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Data released on April 30, 2017

Supporting data for "Draft genome sequence of the Tibetan medicinal herb, Rhodiola crenulata"

Chen, W; Fan, G; Fu, Y; Guan, R; Hao, S; Li, L; Liu, G; Ma, L; Ni, X; Shi, C; Sun, X; Wan, H; Wang, J; Xu, X; You, J; Yue, Z; Zhang, H; Lee, S, M; Liu, X (2017): Supporting data for "Draft genome sequence of the Tibetan medicinal herb, Rhodiola crenulata" GigaScience Database. http://dx.doi.org/10.5524/100301 RIS BibTeX Text

Rhodiola crenulata, one of the well-known Tibetan medicinal herb, is mainly grown in high-altitude regions of Tibet, Yunnan and Sichuan provinces in China. In the past few years, increasing published studies on pharmacological activities of R. crenulata, have strengthened our understanding into its active ingredient composition, pharmacological activity and mechanism of action. The findings also provided strong evidences supporting the important medicinal and economical values of R. crenulata. Meanwhile, some Rhodiola species are becoming endangered because of overexploitation and environmental destruction. However, little is known about the genetic and genomic information of any Rhodiola species.
Here, we reported the first draft assembly of R. crenulata genome, which was 344.5 Mb (25.7Mb Ns), accounting for 82% of the estimated genome size, with the scaffold N50 length of 144.7 kb and the contig N50 length of 25.4 kb. The R. crenulata genome was not only highly heterozygous but also highly repetitive with ratios of 1.12% and 66.15%, respectively, based on the k-mer analysis. Furthermore, 226.6 Mb transposable elements were detected, of which 77.03% were long terminal repeats. In total, 31,517 protein-coding genes were identified, capturing 86.72% of expected plant genes in BUSCO. Additionally, 79.73% of protein-coding genes were functionally annotated.
R. crenulata is an important medicinal plant and also a potentially interesting model species for studying the adaptability of Rhodiola species to extreme environments. The genomic sequences of R. crenulata will be useful for understanding the evolutionary mechanism of stress resistance gene and biosynthesis pathways of the different medicinal ingredients for example, salidroside, in R. crenulata.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix033

Protocols.io:

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Accessions (data included in GigaDB):

SRA: SRP099970
SRA: SRP100622

Keywords:

Rhodiola crenulata Genomics Assembly Annotation BGISeq500 Illumina HiSeq 

Genomic

http://gigadb.org/images/data/cropped/100301.jpg

Funding:

  • Funding body - Ministry of Science and Technology of the People's Republic of China
  • Award ID - 2014AA10A602-4
  • Comment - National High Technology Research and Development Program
  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - JCYJ20150831201123287
  • Comment - Basic research program
  • Funding body - Jiangsu Province
  • Location - China
  • Award ID - BE2016002-3
  • Comment - Key Research & Development Program
  • Awardee - Xiao Sun

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS1981832242839Rhodiola crenulata Description:The DNA sample of Rhodiola crenulata f...
Analyte type:DNA
Geographic location (latitude and longitude):not c...
...
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SRS1992609242839Rhodiola crenulata Description:The RNA sample of Rhodiola crenulata (...
Analyte type:RNA
Geographic location (latitude and longitude):27.03...
...
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SRS1992610242839Rhodiola crenulata Description:The RNA sample of Rhodiola crenulata (...
Analyte type:RNA
Geographic location (latitude and longitude):27.03...
...
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SRS1992611242839Rhodiola crenulata Description:The RNA sample of Rhodiola crenulata (...
Analyte type:RNA
Geographic location (latitude and longitude):27.03...
...
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Displaying 1-4 of 4 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
tabular dataUNKNOWN0.2 KB2017-04-26
otherUNKNOWN0.33 KB2017-04-26
otherUNKNOWN0.32 KB2017-04-26
otherUNKNOWN1.89 MB2017-04-26
otherUNKNOWN4.15 MB2017-04-26
otherUNKNOWN1.09 MB2017-04-26
Genome sequenceFASTA330.88 MB2017-04-26
Coding sequenceFASTA33.47 MB2017-04-26
otherUNKNOWN1.38 MB2017-04-26
otherUNKNOWN2.36 MB2017-04-26
Displaying 1-10 of 14 File(s).

History:

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