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Mück F, Scotti F, Mauvisseau Q, Thorbek BLG, Wangensteen H, de Boer HJ. Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women's health provides progressive qualitative and quantitative insight. Front Pharmacol 2024; 15:1353434. [PMID: 38375033 PMCID: PMC10875096 DOI: 10.3389/fphar.2024.1353434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.
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Affiliation(s)
- Felicitas Mück
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Francesca Scotti
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, United Kingdom
| | | | | | - Helle Wangensteen
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
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2
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Fracasso I, Zaccone C, Oskolkov N, Da Ros L, Dinella A, Belelli Marchesini L, Buzzini P, Sannino C, Turchetti B, Cesco S, Le Roux G, Tonon G, Vernesi C, Mimmo T, Ventura M, Borruso L. Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168159. [PMID: 37923262 DOI: 10.1016/j.scitotenv.2023.168159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.
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Affiliation(s)
- Ilaria Fracasso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
| | - Claudio Zaccone
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 221 00 Lund, Sweden
| | - Luca Da Ros
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Anna Dinella
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luca Belelli Marchesini
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Stefano Cesco
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Gael Le Roux
- Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245 CNRS/UPS/INPT), Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Giustino Tonon
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Tanja Mimmo
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Maurizio Ventura
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
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3
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Adotey G, Alolga RN, Quarcoo A, Yerenkyi P, Otu P, Anang AK, Okine LKN, Gbewonyo WSK, Holliday JC, Lombardi VC. Molecular Identification and Characterization of Five Ganoderma Species from the Lower Volta River Basin of Ghana Based on Nuclear Ribosomal DNA (nrDNA) Sequences. J Fungi (Basel) 2023; 10:6. [PMID: 38276022 PMCID: PMC10817336 DOI: 10.3390/jof10010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Ganoderma is a genus of biomedical fungus that is used in the development of numerous health products throughout the world. The Lower Volta River Basin of Ghana is an undulating land surface covered by extensive vegetation and water bodies and is rich in polypore mushrooms resembling various members of the Ganoderma genus. Despite the extensive biopharmaceutical benefits of Ganoderma spp., the isolates from the Lower Volta River Basin have not been properly characterized, thus limiting their use in the development of biotechnological products. In this study, Ganoderma spp. collected from the Lower Volta River Basin were genetically analyzed using the nuclear ribosomal sequences, the internal transcribed spacer 2 (ITS 2), the complete internal transcribed spacer (ITS), and the nuclear large subunit (nLSU). Blastn search and sequence analysis revealed that the sample we coded as Ganoderma LVRB-2 belongs to G. mbrekobenum, whereas Ganoderma LVRB-1, Ganoderma LVRB-14, and Ganoderma LVRB-16 belong to the species G. enigmaticum. Our analysis further demonstrates that Ganoderma LVRB-17 belongs to the species G. resinaceum. Thus, the five samples collected in the present study were positioned in three different distinct groups, namely G. mbrekobenum, G. enigmaticum, and G. resinaceum. The current data may serve as reference points for future studies.
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Affiliation(s)
- Gideon Adotey
- Science Laboratory Department, Accra Technical University, Barnes Road, P.O. Box GP 561, Accra 00233, Ghana; (A.Q.); (P.Y.); (P.O.)
| | - Raphael N. Alolga
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, China Pharmaceutical University, Nanjing 210009, China;
| | - Abraham Quarcoo
- Science Laboratory Department, Accra Technical University, Barnes Road, P.O. Box GP 561, Accra 00233, Ghana; (A.Q.); (P.Y.); (P.O.)
| | - Paul Yerenkyi
- Science Laboratory Department, Accra Technical University, Barnes Road, P.O. Box GP 561, Accra 00233, Ghana; (A.Q.); (P.Y.); (P.O.)
| | - Phyllis Otu
- Science Laboratory Department, Accra Technical University, Barnes Road, P.O. Box GP 561, Accra 00233, Ghana; (A.Q.); (P.Y.); (P.O.)
| | - Abraham K. Anang
- Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana, Accra 00233, Ghana;
| | - Laud K. N. Okine
- Department of Biochemistry, Cell and Molecular Biology (BCMB), University of Ghana, Accra 00233, Ghana; (L.K.N.O.); (W.S.K.G.)
| | - Winfred S. K. Gbewonyo
- Department of Biochemistry, Cell and Molecular Biology (BCMB), University of Ghana, Accra 00233, Ghana; (L.K.N.O.); (W.S.K.G.)
