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Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis.

ABSTRACT: DNA barcoding of herbal medicines has been mainly concerned with authentication of products in trade and has raised awareness of species substitution and adulteration. More recently DNA barcodes have been included in pharmacopoeias, providing tools for regulatory purposes. The commonly used DNA barcoding regions in plants often fail to resolve identification to species level. This can be especially challenging in evolutionarily complex groups where incipient or reticulate speciation is ongoing. In this study, we take a phylogenomic approach, analyzing whole plastid sequences from the evolutionarily complex genus Berberis in order to develop DNA barcodes for the medicinally important species Berberis aristata. The phylogeny reconstructed from an alignment of ?160 kbp of chloroplast DNA for 57 species reveals that the pharmacopoeial species in question is polyphyletic, complicating development of a species-specific DNA barcode. Instead we propose a DNA barcode that is clade specific, using our phylogeny to define Operational Phylogenetic Units (OPUs). The plastid alignment is then reduced to small, informative DNA regions including nucleotides diagnostic for these OPUs. These DNA barcodes were tested on commercial samples, and shown to discriminate plants in trade and therefore to meet the requirement of a pharmacopoeial standard. The proposed method provides an innovative approach for inferring DNA barcodes for evolutionarily complex groups for regulatory purposes and quality control.

SUBMITTER: Kreuzer M

PROVIDER: S-EPMC6527895 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for <i>Berberis</i>.

Kreuzer Marco M Howard Caroline C Adhikari Bhaskar B Pendry Colin A CA Hawkins Julie A JA

Frontiers in plant science 20190514

DNA barcoding of herbal medicines has been mainly concerned with authentication of products in trade and has raised awareness of species substitution and adulteration. More recently DNA barcodes have been included in pharmacopoeias, providing tools for regulatory purposes. The commonly used DNA barcoding regions in plants often fail to resolve identification to species level. This can be especially challenging in evolutionarily complex groups where incipient or reticulate speciation is ongoing. ...[more]

PMID: 31139202

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Project description:BACKGROUND:Hypercholesterolemia is an important key contributory factor for ischemic heart disease and is associated with age, high blood pressure, a family history of hypercholesterolemia, and diabetes. Chinese herbal medicines have been used for a long time as lipid-lowering agents. OBJECTIVES:To assess the effects of Chinese herbal medicines on hypercholesterolemia. SEARCH STRATEGY:We searched the following databases: The Cochrane Library (issue 8, 2010), MEDLINE (until July 2010), EMBASE (until July 2010 ), Chinese BioMedical Database (until July 2010), Traditional Chinese Medical Literature Analysis and Retrieval System (until July 2010), China National Knowledge Infrastructure (until July 2010), Chinese VIP Information (until July 2010), Chinese Academic Conference Papers Database and Chinese Dissertation Database (until July 2010), and Allied and Complementary Medicine Database (until July 2010). SELECTION CRITERIA:We considered randomized controlled clinical trials in hypercholesterolemic participants comparing Chinese herbal medicines with placebo, no treatment, and pharmacological or non-pharmacological interventions. DATA COLLECTION AND ANALYSIS:Two review authors independently extracted data and assessed the risk of bias. We resolved any disagreements with this assessment through discussion and a decision was achieved based by consensus. We assessed trials for the risk of bias against key criteria: random sequence generation, allocation concealment, blinding of participants, incomplete outcome data, selective outcome reporting and other sources of bias. MAIN RESULTS:We included 22 randomized trials (2130 participants). The mean treatment duration was 2.3 ± 1.3 months (ranging from one to six months). Twenty trials were conducted in China and 18 trials were published in Chinese. Overall, the risk of bias of included trials was high or unclear. Five different herbal medicines were evaluated in the included trials, which compared herbs with conventional medicine in six comparisons (20 trials), or placebo (two trials). There were no outcome data in any of the trials on cardiovascular events and death from any cause. One trial each reported well-being (no significant differences) and economic costs. No serious adverse events were observed. Xuezhikang was the most commonly used herbal formula investigated. A significant effect on total cholesterol (two trial, 254 participants) was shown in favor of Xuezhikang when compared with inositol nicotinate (mean difference (MD) -0.90 mmol/L, 95% confidence interval (CI) -1.13 to -0.68) . AUTHORS' CONCLUSIONS:Some herbal medicines may have cholesterol-lowering effects. Our findings have to be interpreted with caution due to high or unclear risk of bias of the included trials.

