Molecular Authentication of the Medicinal Species of Ligusticum (Ligustici Rhizoma et Radix, "Gao-ben") by Integrating Non-coding Internal Transcribed Spacer 2 (ITS2) and Its Secondary Structure

Molecular identification and studies on genetic diversity and structure-related GC heterogeneity of Spatholobus Suberectus based on ITS2

To determine the role of internal transcribed spacer 2 (ITS2) in the identification of Spatholobus suberectus and explore the genetic diversity of S. suberectus. A total of 292 ITS2s from S. suberectus and 17 other plant species were analysed. S. suberectus was clustered separately in the phylogenetic tree. The genetic distance between species was greater than that within S. suberectus. Synonymous substitution rate (Ks) analysis revealed that ITS2 diverged the most recently within S. suberectus (Ks = 0.0022). These findings suggested that ITS2 is suitable for the identification of S. suberectus. The ITS2s were divided into 8 haplotypes and 4 evolutionary branches on the basis of secondary structure, indicating that there was variation within S. suberectus. Evolutionary analysis revealed that the GC content of paired regions (pGC) was greater than that of unpaired regions (upGC), and the pGC showed a decreasing trend, whereas the upGC remained unchanged. Single-base mutation was the main cause of base pair substitution. In both the initial state and the equilibrium state, the substitution rate of GC was higher than that of AU. The increase in the GC content was partly attributed to GC-biased gene conversion (gBGC). High GC content reflected the high recombination and mutation rates of ITS2, which is the basis for species identification and genetic diversity. We characterized the sequence and structural characteristics of S. suberectus ITS2 in detail, providing a reference and basis for the identification of S. suberectus and its products, as well as the protection and utilization of wild resources.

A comprehensive review of the botany, ethnopharmacology, phytochemistry, pharmacology, quality control and other applications of Ligustici Rhizoma et Radix

ETHNOPHARMACOLOGICAL RELEVANCE

Ligusticum sinense Oliv. and L. jeholense Nakai et Kitag. are globally recognized as medicinal botanical species, specifically the rhizomes and roots. These plant parts are collectively referred to as Ligustici Rhizoma et Radix (LReR), which is recorded in the Pharmacopoeia of the People's Republic of China (Ch. P). LReR enjoys widespread recognition in many countries such as China, Russia, Vietnam, and Korea. It is an herbal remedy traditionally employed for dispelling wind and cold, eliminating dampness, and alleviating pain. Numerous bioactive compounds have been successfully isolated and identified, displaying a diverse array of pharmacological activities and medicinal value.

THE AIM OF THE REVIEW

This review aims to primarily center on the botanical aspects, ethnopharmacology, phytochemistry, pharmacology, toxicity, quality control, and other applications of LReR to furnish a comprehensive and multidimensional foundation for future exploration and utilization.

MATERIALS AND METHODS

Relevant information about LReR was acquired from ancient books, doctoral and master's dissertations, Google Scholar, Web of Science, PubMed, China National Knowledge Infrastructure (CNKI), ScienceDirect, classical literature, and clinical reports. Several electronic databases were also incorporated.

RESULTS

In traditional usage, LReR had been traditionally employed for the treatment of anemofrigid headaches, colds, and joint pain. It possessed therapeutic properties for facial skin disorders, thereby facilitating skin regeneration. It has been subjected to comprehensive chemical analysis, resulting in the identification and isolation of 190 compounds, including phthalides, phenylpropanoids, flavonoids, phenolic acids, triterpenes, steroids, volatile oil, fatty acids, and other constituents. The pharmacological activities have been in-depth explored through modern in vivo and in vitro studies, confirming its anti-inflammatory, analgesic, and anti-melanin effects. Furthermore, it exhibited pharmacological activities such as antioxidant, anticancer, antibacterial, and vasodilatory properties. This study provides a basic to contribute to the advancement of research, medicinal applications and product development related to LReR.

CONCLUSIONS

Considering its traditional and contemporary applications, phytochemical composition, and pharmacological properties, LReR was regarded as a valuable botanical resource for pharmaceutical and pest control purposes. While certain constituents had demonstrated diverse pharmacological activities and application potential, further elucidation was required to fully understand their specific actions and underlying mechanisms. Hence, there was a need to conduct additional investigations to uncover its material foundation and mode of action.