| | | | - Vincent C. Lombardi
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N Virginia St. MS 0320, Reno, NV 89557, USA
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Wang Q, Qiu Z, Chen Y, Song Y, Zhou A, Cao Y, Xiao J, Xiao H, Song M. Review of recent advances on health benefits, microbial transformations, and authenticity identification of Citri reticulatae Pericarpium bioactive compounds. Crit Rev Food Sci Nutr 2023:1-29. [PMID: 37326362 DOI: 10.1080/10408398.2023.2222834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The extensive health-promoting effects of Citri Reticulatae Pericarpium (CRP) have attracted researchers' interest. The difference in storage time, varieties and origin of CRP are closely related to the content of bioactive compounds they contain. The consitituent transformation mediated by environmental microorganisms (bacteria and fungi) and the production of new bioactive components during the storage process may be the main reason for 'the older, the better' of CRP. In addition, the gap in price between different varieties can be as large as 8 times, while the difference due to age can even reach 20 times, making the 'marketing young-CRP as old-CRP and counterfeiting origin' flood the entire market, seriously harming consumers' interests. However, so far, the research on CRP is relatively decentralized. In particular, a summary of the microbial transformation and authenticity identification of CRP has not been reported. Therefore, this review systematically summarized the recent advances on the main bioactive compounds, the major biological activities, the microbial transformation process, the structure, and content changes of the active substances during the transformation process, and authenticity identification of CRP. Furthermore, challenges and perspectives concerning the future research on CRP were proposed.
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Affiliation(s)
- Qun Wang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Zhenyuan Qiu
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yilu Chen
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Yuqing Song
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Aimei Zhou
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Jie Xiao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Mingyue Song
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
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Patel R, Faller AC, Nguyen T, Quan Z, Eminger C, Kaul S, Collins T, Zhang Y, Chang P, Swanson G, Lu Z. Validation of a Real-Time PCR Assay for Identification of Fresh and Processed Carica papaya Botanical Material: Using Synthetic DNA to Supplement Specificity Evaluation. Foods 2023; 12:foods12030530. [PMID: 36766059 PMCID: PMC9913946 DOI: 10.3390/foods12030530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Several commercially important botanicals have a lack of diagnostic testing options that can quickly and unambiguously identify materials of different matrices. Real-time PCR can be a useful, orthogonal approach to identification for its exceptional specificity and sensitivity. Carica papaya L. is a species with a lack of available identification methods, and one which features two distinct commercially relevant matrices: fresh fruit and powdered fruit extract. In this study, we demonstrate the successful design and validation of a real-time PCR assay for detection of papaya DNA extracted from the two matrices. We also propose a technique that can be used during exclusivity panel construction, when genuine botanical samples are not available for certain species: substitution with synthetic DNA. We demonstrate the use of this material to complete a comprehensive specificity evaluation and confidently determine suitable Ct cutoff values. Further, we demonstrate how ddPCR can be used to determine the copy number of the target sequence in a set amount of genomic DNA, to which synthetic DNA samples can be corrected, and how it can verify specificity of the primers and probe. Through the presentation of successful assay validation for papaya detection, this work serves as a guideline for how to approach specificity evaluation when non-target botanical samples are difficult to obtain and otherwise may not have been included in the exclusivity panel.
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Affiliation(s)
- Rajesh Patel
- Quality Control Laboratory, Herbalife International of America, Inc.—Winston-Salem, 3200 Temple School Road, Winston Salem, NC 27107, USA
| | - Adam C. Faller
- Corporate Quality Laboratory, Herbalife International of America, Inc., 950W 190th Street, Torrance, CA 90502, USA
- Correspondence:
| | - Tiffany Nguyen
- Corporate Quality Laboratory, Herbalife International of America, Inc., 950W 190th Street, Torrance, CA 90502, USA
| | - Zheng Quan
- Corporate Quality Laboratory, Herbalife International of America, Inc., 950W 190th Street, Torrance, CA 90502, USA
| | - Corey Eminger
- Quality Control Laboratory, Herbalife International of America, Inc.—Winston-Salem, 3200 Temple School Road, Winston Salem, NC 27107, USA
| | - Swetha Kaul
- Corporate Quality Laboratory, Herbalife International of America, Inc., 950W 190th Street, Torrance, CA 90502, USA
| | - Ted Collins
- Quality Control Laboratory, Herbalife International of America, Inc.—Winston-Salem, 3200 Temple School Road, Winston Salem, NC 27107, USA
| | - Yanjun Zhang
- Corporate Quality, Herbalife International of America, Inc., 990W 190th Street, Torrance, CA 90502, USA
| | - Peter Chang
- Corporate Quality, Herbalife International of America, Inc., 990W 190th Street, Torrance, CA 90502, USA
| | - Gary Swanson
- Corporate Quality, Herbalife International of America, Inc., 990W 190th Street, Torrance, CA 90502, USA
| | - Zhengfei Lu
- Corporate Quality Laboratory, Herbalife International of America, Inc., 950W 190th Street, Torrance, CA 90502, USA
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Chavan D, Adolacion JRT, Crum M, Nandy S, Lee KH, Vu B, Kourentzi K, Sabo A, Willson RC. Isolation and Barcoding of Trace Pollen-free DNA for Authentication of Honey. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14084-14095. [PMID: 36279293 DOI: 10.1021/acs.jafc.2c04309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Adulteration and mislabeling of honey to mask its true origin have become a global concern. Pollen microscopy, the current gold standard for identifying honey's geographical and plant origins, is laborious, requires extensive training, and fails to identify filtered honey and honey spiked with pollen from a more favorable plant to disguise its origins. We successfully isolated pollen-free DNA from filtered honey using three types of adsorbents: (i) anti-dsDNA antibodies coupled to magnetic microspheres; (ii) anion-exchange adsorbent; and (iii) ceramic hydroxyapatite. The internal transcribed spacer 2 region of the captured pollen-free DNA was polymerase chain reaction-amplified and subjected to next-generation sequencing. Using an in-house bioinformatics pipeline, initial experiments showed that anion exchange had the greatest capacity to capture trace pollen-free DNA, and it was successfully applied to isolate DNA from five honey samples. Enrichment of trace pollen-free DNA from filtered honey samples opens a new approach for identifying the true origins of honey.