Project description:BACKGROUND: Herbal products available to consumers in the marketplace may be contaminated or substituted with alternative plant species and fillers that are not listed on the labels. According to the World Health Organization, the adulteration of herbal products is a threat to consumer safety. Our research aimed to investigate herbal product integrity and authenticity with the goal of protecting consumers from health risks associated with product substitution and contamination. METHODS: We used DNA barcoding to conduct a blind test of the authenticity for (i) 44 herbal products representing 12 companies and 30 different species of herbs, and (ii) 50 leaf samples collected from 42 herbal species. Our laboratory also assembled the first standard reference material (SRM) herbal barcode library from 100 herbal species of known provenance that were used to identify the unknown herbal products and leaf samples. RESULTS: We recovered DNA barcodes from most herbal products (91%) and all leaf samples (100%), with 95% species resolution using a tiered approach (rbcL + ITS2). Most (59%) of the products tested contained DNA barcodes from plant species not listed on the labels. Although we were able to authenticate almost half (48%) of the products, one-third of these also contained contaminants and or fillers not listed on the label. Product substitution occurred in 30/44 of the products tested and only 2/12 companies had products without any substitution, contamination or fillers. Some of the contaminants we found pose serious health risks to consumers. CONCLUSIONS: Most of the herbal products tested were of poor quality, including considerable product substitution, contamination and use of fillers. These activities dilute the effectiveness of otherwise useful remedies, lowering the perceived value of all related products because of a lack of consumer confidence in them. We suggest that the herbal industry should embrace DNA barcoding for authenticating herbal products through testing of raw materials used in manufacturing products. The use of an SRM DNA herbal barcode library for testing bulk materials could provide a method for 'best practices? in the manufacturing of herbal products. This would provide consumers with safe, high quality herbal products.

Project description:There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10$\times $ in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.].

Project description:BackgroundChinese herbal medicines (CHMs) are the major interventions of traditional Chinese medicine (TCM), which are typically administered as either single herbs or formulas. The Cochrane systematic reviews (SRs) of CHMs are essential references for evaluating the efficacy and safety of CHMs interventions; they are expected to be accurate and reliable. This study aimed to assess the reporting quality of these SRs, particularly whether necessary information related to CHM was adequately reported.MethodsThe Cochrane Database was systematically searched for all SRs of CHM that were published up to 31 December 2017. The primary analysis was to assess their reporting quality based on 27-item of the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) and 9-item of CHM-related information designed according to TCM theory. Descriptive statistics were additionally used to analyze their baseline characteristics.ResultsA total of 109 Cochrane SRs of CHM were identified from 1999 to 2017. For 27-item of PRISMA, 26 had the reporting compliances higher than 50%, of which 11 were fully reporting (100%). However, for CHM-related information, 65 (59.6%) SRs did not report the specific name of the CHM in the title, 42 (38.5%) lacked TCM-related rationales in the introduction, 62 (56.9%) did not include CHM-related characteristics in the additional analyses, and 77 (70.6%) did not analyze CHM results in terms of TCM-related theories in the discussion. Of 97 SRs that included clinical trials, 38 (39.2%) did not provide the details of composition and dosage of CHMs, 85 (87.6%) did not report the CHM sources, 13 (13.4%) did not provide the dosage form, 95 (97.9%) lacked CHM quality control information, and 57 (58.8%) did not describe details of the controls. For 62 (72.9%) of 85 SRs that included meta-analysis, it was impossible to assess whether meta-analysis had been properly conducted due to inadequate reporting of CHM interventions.ConclusionAlthough the Cochrane SRs of CHM showed reporting compliance with PRISMA checklist, their reporting quality needs improvement, especially about full reporting of CHM interventions and of TCM-related rationales. Reporting guideline of "PRISMA extension for CHM interventions" should be developed thus to improve their quality.

Dataset Information

Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis.

Publications

Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for <i>Berberis</i>.

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