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Gigascience. 2017 Jun 1;6(6):1-5. doi: 10.1093/gigascience/gix033.

Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata.

Fu Y1,2,3, Li L2,3, Hao S2, Guan R2,3, Fan G2,3,4, Shi C2, Wan H2,3, Chen W2, Zhang H2,3, Liu G2, Wang J5, Ma L5, You J6, Ni X2, Yue Z2, Xu X2, Sun X1, Liu X2, Lee SM4.

Author information

1
State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China.
2
BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
3
BGI-Qingdao, No. 2877, Tuanjie Road, Sino-German Ecopark, Qingdao, Shandong Province, 266555, China.
4
State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Dama Road, Macao, China.
5
Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center For Ornamental Horticulture, 2238 Beijing Road, Kunming, 650205, China.
6
The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, School of life Sciences, Fudan University, Songhu Road 2005, Shanghai, 200438, China.

Abstract

Rhodiola crenulata, a well-known medicinal Tibetan herb, is mainly grown in high-altitude regions of the Tibet, Yunnan, and Sichuan provinces in China. In the past few years, increasing numbers of studies have been published on the potential pharmacological activities of R. crenulata, strengthening our understanding into its putitive active ingredient composition, pharmacological activity, and mechanism of action. These findings also provide strong evidence supporting the important medicinal and economical value of R. crenulata. Consequently, 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 report the first draft assembly ofthe R. crenulata genome, which was 344.5 Mb (25.7 Mb Ns), accounting for 82% of the estimated genome size, with a scaffold N50 length of 144.7 kb and a contig N50 length of 25.4 kb. The R. crenulata genome is 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 of 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 the stress resistance gene and the biosynthesis pathways of the different medicinal ingredients, for example, salidroside in R. crenulata.

KEYWORDS:

Rhodiola crenulata; annotation; genome assembly; genomics

PMID:
28475810
PMCID:
PMC5530320
DOI:
10.1093/gigascience/gix033
[Indexed for MEDLINE]
Free PMC Article

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