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Affiliation(s)
- Dimple Chavan
- Department of Biology and Biochemistry, University of Houston, Houston, Texas77204, United States
| | - Jay R T Adolacion
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Mary Crum
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Suman Nandy
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Kyung Hyun Lee
- Center for Clinical Research & Evidence-Based Medicine, The University of Texas Health Science Center at Houston, Houston, Texas77030, United States
| | - Binh Vu
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas77030, United States
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, Houston, Texas77204, United States
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
- Escuela de Medicina y Ciencias de la Salud ITESM, Monterrey, Nuevo León64710, Mexico
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Wang X, Yoo E, Lee S, Cho GT, Lee GA, Yi JY, Du X, Han S, Hyun DY, Ro N, Kim KM. Classification of 17 species Aegilops using DNA barcoding and SNPs, reveals gene flow among Aegilops biuncialis, Aegilops juvenalis, and Aegilops columnaris. FRONTIERS IN PLANT SCIENCE 2022; 13:984825. [PMID: 36275512 PMCID: PMC9583012 DOI: 10.3389/fpls.2022.984825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Rapid changes in agricultural environments caused by global warming pose a major challenge to food production and safety. Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) that shares large numbers of quantitative traits and resistance genes with B and D genomes of Aegilops species, which are responsible for several metabolic functions and biosynthetic processes, particularly in plant adaptation to biotic as well as abiotic stresses. Comparatively, the abundance of the Aegilops gene pool is much higher than that of Triticum. Therefore, we used four universal DNA barcodes for plants (ITS2, matK, rbcL, and psbM-petN) to construct a phylogenetic tree to classify the genus Aegilops. Fourteen species were distinguished among a total of 17 representative species. Aegilops biuncialis, Aegilops juvenalis, and Aegilops umbellulata could not be grouped into any of the clusters in the phylogenetic tree, indicating that these three species could not be distinguished by four DNA barcodes. Therefore, from 2408 SNPs obtained using genotyping by sequencing (GBS), we manually screened 30 SNPs that could be potentially used to classify these three species. The results of gene flow and genetic differentiation index (Fst) showed that the genetic differentiation among the three species was small, and there was bidirectional horizontal gene transfer between the three species, which was consistent with our results that the three species were difficult to classify by DNA barcode.
