DNA barcoding augments conventional methods for identification of medicinal plant species traded at Tanzanian markets

Veldman, Sarina; Ju, Yingzi; Otieno, Joseph; Abihudi, Siri; Posthouwer, Chantal; Gravendeel, Barbara; Andel, Tinde van; Boer, Hugo de

doi:10.1016/j.jep.2019.112495

Cited by 29 publications

(28 citation statements)

References 48 publications

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“…However, these methods suffer from several limitations and hence are not ideal for the analysis of herbal formulations containing multiple plants 33 . DNA is universally present in all plants and is not affected by environmental variations, in contrast to plant metabolites, which are prone to seasonal and climatic variations 34 . The British Pharmacopeia has already included DNA based methods for herbal drug identification 35,36 .…”

Section: Resultsmentioning

confidence: 99%

“…33 DNA is universally present in all plants and is not affected by environmental variations, in contrast to plant metabolites, which are prone to seasonal and climatic variations. 34 The British Pharmacopeia has already included DNA based methods for herbal drug identification. 35,36 The genomic DNA extracted from the fresh leaves of plants used as a reference was found to be intact while total DNA extracted from herbal formulations was sheared.…”

Section: Resultsmentioning

confidence: 99%

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DNA meta‐barcoding using rbcL based mini‐barcode revealed presence of unspecified plant species in Ayurvedic polyherbal formulations

Pandit

Travadi

Sharma

et al. 2021

Phytochemical Analysis

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Introduction Ayurveda takes advantage of the beneficial properties of medicinal plants. High demands in combination with inadequate availability of botanicals and a lack of knowledge with respect to their precise identification lead to adulterations in herbal products. Identification becomes more difficult in complex herbal formulations. Four different polyherbal formulations have been analyzed for the present paper. The targeted plants have different pharmacological properties for various ailments. Objective We aimed to examine the rbcL gene based plant DNA mini‐barcode to identify target and non‐target plants in polyherbal formulations by using high‐throughput next generation sequencing. Methods Degenerate primers of the selected mini‐barcode region have been identified from the literature. A blend of 30 authentic medicinal plant species was used to examine the species resolution capacity of the mini‐barcode. DNA was isolated from herbal formulations, an amplicon library was prepared, and sequencing was performed on an IonS5 system. Data were analyzed using various bioinformatics tools. Results Analysis of control pooled samples revealed the optimum resolving power of the DNA mini‐barcode. Data analysis of the commercial samples revealed that only one herbal formulation contained all plants and matched with listed contents. In two formulations, only 10 out of 21 and 11 out of 20 plants were detected, respectively. Additionally, several non‐listed plants were also detected in these formulations. Two formulations contained >20% reads assigned to non‐target plants. Overall, 21.98% of the reads were assigned to non‐target plants. Conclusion The present study clearly demonstrated the successful application and potential of meta‐barcoding in the quality control of complex herbal matrices. The results strongly suggest that this approach can be used in pharmacovigilance of processed herbal products.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

DNA meta‐barcoding using rbcL based mini‐barcode revealed presence of unspecified plant species in Ayurvedic polyherbal formulations

Pandit

Travadi

Sharma

et al. 2021

Phytochemical Analysis

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“…DNA metabarcoding, which allows for rapid and cost‐effective identification of the biodiversity of the entire sample across a wide range of taxa and habitats, has proved its usefulness for prokaryotic and eukaryotic species identification. Many examples of this approach have been provided in biodiversity assessment of bacteria (e.g., Adamczyk et al., 2019; Cordier, 2019; Thapa, Zhang, & Allen, 2019), fungi (e.g., Hu et al., 2019; Luis et al., 2019; Xiao et al., 2019), plants (e.g., Bell et al., 2019; Tnah et al., 2019; Veldman et al., 2020) and animals from micro‐ to megafauna (e.g., Dopheide et al., 2019; Head et al., 2018; Lynggaard et al., 2019). However, there are still groups of organisms for which metabarcoding could offer new perspectives, especially with regard to high‐throughput identification and diagnostics of pathogens and pests (Tedersoo, Drenkhan, Anslan, Morales‐Rodriguez, & Cleary, 2018).…”

Section: Introductionmentioning

confidence: 99%

A new method of metabarcoding Microsporidia and their hosts reveals high levels of microsporidian infections in mosquitoes (Culicidae)

