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

Dataset type: Genomic
Data released on April 30, 2017

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

DOI10.5524/100301

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.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 28475810)

Accessions (data generated as part of this study):

SRA: SRP099970
SRA: SRP100622





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS1981832242839Rhodiola crenulataRhodiola crenulata Description:The DNA sample of Rhodiola crenulata f...
Analyte type:DNA
Geographic location (latitude and longitude):not c...
...
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SRS1992609242839Rhodiola crenulataRhodiola crenulata Description:The RNA sample of Rhodiola crenulata (...
Analyte type:RNA
Geographic location (country and/or sea,region):Ja...
...
+
SRS1992610242839Rhodiola crenulataRhodiola crenulata Description:The RNA sample of Rhodiola crenulata (...
Analyte type:RNA
Geographic location (country and/or sea,region):Ja...
...
+
SRS1992611242839Rhodiola crenulataRhodiola crenulata Description:The RNA sample of Rhodiola crenulata (...
Analyte type:RNA
Geographic location (country and/or sea,region):Ja...
...
+
Displaying 1-4 of 4 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherUNKNOWN0.33 KB2017-04-26
OtherUNKNOWN0.32 KB2017-04-26
Tabular dataUNKNOWN0.2 KB2017-04-26
OtherUNKNOWN2.36 MB2017-04-26
OtherUNKNOWN1.89 MB2017-04-26
OtherUNKNOWN4.15 MB2017-04-26
ReadmeTEXT2.79 KB2017-04-26
Coding sequenceFASTA33.47 MB2017-04-26
Genome sequenceFASTA330.88 MB2017-04-26
AnnotationGFF13.47 MB2017-04-26
Displaying 1-10 of 14 File(s).
Funding body Awardee Award ID Comments
Ministry of Science and Technology of the People's Republic of China 2014AA10A602-4 National High Technology Research and Development Program
Shenzhen Municipal Government of China JCYJ20150831201123287 Basic research program
Jiangsu Province Xiao Sun BE2016002-3 Key Research & Development Program

Protocols.io:

Date Action
May 19, 2017 Dataset publish
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix033
November 9, 2022 Manuscript Link updated : 10.1093/gigascience/gix033
May 23, 2023 External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.hrkb54w