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Affiliation(s)
- Xiaohan Wang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu, South Korea
| | - Eunae Yoo
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Seungbum Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jung Yoon Yi
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Xiaoxuan Du
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu, South Korea
| | - Seahee Han
- Honam National Institute of Biological Resources, Mokpo, South Korea
| | - Do Yoon Hyun
- Korea National University of Agriculture and Fisheries, Jeonju, South Korea
| | - Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Kyung-Min Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu, South Korea
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Anthoons B, Lagiotis G, Drouzas AD, de Boer H, Madesis P. Barcoding High Resolution Melting (Bar-HRM) enables the discrimination between toxic plants and edible vegetables prior to consumption and after digestion. J Food Sci 2022; 87:4221-4232. [PMID: 35903040 DOI: 10.1111/1750-3841.16253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/18/2022] [Accepted: 06/25/2022] [Indexed: 11/27/2022]
Abstract
The consumption of poisonous plants can lead to serious health problems or even casualties due to various factors, including easy access to poisonous plants due to their common distribution, co-occurrence and resemblance with edible plants, and the lack of regulation in the food product supply chain. Clinical diagnosis of intoxications usually relies on the availability of the plant consumed by the patient and on the morphology of the plant parts found in the patient's stomach. Therefore, given the fragmented nature of ingested plant material, species identification may face serious difficulties, can be inaccurate, and time-consuming. This highlights the need for rapid and reliable tools to identify toxic species. In the present study, we developed an ITS2-high-resolution melting (HRM) assay for: (1) the discrimination of common toxic plants and their edible lookalikes, and (2) the detection of toxic plants in digested samples. More specifically, we designed species-specific ITS2 primers for the authentication of poisonous species in simulated mixtures and verified them with Bar-HRM. Moreover, the developed HRM-based molecular tool was capable of quantifying the toxic species Datura stramonium in simulated mixtures with the edible Amaranthus retroflexus down to at least 0.5% v/v. This study shows that species-specific ITS2 primers can amplify the DNA from fragmented and/or artificially digested samples and that Bar-HRM is capable of detecting poisonous plant species in digested samples even after 4 h. The developed Bar-HRM protocol has important implications for application in medicine, forensics, and the agricultural industry, either to accurately detect the cause of plant intoxications or as a tool for quality control in the supply chain. PRACTICAL APPLICATION: In this work, we established a high-resolution melting DNA-based protocol capable of discriminating between phenotypically similar common toxic and edible plant species in mixtures, even at very low quantities. This technology also proved efficient in detecting the toxic species in mixtures digested in artificial gastric acid, as it would be the case after accidental ingestion. This work is expected to have important implications for application in medicine, forensics, and the agricultural industry, either for identifying the cause of plant intoxications or as a tool for quality control in different steps of the supply chain.
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Affiliation(s)
- Bastien Anthoons
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | | | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, Thessaly, Greece
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9
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Pinya T, Intharuksa A, Yanaso S, Kamnuan S, Phrutivorapongkul A. Conventional and molecular pharmacognostic characters integrated with chemical profiles of five Piper plants in the Thai herbal pharmacopoeia and their admixture/adulteration/substitution situations in Thailand. J Nat Med 2022; 76:605-620. [PMID: 35201516 DOI: 10.1007/s11418-022-01607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/31/2022] [Indexed: 11/28/2022]
Abstract
The morphological and microscopy were combined with DNA-barcoding, together with rapid TLC for the characterization of Piper betle (PB), P. nigrum (PN), P. retrofractum (PR), P. sarmentosum (PS), and P. wallichii (PW), five medicinal Piper plants announced in the Thai Herbal Pharmacopoeia (THP). The authentic plants collected from various locations and voucher Piper products bought from commercial sites in Thailand were studied. The reproductive parts of authentic plants were subjected to ensure their morphological characters. Using sequencing analysis and genetic divergence for analyzing discriminatory performance, ITS2 was selected from eight candidate DNA markers to authenticate the origin of Piper crude drugs together with microscopic and TLC profiles for examining their characters, admixtures, adulterants, and substituents. PB and PR exhibited unique characters of the species, with no admixture, adulteration, and substitution. PN showed no variable characters of morphology and genetics. However, the microscopy could illustrate some commercial products of PN sold in Thailand have been adulterated with rice starch and roasted rice. In the herbal trade, PS has been sold in the form of mixed leaf, root, and stem more than the isolated part, but there is no variable character of the species. PW has shown more than one character of species explained by microscopic, chemical components, and genetic data. In conclusion, the conventional and molecular pharmacognostic data combined with chemical profile of authentic five Piper plants could be applied to indicate the plant origin and clarify the situations of admixture, adulteration, and substitution of the commercial Piper products launched in Thailand.
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Affiliation(s)
- Thawanratn Pinya
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand
| | - Aekkhaluck Intharuksa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand
| | - Suthira Yanaso
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand.,Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmaceutical Sciences, Huachiew Chalermprakiet University, Bang Chalong, Bang Phli, Samutprakan, 10540, Thailand
| | - Suthiwat Kamnuan
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand
| | - Ampai Phrutivorapongkul
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Mueang, Chiang Mai, 50200, Thailand.