DNA barcoding of Notopterygii Rhizoma et Radix (Qiang-huo) and identification of adulteration in its medicinal services

Safety concerns, stemming from the presence of complex and unpredictable adulterants, permeate the entire industrial chain of traditional Chinese medicines (TCMs). The Notopterygii Rhizoma et Radix (NReR) from the Apiaceae family, commonly known as "Qiang-huo", is a widely used herbal medicine. The recent surge in its demand has given rise to a proliferation of counterfeit and substituted products in the market. Traditional identification presents inherent limitations, while DNA mini-barcoding, reliant on sequencing a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In this study, we constructed a comprehensive Internal Transcribed Spacer 2 (ITS2) matrix encompassing genuine NReR and their commonly found adulterants for the first time. Leveraging this matrix, we conducted a thorough assessment of the genetic profiles and sources of NReR available in the Chinese herbal medicine market. Following established DNA barcoding protocols, the intra-specific genetic divergences within NReR species were found to be lower than the inter-specific genetic divergences from other species. Among the 120 samples that were successfully amplified, ITS2 exhibits an outstanding species-level identification efficiency of 100% when evaluated using both the BLASTN and neighbor-joining (NJ) tree methods. We concluded that ITS2 is a mini-barcode that has shown its potential and may become a universal mini-barcode for the quality control of "Qiang-huo", thereby ensuring the safety of clinical medication.

Existing status and future advancements of adulteration detection techniques in herbal products

BACKGROUND

Herbal products have been commonly used all over the world for centuries. Its products have gained remarkable acceptance as therapeutic agents for a variety of disorders. However, following recent research disclosing discrepancies between labeling and actual components of herbal products, there is growing concern about the efficacy, quality and safety of the products. The admixture and adulteration of herbal medicinal products pose a risk of serious health compromise and the well-being of the consumers. To prevent adulteration in raw ingredients and final herbal products, it is necessary to use approaches to assess both genomes as well as metabolomics of the products; this offers quality assurance in terms of product identification and purity. The combinations of molecular and analytical methods are inevitable for thorough verification and quality control of herbal medicine.

METHODS AND RESULTS

This review discusses the combination of DNA barcoding, DNA metabarcoding, mass spectroscopy as well as HPLC for the authentication of herbal medicine and determination of the level of adulteration. It also discusses the roles of PCR and real-time PCR techniques in validating and ensuring the quality, purity and identity of the herbal products.

CONCLUSIONS

In conclusion, each technique has its own pros and cons, but the cumulative of both the chemical and molecular methods is proven to be the best strategy for adulteration detection. Moreover, CRISPR diagnosis tools equipped with multiplexing techniques may be implemented for screening adulteration from herbal drugs, this will play a crucial role in herbal product authentication in the future.

Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses

BACKGROUND

Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced.

RESULTS

The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029-155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61-67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported.

CONCLUSIONS

The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.

DNA Barcoding, Phylogenetic Analysis and Secondary Structure Predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana

Nepentheceae, the most prominent carnivorous family in the Caryophyllales order, comprises the Nepenthes genus, which has modified leaf trap characteristics. Although most Nepenthes species have unique morphologies, their vegetative stages are identical, making identification based on morphology difficult. DNA barcoding is seen as a potential tool for plant identification, with small DNA segments amplified for species identification. In this study, three barcode loci; ribulose-bisphosphate carboxylase (rbcL), intergenic spacer 1 (ITS1) and intergenic spacer 2 (ITS2) and the usefulness of the ITS1 and ITS2 secondary structure for the molecular identification of Nepenthes species were investigated. An analysis of barcodes was conducted using BLASTn, pairwise genetic distance and diversity, followed by secondary structure prediction. The findings reveal that PCR and sequencing were both 100% successful. The present study showed the successful amplification of all targeted DNA barcodes at different sizes. Among the three barcodes, rbcL was the least efficient as a DNA barcode compared to ITS1 and ITS2. The ITS1 nucleotide analysis revealed that the ITS1 barcode had more variations compared to ITS2. The mean genetic distance (K2P) between them was higher for interspecies compared to intraspecies. The results showed that the DNA barcoding gap existed among Nepenthes species, and differences in the secondary structure distinguish the Nepenthes. The secondary structure generated in this study was found to successfully discriminate between the Nepenthes species, leading to enhanced resolutions.

Phylogenetic position of Ligusticopsis (Apiaceae, Apioideae): evidence from molecular data and carpological characters

