Sequencing analysis of the medicinal plant Stemona tuberosa and five related species existing in Thailand based on trnH-psbA chloroplast DNA

DNA barcoding of species of Bacopa coupled with high-resolution melting analysis

In Thailand, there are three species of Bacopa, namely, B. monnieri, B. caroliniana, and B. floribunda. Among these species of Bacopa, B. monnieri is the only medicinal species, used for the treatment of cognitive impairment and improvement of cognitive abilities because of its bioactive constituents, bacoside A and B. However, because of the similar characteristics of these species, it is difficult to differentiate among related species, resulting in confusion during identification. For this reason, and to ensure therapeutic quality for consumers, authentication is important. In this study, the three abovementioned species of Bacopa were evaluated using barcoding coupled with high-resolution melting (Bar-HRM) analysis based on primers designed for the trnL-F sequences of the three species. The melting profiles of the trnL-F amplicons of B. caroliniana and B. floribunda were clearly different from the melting profile of the trnL-F amplicon from B. monnieri; thus, the species could be discriminated by Bar-HRM analysis. Bar-HRM was then used to authenticate commercial products in various forms. The melting curves of the six commercial samples indicated that all the tested products contained genuine B. monnieri species. This method provides an efficient and reliable authentication system for future commercial herbal products and offers a reference system for quality control.

The changing epitome of species identification - DNA barcoding

The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.

Effect of Stemona spp. against Rhipicephalus microplus

Stemona plants have been traditionally used against various insects in Thailand and Southeast Asian countries. The acaricidal efficacy of 9 species of Stemona grown in Thailand was evaluated against dairy cattle tick, Rhipicephalus microplus using adult immersion test and in vivo evaluation on infested calves. From the ten Stemona root extracts used in this study, S. collinsiae of a concentration 250 mg/ml possessed the highest activity. In vivo study revealed that S. collinsiae extract could significantly reduce the attached ticks on calf skin compared to the control and promoted not significantly different efficacy from flumethrin, a common pyrethroid used in dairy farms. No side effect was found on calves during the experiment. The results confirmed traditional use of S. collinsiae as a better source of insecticide than other species and could be used as guidance for further development of S. collinsiae as a herbal acaricide.

The diversity of Stemona stilbenoids as a result of storage and fungal infection

In relation to their biogenetic origin, 68 Stemona stilbenoids have been grouped into four structural types and are listed in order of increasing substitution pattern. Besides different hydroxylations and methoxylations, the rare C-methylations of the aromatic rings represent a typical chemical feature of these compounds. The formation of phenylbenzofurans constitutes another important chemical character separating Stemona species into two groups consistent with morphological and DNA data. Fungal infection leads to an increasing accumulation of stilbenes, dihydrostilbenes, and phenylbenzofurans with unsubstituted A-rings, suggesting the ecological role of these compounds as phytoalexins. Further oxygenations and methylations of both rings are interpreted as a result of aging or the drying processes. Bioautographic tests on TLC plates and germ-tube inhibition assays in microwells against four different fungi exhibited antifungal activities for almost all stilbenoids tested. Some derivatives also showed effects against yeasts and bacteria. Further activities may also be seen as dormancy-inducing factors of Stemona species occurring in periodically dry habitats. A leucotriene biosynthesis inhibition assay using 15 stilbenoids showed interesting structure-activity relationships, with more potent effects of some compounds than the commercial 5-lipoxygenase inhibitor zileuton being observed. Potential neuroprotective activities have been reported for three dihydrostilbene glucosides against 6-hydroxydopamine-induced neurotoxicity in human neuroblastoma SH-SY5Y cells.

Discrimination of the Thai rejuvenating herbs Pueraria candollei (White Kwao Khruea), Butea superba (Red Kwao Khruea), and Mucuna collettii (Black Kwao Khruea) using PCR-RFLP

The tuberous roots of Pueraria candollei (White Kwao Khruea), Butea superba (Red Kwao Khruea) and Mucuna collettii (Black Kwao Khruea), which belong to the family Leguminosae, are used as rejuvenating herbs in traditional Thai medicine. Although all of these species have an indication for rejuvenation, each differs in its medicinal properties. Two varieties of P. candollei, var. mirifica and var. candollei, affect females, whereas B. superba and M. collettii exhibit effects on males. However, the identification of these roots according to the name "Kwao Khruea" is confusing due to the similarity in their features. Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) was utilised to identify plant origin. The partial matK gene was amplified and subjected to restriction enzyme digestion with DdeI and TaqI. The restriction fragments generated differed in number and size. To test the reliability of the method, an admixture of the different Kwao Khruea species containing equal amounts of DNA was tested. The results showed combined restriction patterns, and each species could be detected in the background of the others. The method was also used to authenticate eight different crude drugs sold as various types of Kwao Khruea in Thai markets. The results showed that the misidentification of commercial drugs remains a problem in crude drug markets. The PCR-RFLP analysis developed here provides a simple and accurate discrimination of these rejuvenating "Kwao Khruea" species.

Plant genetics for forensic applications

An emerging application for plant DNA fingerprinting and barcoding involves forensic investigations. Examples of DNA analysis of botanical evidence include crime scene analysis, identifying the source of commercial plant products, and investigation of trade in illicit drugs. Here, we review real and potential applications of DNA-based forensic botany and provide a protocol for microsatellite genotyping of leaf material, a protocol that could be used to link a suspect to a victim or to a crime scene.

Molecular analysis of Stemona plants in China based on sequences of four chloroplast DNA regions

Stemona sessilifolia, S. japonica and S. tuberosa are the three original sources of Stemonae Radix specified in the Chinese Pharmacopoeia (CP), and have been traditionally used for antitussive and insecticidal remedy. Significant variations in alkaloids composition and content, as well as different degrees of antitussive activities were found among them. In order to identify the genuine sources of Stemonae Radix accurately in genetic level, we determined the nucleotide sequences of chloroplast DNA trnL-trnF, trnH-psbA, petB-petD and trnK-rps16 regions of the species recorded in CP and S. parviflora, as well as the common counterfeits of Stemonae Radix, Asparagus species. The results revealed that the sequences of petB-petD and trnK-rps16 regions, showing relatively high substitution rate, were more informative than those of trnL-trnF and trnH-psbA regions. The sequences from all the four regions provided useful information to discriminate the three CP species from each other and from S. parviflora and the counterfeits. A phylogenetic tree reconstructed by the trnH-psbA sequences for 9 Stemona species distributed in China and Thailand showed that the three CP species belonged to the same clade, among which S. japonica and S. sessillifolia formed a sister group, showing closer relations to each other than to S. tuberosa. By contrast, S. parviflora was genetically far from the three CP species. Intra-species variations were observed in the three CP species. Especially, in S. tuberosa two types of petB-petD sequence and four types each of trnL-trnF, trnK-rps16 and trnH-psbA sequences resulted in 6 haplotypes; whereas, these differences had no relation with the different chemical types, but seemed to be consistent with geographical distribution.