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10
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Sokołowska J, Fuchs H, Celiński K. Assessment of ITS2 Region Relevance for Taxa Discrimination and Phylogenetic Inference among Pinaceae. PLANTS 2022; 11:plants11081078. [PMID: 35448806 PMCID: PMC9029031 DOI: 10.3390/plants11081078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
The internal transcribed spacer 2 (ITS2) is one of the best-known universal DNA barcode regions. This short nuclear region is commonly used not only to discriminate taxa, but also to reconstruct phylogenetic relationships. However, the efficiency of using ITS2 in these applications depends on many factors, including the family under study. Pinaceae represents the largest family of extant gymnosperms, with many species of great ecological, economic, and medical importance. Moreover, many members of this family are representatives of rare, protected, or endangered species. A simple method for the identification of Pinaceae species based on DNA is necessary for their effective protection, authentication of products containing Pinaceae representatives, or phylogenetic inference. In this study, for the first time, we conducted a comprehensive study summarizing the legitimacy of using the ITS2 region for these purposes. A total of 368 sequences representing 71 closely and distantly related taxa of the seven genera and three subfamilies of Pinaceae were characterized for genetic variability and divergence. Intra- and interspecies distances of ITS2 sequences as well as rates of sequence identification and taxa discrimination among Pinaceae at various taxonomic levels, i.e., the species complex, genus, subfamily, and family, were also determined. Our study provides a critical assessment of the suitability of the ITS2 nuclear DNA region for taxa discrimination among Pinaceae. The obtained results clearly show that its usefulness for this purpose is limited.
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Affiliation(s)
- Joanna Sokołowska
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, School of Natural Sciences, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
| | - Hanna Fuchs
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland;
| | - Konrad Celiński
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, School of Natural Sciences, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
- Correspondence:
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11
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Jia H, Liu Y, Li X, Li H, Pan Y, Hu C, Zhou X, Wyckhuys KAG, Wu K. Windborne migration amplifies insect-mediated pollination services. eLife 2022; 11:76230. [PMID: 35416148 PMCID: PMC9042232 DOI: 10.7554/elife.76230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Worldwide, hoverflies (Syrphidae: Diptera) provide crucial ecosystem services such as pollination and biological pest control. Although many hoverfly species exhibit migratory behavior, the spatiotemporal facets of these movement dynamics, and their ecosystem services implications are poorly understood. In this study, we use long-term (16-year) trapping records, trajectory analysis, and intrinsic (i.e., isotope, genetic, pollen) markers to describe migration patterns of the hoverfly Episyrphus balteatus in northern China. Our work reveals how E. balteatus migrate northward during spring–summer and exhibits return (long-range) migration during autumn. The extensive genetic mixing and high genetic diversity of E. balteatus populations underscore its adaptive capacity to environmental disturbances, for example, climate change. Pollen markers and molecular gut analysis further illuminate how E. balteatus visits min. 1012 flowering plant species (39 orders) over space and time. By thus delineating E. balteatus transregional movements and pollination networks, we advance our understanding of its migration ecology and facilitate the design of targeted strategies to conserve and enhance its ecosystem services.
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Affiliation(s)
- Huiru Jia
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongqiang Liu
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xaiokang Li
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Li
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunfei Pan
- Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Xainyong Zhou
- Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Kongming Wu
- Chinese Academy of Agricultural Sciences, Beijing, China
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12
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Zhang G, Wang H, Shi L, Liu Y, Yao R, Sui C, Yang C, Ji H, Wang Q, Wei J. Identification of the original plants of cultivated Bupleuri Radix based on DNA barcoding and chloroplast genome analysis. PeerJ 2022; 10:e13208. [PMID: 35433122 PMCID: PMC9012172 DOI: 10.7717/peerj.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/10/2022] [Indexed: 01/12/2023] Open
Abstract
Bupleuri Radix is the dry root of certain species of the genus Bupleurum and is commonly used in traditional Chinese medicine. The increasing global demand for Bupleuri Radix cannot be fulfilled with wild populations only. Therefore, cultivated Bupleurum is now the main commercial source of this medicinal product. Different species of Bupleurum show different medicinal properties and clinical effects, making reliable authentication and assignment of correct botanical origin for medicinal species critical. However, accurate identification of the cultivated Bupleurum species is difficult due to dramatic morphological variations resulting from cultivation. In this study, we sampled 56 cultivated Bupleurum populations of six different morphotypes (Types A-F) from the main production areas of China, and 10 wild populations of four species were used as reference materials. Conventional DNA barcoding was conducted to identify cultivated Bupleurum species. Additionally, verification based on complete chloroplast genomes was performed and new chloroplast markers were developed and evaluated. The combination of these methods resulted in the successful identification of all cultivated Bupleurum individuals. Three chloroplast regions are recommended as additional barcodes for the genus: ycf4_cemA, psaJ_rpl33, and ndhE_ndhG. This is a reliable and promising strategy that can be applied to the authentication of natural products and the identification of other medicinal plant species with similar taxonomic problems.
