Supporting data for "Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)".

Dataset type: Genomic
Data released on December 04, 2015

Zhang G; Tian Y; Yang S; Wang W; Sheng J; Dong Y; Chen W (2015): Supporting data for "Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)". GigaScience Database. http://dx.doi.org/10.5524/100164

DOI10.5524/100164

Danshen (Salvia miltiorrhiza Bunge) of Lamiaceae family, also known as Chinese red sage, is valued in the traditional Chinese medicine mainly to treat cardiovascular and cerebrovascular diseases. Because of this pharmacological prospect, continuous research aims to identify novel bioactive compounds and their biosynthetic pathways in danshen. So far, only EST and RNA-seq data for this herbal plant are available to the public. We therefore propose that the construction of a reference danshen genome will help elucidate the biosynthetic steps for important secondary metabolites, thereby pushing forward the investigation of novel drugs from the plant.
Here we present the 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 draft genome is approximately 641 Mb, with a contig N50 size of 82.8kb and scaffold N50 size of 1.2 Mb.
Further analyses predicted 27,986 protein-coding genes and 1,147 unique gene families in the danshen genome.

Additional details

Read the peer-reviewed publication(s):

Zhang, G., Tian, Y., Zhang, J., Shu, L., Yang, S., Wang, W., … Chen, W. (2015). Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge). GigaScience, 4(1). doi:10.1186/s13742-015-0104-3

Accessions (data generated as part of this study):

BioProject: PRJNA287594





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Salvia miltiorrhiza226208Salvia miltiorrhizaSalvia miltiorrhiza Age:1
Tissue:leaf
Alternative accession-SRA Sample:SRS967127
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AnnotationGFF10.22 MB2015-12-04
AnnotationGFF10.7 MB2015-12-04
AnnotationGFF10.75 MB2015-12-04
AnnotationGFF1.74 MB2015-12-04
AnnotationGFF17.7 MB2015-12-04
OtherTEXT4.77 MB2015-12-04
AnnotationGFF5.37 MB2015-12-04
AnnotationGFF9.85 MB2015-12-04
AnnotationGFF14.53 MB2015-12-04
AnnotationGFF642.7 KB2015-12-04
Displaying 1-10 of 24 File(s).
Date Action
December 4, 2015 Dataset publish
December 29, 2015 Manuscript Link added : 10.1186/s13742-015-0104-3