1. Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata
- Author
-
Liangwei Li, Jianling You, Chengcheng Shi, Zhen Yue, Guangyi Fan, Jihua Wang, Lulin Ma, Xuemei Ni, Shijie Hao, Yuanyuan Fu, Xun Xu, Xin Liu, Guo-Cheng Liu, Rui Guan, Wenbin Chen, Xiao Sun, Simon Ming-Yuen Lee, Haibo Wan, and He Zhang
- Subjects
0301 basic medicine ,Health Informatics ,Genomics ,Rhodiola crenulata ,Data Note ,Genome ,DNA sequencing ,03 medical and health sciences ,0302 clinical medicine ,Genome Size ,Rhodiola ,Botany ,genomics ,Medicine, Tibetan Traditional ,Medicinal plants ,Genome size ,Gene ,Whole genome sequencing ,biology ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,biology.organism_classification ,Computer Science Applications ,030104 developmental biology ,annotation ,030220 oncology & carcinogenesis ,DNA Transposable Elements ,genome assembly ,Genome, Plant - 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.
- Published
- 2017