Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia

Quantification of adulteration in traded ayurvedic raw drugs employing machine learning approaches with DNA barcode database

Adulteration of expensive raw drugs with inferior taxa has become a routine practice, conceding the quality and safety of derived herbal products. In this regard, the study addresses the development of an integrated approach encompassing DNA barcode and HPTLC fingerprinting to authenticate chiefly traded ayurvedic raw drugs in south India [viz. Saraca asoca (Roxb.) Willd., Terminalia arjuna (Roxb. ex DC.) Wight and Arn., Sida alnifolia L. and Desmodium gangeticum (L.) DC.] from its adulterants. Consortium of Barcode of Life (CBOL) recommended DNA barcode gene regions viz. nuclear ribosomal-Internal Transcribed Spacer (nrDNA-ITS), maturase K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and psbA-trnH spacer regions along with HPTLC profiling were experimented and a reference database was created. Further, an integrated analytical approach employing genetic distance-based Maximum Likelihood phylogenetic tree and Artificial Intelligence (AI)based Machine Learning Algorithms (MLA)-Waikato Environment for Knowledge Analysis (WEKA) and Barcoding with Logic (BLOG) were employed to prove efficacy of DNA barcode tool. Even though, among the four barcodes, psbA-trnH (S. alnifolia and its adulterants, T. arjuna and its adulterants) or ITS region (S. asoca and its adulterants, D. gangeticum and its adulterants) showed highest inter specific divergences in the selected Biological Reference Materials (BRMs), rbcL or matK barcode regions alone were successful for authentication of traded samples. The automated species identification techniques, WEKA and BLOG, experimented for the first time in India for raw drug validation, could achieve rapid and precise identification. A national certification agency for raw drug authentication employing an integrated approach involving a DNA barcoding tool along with standard organoleptic and analytical methods can strengthen and ensure safety and quality of herbal medicines in India.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03001-5.

DNA barcodes for the identification of Stephania (Menispermaceae) species

Stephania is a medicinal plants-rich genus of Menispermaceae. However, the identification of morphologically-similar species in Stephania is difficult using the currently reported methods. The indiscriminate overexploitation of Stephania plants has resulted in clinical misuse and endangerment of many species, which necessitates the development of an efficient and reliable method for species authentication. Therefore, six candidate DNA barcode sequences (ITS, ITS2, psbA-trnH, matK, rbcL, and trnL-F) were tested for their capacity to identify Stephania species. The barcodes were analyzed either as a single region or in combination by tree-based [neighbor-joining (NJ) and Bayesian inference (BI)], distance-based (PWG-distance), and sequence similarity-based (TaxonDNA) methods. Amplification and sequencing success rates were 100% for all six candidate barcodes. A comparison of six barcode regions showed that ITS exhibited the highest number of variable and informative sites (182/179), followed by psbA-trnH (173/162). DNA barcoding gap assessment showed that interspecific distances of the six barcodes were greater than intraspecific distances. The identification results showed that species discrimination rates of combination barcodes were higher than those of single-region barcodes. Based on best match and best close match methods, the ITS+psbA-trnH combination exhibited the highest discrimination power (93.93%). Further, all Stephania species could be resolved in the phylogenetic trees based on ITS+psbA-trnH (NJ, BI). This study demonstrates that DNA barcoding is an efficient method to identify Stephania species and recommends that the ITS+psbA-trnH combination is the best DNA barcode for the identification of Stephania species.

Employing barcoding markers to authenticate selected endangered medicinal plants traded in Indian markets

The high demand of medicinal plants and their unrestricted collection have rendered many of these as rare or endangered. The restrictions imposed on their collection and trade are difficult to implement because of the inability to identify them in fragmented form. The rarity of these plants in nature and lack of their cultivation raise doubt about the authenticity of the herbals sold in markets. Therefore, in the present investigation, ITS/ITS2, matK, rbcL and rpoC1 sequences of fourteen species of important medicinal plants, some of which are endangered, were generated and checked for their species-specificity (sequences having maximum similarity only with their own) by BLAST1 and/or BOLD identifications. ITS sequences of 12 species were species-specific. However, ITS2 of only 10 of these 12 species were species-specific. As for the chloroplast loci, rbcL and rpoC1 sequences of all 14 species could be obtained, while matK sequences of only 10 of these could be generated. Of the retrieved sequences, rbcL, rpoC1 and matK sequences of 7, 11 and 7 species, respectively, were species-specific. The sequences of the targeted loci from the herbal samples of these species were difficult to retrieve because of failure in the amplification or sequencing. Nevertheless, based on ITS2 and/or one or more of the chloroplast loci targeted, the botanical identities of 22 herbal market samples were checked by phylogenetic tree, BLAST1 and BOLD identification methods. Of these 22 samples, only one of each of Rauvolfia serpentina and Picrorhiza kurroa were found to be authentic.

Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs

Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes (rbcL and matK) and intergenic spacers (psbA-trnH and ITS) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S. italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 (S. alexandrina crude drug sample from Bangalore) and HSA06 (S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S. italica subsp. micrantha. Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply chain. CIMAP Communication Number: CIMAP/PUB/2017/31.

Character-based DNA barcoding for authentication and conservation of IUCN Red listed threatened species of genus Decalepis (Apocynaceae)

The steno-endemic species of genus Decalepis are highly threatened by destructive wild harvesting. The medicinally important fleshy tuberous roots of Decalepis hamiltonii are traded as substitute, to meet the international market demand of Hemidesmus indicus. In addition, the tuberous roots of all three species of Decalepis possess similar exudates and texture, which challenges the ability of conventional techniques alone to perform accurate species authentication. This study was undertaken to generate DNA barcodes that could be utilized in monitoring and curtailing the illegal trade of these endangered species. The DNA barcode reference library was developed in BOLD database platform for candidate barcodes rbcL, matK, psbA-trnH, ITS and ITS2. The average intra-specific variations (0-0.27%) were less than the distance to nearest neighbour (0.4-11.67%) with matK and ITS. Anchoring the coding region rbcL in multigene tiered approach, the combination rbcL + matK + ITS yielded 100% species resolution, using the least number of loci combinations either with PAUP or BLOG methods to support a character-based approach. Species-specific SNP position (230 bp) in the matK region that is characteristic of D. hamiltonii could be used to design specific assays, enhancing its applicability for direct use in CITES enforcement for distinguishing it from H. indicus.