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Affiliation(s)
- Gaixia Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruyu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chun Sui
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengmin Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongliang Ji
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiuling Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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13
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Osman MF, Lee SY, Sarbini SR, Mohd Faudzi SM, Khamis S, Zainudin BH, Shaari K. Metabolomics-Driven Discovery of an Introduced Species and Two Malaysian Piper betle L. Variants. PLANTS 2021; 10:plants10112510. [PMID: 34834873 PMCID: PMC8622403 DOI: 10.3390/plants10112510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 11/23/2022]
Abstract
The differences in pungency of “sirih” imply the probable occurrence of several variants of Piper betle L. in Malaysia. However, the metabolite profiles underlying the pungency of the different variants remain a subject of further research. The differences in metabolite profiles of selected Malaysian P. betle variants were thus investigated; specifically, the leaf aqueous methanolic extracts and essential oils were analyzed via 1H-NMR and GC-MS metabolomics, respectively. Principal component analysis (PCA) of the 1H-NMR spectral data showed quantitative differences in the metabolite profiles of “sirih melayu” and “sirih india” and revealed an ambiguous group of samples with low acetic acid content, which was identified as Piper rubro-venosum hort. ex Rodigas based on DNA sequences of the internal transcribed spacer 2 (ITS2) region. The finding was supported by PCA of two GC-MS datasets of P. betle samples obtained from several states in Peninsular Malaysia, which displayed clustering of the samples into “sirih melayu” and “sirih india” groups. Higher abundance of chavicol acetate was consistently found to be characteristic of “sirih melayu”. The present research has provided preliminary evidence supporting the notion of occurrence of two P. betle variants in Malaysia based on chemical profiles, which may be related to the different genders of P. betle.
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Affiliation(s)
- Muhamad Faris Osman
- Natural Medicines and Products Research Laboratory (NaturMeds), Institute of Bioscience, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia; (M.F.O.); (S.Y.L.); (S.M.M.F.)
- Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia
| | - Soo Yee Lee
- Natural Medicines and Products Research Laboratory (NaturMeds), Institute of Bioscience, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia; (M.F.O.); (S.Y.L.); (S.M.M.F.)
| | - Shahrul Razid Sarbini
- Department of Crop Science, Faculty of Agricultural Science and Forestry, Universiti Putra Malaysia, Bintulu 97008, Sarawak, Malaysia;
| | - Siti Munirah Mohd Faudzi
- Natural Medicines and Products Research Laboratory (NaturMeds), Institute of Bioscience, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia; (M.F.O.); (S.Y.L.); (S.M.M.F.)
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Shamsul Khamis
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, Bangi 43600, Selangor, Malaysia;
| | - Badrul Hisyam Zainudin
- Analytical Services Laboratory, Chemistry and Technology Division, Malaysian Cocoa Board, Cocoa Innovation and Technology Centre, Lot 12621 Kawasan Perindustrian Nilai, Nilai 71800, Negeri Sembilan, Malaysia;
| | - Khozirah Shaari
- Natural Medicines and Products Research Laboratory (NaturMeds), Institute of Bioscience, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia; (M.F.O.); (S.Y.L.); (S.M.M.F.)
- Correspondence: ; Tel.: +60-13-3420686
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14
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Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than. PLANTS 2021; 10:plants10102023. [PMID: 34685831 PMCID: PMC8540904 DOI: 10.3390/plants10102023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022]
Abstract
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.
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15
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Geographic source estimation using airborne plant environmental DNA in dust. Sci Rep 2021; 11:16238. [PMID: 34376726 PMCID: PMC8355115 DOI: 10.1038/s41598-021-95702-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Information obtained from the analysis of dust, particularly biological particles such as pollen, plant parts, and fungal spores, has great utility in forensic geolocation. As an alternative to manual microscopic analysis of dust components, we developed a pipeline that utilizes the airborne plant environmental DNA (eDNA) in settled dust to estimate geographic origin. Metabarcoding of settled airborne eDNA was used to identify plant species whose geographic distributions were then derived from occurrence records in the USGS Biodiversity in Service of Our Nation (BISON) database. The distributions for all plant species identified in a sample were used to generate a probabilistic estimate of the sample source. With settled dust collected at four U.S. sites over a 15-month period, we demonstrated positive regional geolocation (within 600 km2 of the collection point) with 47.6% (20 of 42) of the samples analyzed. Attribution accuracy and resolution was dependent on the number of plant species identified in a dust sample, which was greatly affected by the season of collection. In dust samples that yielded a minimum of 20 identified plant species, positive regional attribution was achieved with 66.7% (16 of 24 samples). For broader demonstration, citizen-collected dust samples collected from 31 diverse U.S. sites were analyzed, and trace plant eDNA provided relevant regional attribution information on provenance in 32.2% of samples. This showed that analysis of airborne plant eDNA in settled dust can provide an accurate estimate regional provenance within the U.S., and relevant forensic information, for a substantial fraction of samples analyzed.
