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[Transcriptomic data analyses of wild and cultivated Angelica sinensis root by high-throughput sequencing technology].
Zhongguo Zhong Yao Za Zhi. 2020 Apr; 45(8):1879-1886.ZZ

Abstract

The root of Angelica sinensis is known throughout Asia for its traditional efficacy in invigorating and promoting blood circulation. The wild germplasm resources of A. sinensis was in short supply, and most of the commercial medicinal materials come from cultivation. To obtain the differences in the transcriptional levels of wild and cultivated of A. sinensis, the full-length transcriptome of A. sinensis was analyzed using PacBio SMRT three-generation high-throughput sequencing technology. Using the high-throughput sequencing platform Illumina HiSeq X Ten PE150, a root transcriptome dataset of wild and cultivated A.sinensis was obtained. The transcriptome sequencing analyses obtained 16.5 Gb database in wild and cultivated A.sinensis, after assembly steps, we obtain 113 906 transcript sequences(insfroms) with an average length of 1 466 nt. BLAST analysis indicated that 109 113(accounting for 95.79% of the total insfroms), 93 276(81.89%),60 638(53.24%),48 928(42.95%),42 876(37.64%)isofroms were successfully annotated in the NR, Swiss-port, GO, KO and KOG databases, respectively. The annotation information can be classified into three categories of biological processes, cellular components and molecular functions of GO classification, involving 128 KEGG standard metabolic pathways. Analysis of 25 463 differential insfroms, 15 090 higher expression in wild A. sinensis, and 10 373 higher in cultivated A. sinensis. In the enrichment analysis of GO and KEGG, differential insfroms were concentrated on the pathway of plant-pathogen interaction, MAPK signaling pathway-plant and plant hormone signal transduction. In this study, high-throughput sequencing was used to obtain the full-length transcription information of A. sinensis, and the overall characteristics of A. sinensis genetic information were clarified. By comparing the differential expression of wild and cultivated A. sinensis at the genetic level, it provides basic information for further screening and breeding of A. sinensis germplasm resources, resistance research and secondary metabolic pathway analysis.

Authors+Show Affiliations

Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine Nanjing 210023, China.Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine Nanjing 210023, China.Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine Nanjing 210023, China.Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine Nanjing 210023, China.Gansu Province Min County Chinese Herbal Medicine Production Technical Guidance Station Dingxi 748400, China.Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine Nanjing 210023, China.Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine Nanjing 210023, China.Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine Nanjing 210023, China.Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine Nanjing 210023, China.

Pub Type(s)

Journal Article

Language

chi

PubMed ID

32489073

Citation

Feng, Wei-Meng, et al. "[Transcriptomic Data Analyses of Wild and Cultivated Angelica Sinensis Root By High-throughput Sequencing Technology]." Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica, vol. 45, no. 8, 2020, pp. 1879-1886.
Feng WM, Liu P, Yan H, et al. [Transcriptomic data analyses of wild and cultivated Angelica sinensis root by high-throughput sequencing technology]. Zhongguo Zhong Yao Za Zhi. 2020;45(8):1879-1886.
Feng, W. M., Liu, P., Yan, H., Yu, G., Guo, Z. X., Zhu, L., Ma, J. W., Qian, D. W., & Duan, J. A. (2020). [Transcriptomic data analyses of wild and cultivated Angelica sinensis root by high-throughput sequencing technology]. Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica, 45(8), 1879-1886. https://doi.org/10.19540/j.cnki.cjcmm.20200208.101
Feng WM, et al. [Transcriptomic Data Analyses of Wild and Cultivated Angelica Sinensis Root By High-throughput Sequencing Technology]. Zhongguo Zhong Yao Za Zhi. 2020;45(8):1879-1886. PubMed PMID: 32489073.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - [Transcriptomic data analyses of wild and cultivated Angelica sinensis root by high-throughput sequencing technology]. AU - Feng,Wei-Meng, AU - Liu,Pei, AU - Yan,Hui, AU - Yu,Guang, AU - Guo,Zeng-Xiang, AU - Zhu,Lei, AU - Ma,Jun-Wei, AU - Qian,Da-Wei, AU - Duan,Jin-Ao, PY - 2020/6/4/entrez PY - 2020/6/4/pubmed PY - 2020/9/18/medline KW - Angelica sinensis KW - metabolism pathway KW - transcriptome KW - wild and cultivated SP - 1879 EP - 1886 JF - Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica JO - Zhongguo Zhong Yao Za Zhi VL - 45 IS - 8 N2 - The root of Angelica sinensis is known throughout Asia for its traditional efficacy in invigorating and promoting blood circulation. The wild germplasm resources of A. sinensis was in short supply, and most of the commercial medicinal materials come from cultivation. To obtain the differences in the transcriptional levels of wild and cultivated of A. sinensis, the full-length transcriptome of A. sinensis was analyzed using PacBio SMRT three-generation high-throughput sequencing technology. Using the high-throughput sequencing platform Illumina HiSeq X Ten PE150, a root transcriptome dataset of wild and cultivated A.sinensis was obtained. The transcriptome sequencing analyses obtained 16.5 Gb database in wild and cultivated A.sinensis, after assembly steps, we obtain 113 906 transcript sequences(insfroms) with an average length of 1 466 nt. BLAST analysis indicated that 109 113(accounting for 95.79% of the total insfroms), 93 276(81.89%),60 638(53.24%),48 928(42.95%),42 876(37.64%)isofroms were successfully annotated in the NR, Swiss-port, GO, KO and KOG databases, respectively. The annotation information can be classified into three categories of biological processes, cellular components and molecular functions of GO classification, involving 128 KEGG standard metabolic pathways. Analysis of 25 463 differential insfroms, 15 090 higher expression in wild A. sinensis, and 10 373 higher in cultivated A. sinensis. In the enrichment analysis of GO and KEGG, differential insfroms were concentrated on the pathway of plant-pathogen interaction, MAPK signaling pathway-plant and plant hormone signal transduction. In this study, high-throughput sequencing was used to obtain the full-length transcription information of A. sinensis, and the overall characteristics of A. sinensis genetic information were clarified. By comparing the differential expression of wild and cultivated A. sinensis at the genetic level, it provides basic information for further screening and breeding of A. sinensis germplasm resources, resistance research and secondary metabolic pathway analysis. SN - 1001-5302 UR - https://www.unboundmedicine.com/medline/citation/32489073/[Transcriptomic_data_analyses_of_wild_and_cultivated_Angelica_sinensis_root_by_high-throughput_sequencing_technology]. L2 - https://antibodies.cancer.gov/detail/CPTC-CD48-1 DB - PRIME DP - Unbound Medicine ER -