Ligusticopsis (Apiaceae, Apioideae) is now considered to have an East-Asia and Sino-Himalaya distribution. The genus was not recognized as a natural and separate genus and was treated as a synonym of Ligusticum both in Flora Reipublicae Popularis Sinicae and Flora of China since first established, though Pimenov et al. have made many taxonomic revisions to Ligusticopsis, phylogenetic relationships between Ligusticopsis and Ligusticum have been in dispute. Thirty-four plastomes and 35 nrITS from Apioideae were analysed by RAxML and MrBayes to reconstruct the phylogenetic relationships, along with carpology of 10 species and comparative analyses of 17 plastomes to investigate the evidence supporting the independence of Ligusticopsis. As a result, nine species suggested to be Ligusticopsis formed a highly supported monophyletic branch (Subclade A) inside Selineae both in maximum likelihood and Bayesian inference; the results of the comparative analyses further supported the monophyly of Subclade A, mainly in the location of genes at the IRa/LSC boundary, the sequence diversity exhibited by various genes (e.g. trnH-GUG-psbA and ycf2) and same codon biases in terminator TAA (relative synonymous codon usage = 1.75). Species in Subclade A also had shared characters in mericarps, combined with other characters of the plant, 'base clothed in fibrous remnant sheaths, pinnate bracts, pinnate bracteoles longer than rays of umbellule, mericarps strongly compressed dorsally, median and lateral ribs filiform or keeled, marginal ribs winged, and numerous vittae in commissure and each furrow' should be the most important and diagnostic characters of Ligusticopsis. Our phylogenetic trees and other analyses supported the previous taxonomic treatments of Pimenov et al. that Ligusticopsis should be a natural and separate genus rather than a synonym of Ligusticum.

Study on the identification and evaluation of growth years for Paris polyphylla var. yunnanensis using deep learning combined with 2DCOS

Paris polyphylla var. yunnanensis, as perennial plants, its quality is closely related to growth period. Different harvest years determine the dry matter accumulation of its medicinal parts and the dynamic accumulation of active ingredients, as well as its economic value and medicinal value. Therefore, it is necessary to establish a systematic evaluation method for the identification and evaluation of P. polyphylla var. yunnanensis with different growth years. Deep learning has a powerful ability in recognition. This study extends it to the identification analysis of medicinal plants from the perspective of spectrum. For the first time, two-dimensional correlation spectroscopy (2DCOS) based on the attenuated total reflection Fourier transformed infrared spectroscopy (ATR-FTIR) combined with residual neural network (Resnet) was used to identify growth years. 525 samples were collected, 4725 2DCOS images were drawn, and the dry matter accumulation in rhizomes of different growth years and different sampling sites were briefly analyzed. The results show that the eight-year-old P. polyphylla var. yunnanensis in Dali has higher economic value and medicinal value. The synchronous 2DCOS models based on ATR-FTIR can realize the identification of growth years with accuracy of 100%. Synchronous 2DCOS are more suitable for the identification of medicinal plants with complex systems. 2DCOS images with different colors and second derivative processing cannot optimize the modeling results. In summary, the method we established is innovative and feasible. It not only solved the identification of growth years, expanded the application field of deep learning, but could also be extended to further research on other medicinal plants.

Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

The Pikad Tri-phol-sa-mut-than (TS) remedy, a Thai traditional medicine, is officially recorded in Tamra Paetsart Sonkrau Chabub Anurak for its capabilities in treating kidney deficiency. TS remedy is composed of three fruit species—Aegle marmelos (L.) Corrêa., Coriandrum sativum L., and Morinda citrifolia L.—in an equal part by weight. The quality of the raw material is one of the essential factors that can affect the effectiveness and safety of treatment by herbal remedy. The pharmacognostic evaluation and DNA barcode of the three fruit species and TS remedy were performed in this study to authenticate them from contamination, and to provide the scientific database for further uses. Macroscopic and microscopic examination, chemical profile by TLC, and DNA barcoding were employed to positively identify the raw materials bought from the herbal market, especially the powder form. Consequently, the outcomes of this investigation can be used to develop an essential and effective tool for the authentication of crude drugs and herbal remedies.

Verification of Thai ethnobotanical medicine "Kamlang Suea Khrong" driven by multiplex PCR and powerful TLC techniques

Kamlang Suea Khrong (KSK) crude drug, a traditional Thai medicine used for oral tonic and analgesic purposes, is obtained from three origins: the inner stem bark of Betula alnoides (BA) or the stems of Strychnos axillaris (SA) or Ziziphus attopensis (ZA). According to the previous reports, SA contains strychnine-type alkaloids that probably cause poisoning; however, only organoleptic approaches are insufficient to differentiate SA from the other plant materials. To ensure the botanical origin of KSK crude drug, powerful and reliable tools are desperately needed. Therefore, molecular and chemical identification methods, DNA barcoding and thin-layer chromatography (TLC), were investigated. Reference databases, i.e., the ITS region and phytochemical profile of the authentic plant species, were conducted. In case of molecular analysis, multiplex polymerase chain reaction (PCR) based on species-specific primers was applied. Regarding species-specific primers designation, the suitability of three candidate barcode regions (ITS, ITS1, and ITS2) was evaluated by genetic distance using K2P model. ITS2 presented the highest interspecific variability was verified its discrimination power by tree topology. Accordingly, ITS2 was used to create primers that successfully specified plant species of authentic samples. For chemical analysis, TLC with toluene:ethyl acetate:ammonia (1:9:0.025) and hierarchical clustering were operated to identify the authentic crude drugs. The developed multiplex PCR and TLC methods were then applied to identify five commercial KSK crude drugs (CK1-CK5). Both methods correspondingly indicated that CK1-CK2 and CK3-CK5 were originated from BA and ZA, respectively. Molecular and chemical approaches are convenient and effective identification methods that can be performed for the routine quality-control of the KSK crude drugs for consumer reliance. According to chemical analysis, the results indicated BA, SA, and ZA have distinct chemical profiles, leading to differences in pharmacological activities. Consequently, further scientific investigations are required to ensure the quality and safety of Thai ethnobotanical medicine known as KSK.