Trzebny

Słodkowicz-Kowalska

Becnel

et al. 2020

Molecular Ecology Resources

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DNA metabarcoding offers new perspectives, especially with regard to the highthroughput identification and diagnostics of pathogens. Microsporidia are an example of widely distributed, opportunistic and pathogenic microorganisms in which molecular identification is important for both environmental research and clinical diagnostics. We have developed a method for parallel detection of both microsporidian infection and the host species. We designed new primer sets: one specific for the classical Microsporidia (targeting the hypervariable V5 region of small subunit [ssu] rDNA), and a second one targeting a shortened fragment of the COI gene (standard metazoan DNA-barcode); both markers are well suited for next generation sequencing. Analysis of the ssu rDNA data set representing 607 microsporidian species (120 genera) indicated that the V5 region enables identification of >98% species in the data set (596/607). To test the method, we used microsporidians that infect mosquitoes in natural populations. Using mini-COI data, all field-collected mosquitoes were unambiguously assigned to seven species; among them almost 60% of specimens were positive for at least 11 different microsporidian species, including a new microsporidian ssu rDNA sequence (Microsporidium sp. PL01). Phylogenetic analysis showed that this species belongs to one of the two main clades in the Terresporidia. We found a high rate of microsporidian co-infections (9.4%). The numbers of sequence reads for the operational taxonomic units suggest that the occurrence of Nosema spp. in co-infections could benefit them; however, this observation should be retested using a more intensive host sampling. Our results show that DNA barcoding is a rapid and cost-effective method for deciphering sample diversity in greater resolution, including the hidden biodiversity that may be overlooked using classical methodology.

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“…In addition to the traditional methods recommended in the THP, DNA barcoding with selected gene candidates, such as matK, rbcL, ITS, and psbA-trnH spacer, has been applied for discrimination of plant species [28][29][30] . In this study, DNA barcoding analysis was performed for comparison of C. cinereum and E. sonchifolia sequences.…”

Section: Discussionmentioning

confidence: 99%

“…The rbc L gene revealed the lowest nucleotide variation (5.13%) among the DNA barcode regions, which correlated with results from previous work 28 . Recently, Veldman et al 29 showed that rbc L exhibited very low discriminatory power, making it suitable for identification of plants at the family level. In this study, the full-length mat K sequence was obtained even though it has been reported that mat K has a low sequencing success rate in medicinal plants because of low primer universality 30 .…”

Section: Discussionmentioning

confidence: 99%

Differentiation of Cyanthillium cinereum, a smoking cessation herb, from its adulterant Emilia sonchifolia using macroscopic and microscopic examination, HPTLC profiles and DNA barcodes

Thongkhao

Pongkittiphan

Phadungcharoen

et al. 2020

Sci Rep

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Cyanthillium cinereum (L.) H.Rob. is one of the most popular herbal smoking cessation aids currently used in Thailand, and its adulteration with Emilia sonchifolia (L.) DC. is often found in the herbal market. Therefore, the quality of the raw material must be considered. This work aimed to integrate macro- and microscopic, chemical and genetic authentication strategies to differentiate C. cinereum raw material from its adulterant. Different morphological features between C. cinereum and E. sonchifolia were simply recognized at the leaf base. For microscopic characteristics, trichome and pappus features were different between the two plants. HPTLC profiles showed a distinct band that could be used to unambiguously differentiate C. cinereum from E. sonchifolia. Four triterpenoid compounds, β-amyrin, taraxasterol, lupeol, and betulin, were identified from the distinct HPTLC band of C. cinereum. The use of core DNA barcode regions; rbcL, matK, ITS and psbA-trnH provided species-level resolution to differentiate the two plants. Taken together, the integration of macroscopic and microscopic characterization, phytochemical analysis by HPTLC and DNA barcoding distinguished C. cinereum from E. sonchifolia. The signatures of C. cinereum obtained here can help manufacturers to increase the quality control of C. cinereum raw material in commercialized smoking cessation products.

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DNA barcoding augments conventional methods for identification of medicinal plant species traded at Tanzanian markets

Cited by 29 publications

References 48 publications

DNA meta‐barcoding using rbcL based mini‐barcode revealed presence of unspecified plant species in Ayurvedic polyherbal formulations

DNA meta‐barcoding using rbcL based mini‐barcode revealed presence of unspecified plant species in Ayurvedic polyherbal formulations

A new method of metabarcoding Microsporidia and their hosts reveals high levels of microsporidian infections in mosquitoes (Culicidae)

Differentiation of Cyanthillium cinereum, a smoking cessation herb, from its adulterant Emilia sonchifolia using macroscopic and microscopic examination, HPTLC profiles and DNA barcodes

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