title: Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge).
abstract: 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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  The draft danshen genome will provide a valuable resource for the investigation of novel bioactive compounds in this Chinese herb.
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201 China.
authors.forename: Guanghui
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201 China ; College of Life Sciences, Jilin University, Changchun, 130012 China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Tian
authors.affiliation: College of Life Sciences, Huazhong University of Science and Technology, Wuhan, 430074 China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.affiliation: College of Life Science, Kunming University of Science and Technology, Kunming, 650504 China.
authors.forename: Liping
authors.initials: L
authors.lastname: Shu
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201 China.
authors.forename: Shengchao
authors.initials: S
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.affiliation: Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201 China.
authors.forename: Jun
authors.initials: J
authors.lastname: Sheng
authors.affiliation: College of Life Science, Kunming University of Science and Technology, Kunming, 650504 China ; Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201 China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201 China ; Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201 China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
mesh_terms: D030541:Databases, Genetic; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D012091:Repetitive Sequences, Nucleic Acid; D027561:Salvia miltiorrhiza / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
keywords: High heterozygous genome assembly; Illumina sequencing; PacBio sequencing; Salvia miltiorrhiza Bunge