De novo sequencing and analysis of the transcriptome of Panax ginseng in the leaf-expansion period.
Panax ginseng, a traditional Chinese medicine, is used worldwide for its variety of health benefits and its treatment efficacy. However, it is difficult to cultivate due to its vulnerability to environmental stresses. The present study provided the first report, to the best of our knowledge, of transcriptome analysis of ginseng at the leaf‑expansion stage. Using the Illumina sequencing platform, >40,000,000 high‑quality paired‑end reads were obtained and assembled into 100,533 unique sequences. When the sequences were searched against the publicly available National Center for Biotechnology Information protein database using The Basic Local Alignment Search Tool, 61,599 sequences exhibited similarity to known proteins. Functional annotation and classification, including use of the Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases, revealed that the activated genes in ginseng were predominantly ribonuclease‑like storage genes, environmental stress genes, pathogenesis-related genes and other antioxidant genes. A number of candidate genes in environmental stress‑associated pathways were also identified. These novel data provide useful information on the growth and development stages of ginseng, and serve as an important public information platform for further understanding of the molecular mechanisms and functional genomics of ginseng.
Center of Chinese Medicine and Bio‑Engineering Research, Changchun University of Chinese Medicine, Changchun, Jilin 130000, P.R. China.
Shichao
S
Liu
Center of Chinese Medicine and Bio‑Engineering Research, Changchun University of Chinese Medicine, Changchun, Jilin 130000, P.R. China.
Siming
S
Wang
Center of Chinese Medicine and Bio‑Engineering Research, Changchun University of Chinese Medicine, Changchun, Jilin 130000, P.R. China.
Meichen
M
Liu
Department of Bio‑Pharmaceutical Development, GeneScience Pharmaceuticals Co., Ltd., Changchun, Jilin 130000, P.R. China.
Fei
F
Yang
Center of Chinese Medicine and Bio‑Engineering Research, Changchun University of Chinese Medicine, Changchun, Jilin 130000, P.R. China.
Hui
H
Zhang
College of Life Sciences, Jilin University, Changchun, Jilin 130000, P.R. China.
Shiyang
S
Liu
Center of Chinese Medicine and Bio‑Engineering Research, Changchun University of Chinese Medicine, Changchun, Jilin 130000, P.R. China.
Qun
Q
Wang
Center of Chinese Medicine and Bio‑Engineering Research, Changchun University of Chinese Medicine, Changchun, Jilin 130000, P.R. China.
Yu
Y
Zhao
D019295:Computational Biology / Q000379:methods; D004777:Environment; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D059647:Gene-Environment Interaction; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D005894:Panax / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome