Application of phylogenomics in Chinese medicine resources / 中国中药杂志

China is rich in the diversified Chinese medicine resources and is notable for the wide and long-term applications of Chinese medicine. However,the lack of genomic information on medicinal taxa leads to problems in relation to resource conservation and the downstream application of traditional Chinese medicine resources,which restricts the modernization process of traditional Chinese medicine. Molecular phylogenetics is an important tool to understand the origin and evolution of the earth's biodiversity and promote the conservation and use of medicinal taxa. With the development of sequencing technology,the combination of genomic data extends the traditional molecular phylogenetics to the research level of phylogenomics,making it more powerfully applied to all aspects of biological research. Undoubtedly,carrying out phylogenomic research on Chinese medicine species will greatly promote their resources conservation,molecular evaluation and identification,and the exploration and utilization of natural pharmacodynamic components,promoting the modernization of traditional Chinese medicine. This article starts with a brief introduction of the developing history and basic research methods of phylogenomics,and then reviews the current research progress in phylogenomics related to traditional Chinese medicine resources. Finally,it discusses the problems existing in the current research and the next direction of phylogenomics research in medicinal taxa. The article will hopefully provide a reference for relevant researches in future.

Current Status and Prospect of Discipline Construction of Herbgenomics / 中国实验方剂学杂志

Herbgenomics is an interdisciplinary subject between traditional Chinese medicine(TCM) and genomics.It is a comprehensive discipline covering multi-omics research in both medicinal organisms of TCM and the relationship of TCM to human body.It has been widely used in the research fields of medicinal model organisms,synthetic biology of TCM,identification of TCM molecules and breeding of medicinal plant cultivars,pharmacokinetics,and the study on the geoherbalism and medicinal of TCM.With the release of important documents,such as the Law of the People's Republic of China on TCM and the Outline of TCM Development Strategy(2016-2030),the Chinese medicine industry has entered a new and high-level development opportunity and the herbgenomic research area has got a landmark achievement.The training of well-rounded students and researchers is a key point for the development of TCM industry and the reform of medical colleges and universities.Therefore,the establishment of herbgenomics is particularly important for the modernization of TCM.At present,many colleges and universities have set up the course of Herbgenomics among graduate students and undergraduates,and initially formed a distinctive herbal genomics talent training system.This paper introduces the herbgenomics from the progress of the research,the development of teaching courses,the background of the textbook,the main content and key technologies of the discipline and the prospect of discipline construction,in order to provide theoretical basis and methodological support for the discipline construction,personal training and scientific research of herbgenomics.

Application of HRM combined with DNA barcoding to analysis of the Armeniacae semen amarum mixed in Persicae semen / 药学学报

Persicae semen has been used for years as a traditional Chinese medicine to treat diseases. Because of their similar morphologies, Persicae semen was commonly inadvertently mixed with Armeniacae semen amarum (a toxic herbal seed). Development of a reliable method for discriminating Persicae semen from its adulterant is necessary to reduce confusion for the drug safety in clinical practices. This study evaluates the efficiency of high-resolution melting (HRM) combined with internal transcribed spacer 2 (ITS2) to analyze Persicae semen. Our findings show that HRM allows not only the identification of adulteration but also the quantification of the most common admixture. HRM sensitivity in adulterant detection was assessed through the analysis of mixing samples with different proportions of Prunus persica and Prunus armeniaca control. The results are presented as a linear regression with r of 0.96 and imply the capability of the method to detect adulteration. In particular, HRM detected seeds of Prunus persica in Prunus armeniaca at concentrations as low as 1%, and commercial products labeled as ‘Persicae semen’ were purchased from markets and could rapid authenticated by HRM analyses. This study is significant in the verification of the authenticity in the quality control of herbal medicine. In the near future, it is promising to be the main trend for identifying traditional Chinese medicinal materials.

Application of high resolution melting curve to identification of Cimicifugae Rhizoma / 药学学报

High-resolution-melting analysis (HRM) is a new technology derived from qPCR and is widely used in the study of polymorphism, genotyping, and single nucleotide mutation. Advantages of HRM include cost-effectiveness and time-efficiency over PCR-based genotyping. However, the application of HRM in the authentication of herbal products is still limited with few studies on the classification and identification of herbal products. In this study, Cimicifugae Rhizoma was used as an example to verify the stability and accuracy of HRM technique in identification of Chinese materia medica. HRM assay was established for identification based on ITS2 region of Cimicifugae Rhizomas and its adulterants (including 41 samples). Our findings showed that HRM allows not only the identification of adulteration but also the quantification of the most common admixture. This study is significant for better quality in the verification of the authenticity of herbal medicine. The method is promising for future identification of traditional Chinese medicinal materials.

ITS2 barcoding DNA region combined with high resolution melting (HRM) analysis of Hyoscyami Semen, the mature seed of Hyoscyamus niger / 中国天然药物

Hyoscyami Semen, the mature dried seed of Hyoscyamus niger L., has long been used as a traditional Chinese medicine to treat human diseases. Hyoscyami Semen is found in local markets in China. In markets, sellers and buyers commonly inadvertently mix the seeds of H. niger with the seeds of related species such as Hygrophila salicifolia (Vahl) Nees, Astragalus complanatus R. Br., Cuscuta australis R. Br., Cuscuta chinensis Lam., and Impatiens balsamina L. because of their similar morphologies or similar names. Thus, developing a reliable method for discriminating H. niger seeds from its adulterants is necessary to reduce confusion and ensure the safe use of Hyoscyami Semen. The present study was designed to evaluate the efficiency of high-resolution melting analysis combined with DNA barcoding (Bar-HRM) with internal transcribed spacer 2 to discriminate H. niger. Our results show that Bar-HRM successfully identified the adulterants and detected the proportion of H. niger DNA extract within an admixture. In particular, HRM detected H. niger DNA extract in A. complanatus DNA extract at concentrations as low as 1%. In conclusion, the Bar-HRM method developed in the present study for authenticating H. niger is rapid and cost-effective. It can be used in the future to guarantee the purity of Hyoscyami Semen for the clinical use.

Identification of moutan cortex and its adulterants by ITS2 sequence / 中国中药杂志

To explore a new method to identify Moutan Cortex to guarantee its safe use, internal transcribed spacer 2 (ITS2) sequence was used to identify Moutan Cortex and its adulterants. DNA was extracted and target fragments were amplified. Sequences were analyzed and assembled by CodonCode Aligner V3.7.1. Genetic distances were computed and phylogenetic tree was constructed based on kimura 2-parameter (K2P) model by MEGA 5.0. The length of the 20 ITS2 sequences of Moutan Cortex from nine different places is 227 bp, and no variation site was detected. The maximum inter-specificK2P distance of Moutan Cortex is 0, the minimum intra-specific K2P distance is 0.041, the average intra-specific K2P distance is 0.222. According to NJ analysis, Moutan Cortex from different places can get together as one branch with bootstrap support values 99%, which indicates Moutan Cortex can be easily distinguished from its adulterants. Using ITS2 sequence can accurately identify Moutan Cortex and its adulterants, it is an effective supplementary to traditional identification methods.

High-throughput pyrosequencing of the complete chloroplast genome of Magnolia officinalis and its application in species identification / 药学学报

Chloroplast genome sequences have comprehensive application prospects in DNA barcoding and chloroplast engineering in traditional Chinese medicine. The complete chloroplast genome of Magnolia officinalis sequenced by high-throughput pyrosequencing and a sequencing procedure was established. Fourteen contigs were obtained after de nove assembly. The sequencing percent of coverage was 99.99%. The chloroplast genome is 160 183 bp in size, and has a typical quadripartite structure with the large (LSC, 88 210 bp) and small copy (SSC, 18 843 bp) regions separated by two copies of an inverted repeat (IRs, 26 565 bp each). chloroplast genes were successfully annotated, of which 17 genes located in each IR region. The chloroplast genome features in Magnolia officinalis are nearly identical to those from other Magnoliid chloroplast genomes. Phylogenetic analyses were performed based on 81 shared coding-genes for a total of 9 Magnolia samples of 5 closely related species. Results showed that distinguishing among species was generally straightforward at the species and population level. This study confirmed the effectiveness of our chloroplast genome sequencing procedure. The chloroplast genome can provide distinguishing differences to help identify Magnolia officinalis and its closely related plants.