIGASCIENCE
卷号	4 期号:X 页码:e62
合作性质	其它
摘要	Background: 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. Findings: We assembled the highly heterozygous danshen genome with the help of 395 x raw read coverage using Illumina technologies and about 10 x 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. Conclusions: The draft danshen genome will provide a valuable resource for the investigation of novel bioactive compounds in this Chinese herb.
关键词	High Heterozygous Genome Assembly Illumina Sequencing Pacbio Sequencing Salvia Miltiorrhiza Bunge
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/9512
专题	基因起源组遗传资源与进化国家重点实验室
通讯作者	loyalyang@163.com; wchenntr@gmail.com
作者单位	1.Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming 650201, China 2.Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China 3.College of Life Sciences, Jilin University, Changchun 130012, China. 4.College of Life Sciences, Huazhong University of Science and Technology, Wuhan 430074, China 5.College of Life Science, Kunming University of Science and Technology, Kunming 650504, China 6.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 7.Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China
推荐引用方式 GB/T 7714	Zhang GH,Tian Y,Zhang J,et al. Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)[J]. GIGASCIENCE,2015,4(X):e62.
APA	Zhang GH.,Tian Y.,Zhang J.,Shu LP.,Yang SC.,...&wchenntr@gmail.com.(2015).Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge).GIGASCIENCE,4(X),e62.
MLA	Zhang GH,et al."Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)".GIGASCIENCE 4.X(2015):e62.

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A2015122102.pdf（411KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文