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16
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Lv YN, Yang CY, Shi LC, Zhang ZL, Xu AS, Zhang LX, Li XL, Li HT. Identification of medicinal plants within the Apocynaceae family using ITS2 and psbA-trnH barcodes. Chin J Nat Med 2021; 18:594-605. [PMID: 32768166 DOI: 10.1016/s1875-5364(20)30071-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Indexed: 02/02/2023]
Abstract
To ensure the safety of medications, it is vital to accurately authenticate species of the Apocynaceae family, which is rich in poisonous medicinal plants. We identified Apocynaceae species by using nuclear internal transcribed spacer 2 (ITS2) and psbA-trnH based on experimental data. The identification ability of ITS2 and psbA-trnH was assessed using specific genetic divergence, BLAST1, and neighbor-joining trees. For DNA barcoding, ITS2 and psbA-trnH regions of 122 plant samples of 31 species from 19 genera in the Apocynaceae family were amplified. The PCR amplification for ITS2 and psbA-trnH sequences was 100%. The sequencing success rates for ITS2 and psbA-trnH sequences were 81% and 61%, respectively. Additional data involved 53 sequences of the ITS2 region and 38 sequences of the psbA-trnH region were downloaded from GenBank. Moreover, the analysis showed that the inter-specific divergence of Apocynaceae species was greater than its intra-specific variations. The results indicated that, using the BLAST1 method, ITS2 showed a high identification efficiency of 97% and 100% of the samples at the species and genus levels, respectively, via BLAST1, and psbA-trnH successfully identified 95% and 100% of the samples at the species and genus levels, respectively. The barcode combination of ITS2/psbA-trnH successfully identified 98% and 100% of samples at the species and genus levels, respectively. Subsequently, the neighbor joining tree method also showed that barcode ITS2 and psbA-trnH could distinguish among the species within the Apocynaceae family. ITS2 is a core barcode and psbA-trnH is a supplementary barcode for identifying species in the Apocynaceae family. These results will help to improve DNA barcoding reference databases for herbal drugs and other herbal raw materials.
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Affiliation(s)
- Ya-Na Lv
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Chun-Yong Yang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Lin-Chun Shi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zhong-Lian Zhang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - An-Shun Xu
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China
| | - Li-Xia Zhang
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xue-Lan Li
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Hai-Tao Li
- Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong 666100, China; Key Laborartory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Jinghong 666100, China; Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Tu Y, Wang K, Jia X, Tan L, Han B, Zhang Q, Li Y, He C. Isolation and Identification of Antiarthritic Constituents from Glycine tabacina and Network Pharmacology-Based Prediction of Their Protective Mechanisms against Rheumatoid Arthritis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10664-10677. [PMID: 32530618 DOI: 10.1021/acs.jafc.0c00878] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glycine tabacina (Labill.) Benth is an edible medicinal herb for rheumatoid arthritis (RA) treatment in folk medicine. Current phytochemical research on this dried herb led to the isolation of eight new coumestans, named glytabastan A-H (1-8), and twenty-three known compounds 9-31. Their structures were elucidated using spectroscopic methods. The antiarthritic activities of all isolates were evaluated, and the results showed that coumestans 1-6 and 8-10 could inhibit arthritic inflammation in vitro, while coumestans 1, 2, 9, and 10 significantly blocked the osteoclastogenesis induced by receptor activator of nuclear factor (NF) κB ligand (RANKL). Moreover, network pharmacological analysis revealed that the anti-RA effect of G. tabacina involved multitargets, multipathways such as PI3K/Akt and MAPK signaling pathways, and various biological processes such as inflammatory response and cytokine-mediated signaling pathways. These results suggested that this species and its novel coumestans could serve as potential antiarthritic agents for functional food or medicinal use.
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Affiliation(s)
- Yanbei Tu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Kai Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Xuejing Jia
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Lihua Tan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Bing Han
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Qingwen Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Yanfang Li
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Chengwei He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
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18
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DNA barcodes for delineating Clerodendrum species of North East India. Sci Rep 2020; 10:13490. [PMID: 32778674 PMCID: PMC7417596 DOI: 10.1038/s41598-020-70405-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
The diversified genus of Clerodendrum with its complex evolutionary history leads to taxonomic mystification. Unlike traditional taxonomic methods, DNA barcoding could be a promising tool for the identification and conservation of Clerodendrum species. This study was attempted to develop an efficient barcode locus in Clerodendrum species of North East India. We evaluated four barcode candidates (ITS2, matK, rbcL, ycf1) and its combinations in different Clerodendrum species. The reliability of barcodes to distinguish the species were calculated using genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods. The results exemplify that matK posse’s maximum number of variables and parsimony-informative sites (103/100), intra- (0.021 ± 0.001) and inter- (0.086 ± 0.005) specific divergences and species resolution rate (89.1%) followed by ITS2, ycf1, and rbcL. Among the combinatorial locus, ITS2 + matK showed the best species discrimination with distinctive barcode gaps. Therefore, we tentatively suggest that the combination of ITS2 + matK as core barcode for Clerodendrum and converted into quick response (QR) code. Hence, this finding indicates that DNA barcoding could provide consistent resources for species discrimination and resolve taxonomic controversies of the genus as well as set a preliminary assessment toward its biodiversity.