Internal transcribed spacer primer evaluation for vascular plant metabarcoding

The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.

Molecular Identification and Phylogenetic Analysis of the Traditional Chinese Medicinal Plant Kochia scoparia Using ITS2 Barcoding

Kochia scoparia has high medicinal and economic value. However, with similar morphological features, adulterants and some closely related species of K. scoparia are increasingly sold in the medicinal markets, leading to potential safety risks. In this study, 128 internal transcribed spacer 2 (ITS2) sequences were collected to distinguish K. scoparia from its closely related species and adulterants. Then, sequence alignment, sequence characteristics analysis, and genetic distance calculations were performed using MEGA 6.06 software, and the phylogenetic trees were reconstructed using both MEGA 6.06 and IQ-Tree software. Finally, the secondary structure of ITS2 was modeled using the prediction tool in the ITS2 database. The results showed that ITS2 sequences of K. scoparia ranged in length from 226 to 227 bp, with a mean GC content of 55.3%. The maximum intraspecific distance was zero, while the minimum interspecific distance from closely related species and adulterants was 0.009 and 0.242, respectively. Kochia scoparia formed an independent clade in the phylogenetic trees, and its secondary structure exhibited enough variation to be separated from that of other species. In summary, ITS2 can be used as a mini-barcode for distinguishing K. scoparia from closely related species and adulterants. Its phylogenetic trees could illustrate the evolutionary process of K. scoparia in the Camphorosmeae. The phylogenetic results using ITS2 barcode further supported the internationally recognized revised classifications of Kochia and Bassia genera as a combined Bassia genus, together with the establishment of new genera Grubovia and Sedobassia, which we suggest is accepted by the Flora of China. Graphical abstract .

Recent advances of novel technologies for quality consistency assessment of natural herbal medicines and preparations

Quality consistency is one of the basic attributes of medicines, but it is also a difficult problem that natural medicines and their preparations must face. The complex chemical composition and comprehensive pharmacological action of natural medicines make it difficult to simply apply the commonly used evaluation methods in chemical drugs. It is thus urgent to explore the novel evaluation methods suitable for the characteristics of natural medicines. With the rapid development of analytical techniques and the deepening understanding of the quality of natural herbs, increasing numbers of researchers have proposed many new ideas and technologies. This review mainly focuses on the basic principles, technical characteristics and application examples of the chemical evaluation, biological evaluation methods and their combination in quality consistency evaluation of natural herbs. On the bases of chemical evaluation and clinical efficacy, new methods reflecting their pharmacodynamic mechanism and safety characteristics will be developed, and gradually towards accurate quality control, to achieve the goal of quality consistency. We hope that this manuscript can provide new ideas and technical references for the quality consistency of natural drugs and their preparations, thus better guarantee their clinical efficacy and safety, and better promote industrial development.

DMSO and betaine significantly enhance the PCR amplification of ITS2 DNA barcodes from plants

ITS2 marker is highly efficient in species discrimination but its application in DNA barcoding is limited due to huge variations in the PCR success rate. We have hypothesized that higher GC content and the resultant secondary structures formed during annealing might hinder the PCR amplification of ITS2. To test this hypothesis, we selected 12 species from 12 different families in which ITS2 was not amplified under standard PCR reaction conditions. In these samples, DMSO, formamide, betaine, and 7-deaza-dGTP were evaluated for their ability to improve the PCR success rate. The highest PCR success rate (91.6%) was observed with 5% DMSO, followed by 1 M betaine (75%), 50 μM 7-deaza-dGTP (33.3%), and 3% formamide (16.6%). The one sample that did not amplify with DMSO was amplified by adding 1 M betaine. However, combining DMSO and betaine in the same reaction did not improve the PCR. Therefore, to achieve the highest PCR success rate for ITS2, it is recommended to include 5% DMSO by default and substitute it with 1 M betaine only in the case of failed reactions. When this strategy was tested in 50 species from 43 genera and 29 families, the PCR success rate of ITS2 increased from 42% to 100%.