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Tu Y, Wang K, Tan L, Han B, Hu Y, Ding H, He C. Dolichosin A, a coumestan isolated from Glycine tabacina, inhibits IL-1β-induced inflammation in SW982 human synovial cells and suppresses RANKL-induced osteoclastogenesis: From network pharmacology to experimental pharmacology. JOURNAL OF ETHNOPHARMACOLOGY 2020; 258:112855. [PMID: 32376366 DOI: 10.1016/j.jep.2020.112855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/05/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Glycine tabacina (Labill.) Benth has been used as a traditional Chinese herbal medicine for the treatment of rheumatoid arthritis (RA) and joint infection. It is also one of the sources of the renowned native herbal medicine 'I-Tiao-Gung' in Taiwan. AIM OF THE STUDY This study aimed to investigate anti-arthritic effects and underlying mechanisms of dolichosin A (DoA), a coumestan compound isolated from G. tabacina, by the integration of network pharmacology and experimental pharmacology. MATERIALS AND METHODS Putative therapeutic targets and potential pharmacological mechanisms of DoA for RA treatment were predicted by network pharmacology approach. The regulated network of DoA acting on RA was constructed using Cytoscape 3.7.1. Anti-arthritic effects of DoA and predicted mechanisms were further validated using IL-1β-induced SW982 human synovial cell model and RANKL-induced osteoclastogenesis model. RESULTS A regulatory network of DoA-targets-pathways-RA was successfully constructed using network pharmacology approach. In this network, 65 candidate targets of DoA related to its therapeutic effect on RA were identified and the functional enrichment analysis revealed that these candidate targets were significantly involved in 12 central signaling pathways such as PI3K/AKT pathway, MAPK pathway and osteoclast differentiation. Furthermore, we found that DoA could significantly inhibit IL-1β-induced inflammation in SW982 human synovial cells, as evidenced by the decreased levels of pro-inflammatory mediators (TNF-α, IL-6 and COX-2) and MMP-3. DoA also suppressed RANKL-induced osteoclastogenesis in vitro, as evidenced by decreased number of TRAP-positive multinucleated osteoclasts and reduced TRAP activity. Further experimental mechanism evidence confirmed the predicted results of network pharmacology that the blockade of PI3K/AKT and MAPK pathways activation was closely associated with these regulated processes of DoA. CONCLUSIONS Our results demonstrated that DoA exhibited strong anti-arthritic activity through suppressing PI3K/AKT and MAPK pathways activation in activated synovial cells and osteoclasts, suggesting its potential as a hopeful candidate for the development of novel agents for the prevention and treatment of RA.
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Affiliation(s)
- Yanbei Tu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, SAR, 999078, China
| | - Kai Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, SAR, 999078, China
| | - Lihua Tan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, SAR, 999078, China
| | - Bing Han
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, SAR, 999078, China
| | - Yuanjia Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, SAR, 999078, China
| | - Hang Ding
- Department of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, Guangdong, 523808, China.
| | - Chengwei He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, SAR, 999078, China.
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20
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Tan L, Tu Y, Wang K, Han B, Peng H, He C. Exploring protective effect of Glycine tabacina aqueous extract against nephrotic syndrome by network pharmacology and experimental verification. Chin Med 2020; 15:79. [PMID: 32765640 PMCID: PMC7395350 DOI: 10.1186/s13020-020-00361-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
Background Glycine tabacina (Labill.) Benth, one of the traditional Chinese herbal medicines, has been used for treatment of nephritis, osteoporosis, rheumatism, and menopausal syndrome. The aim of this study was to illuminate the therapeutic effect and mechanism of Glycine tabacina aqueous extract (GATE) in the treatment of nephrotic syndrome (NS). Methods UHPLC-DAD-MS/MS was used to analyze the chemical profile of GATE. Adriamycin (ADR)-induced NS mouse model and network pharmacology methods were conducted to explore the protective effect and mechanism of GATE on NS treatment. Results GATE administration significantly ameliorated symptoms of proteinuria and hyperlipidemia in NS mice, as evidenced by reduced excretion of urine protein and albumin, and decreased plasma levels of total cholesterol and triglyceride. Decreased blood urea nitrogen (BUN) and creatinine levels in NS mice suggested that GATE could prevent renal function decline caused by ADR. GATE treatment also inhibited ADR-induced pathological lesions of renal tissues as indicated by periodic acid Schiff staining. Six flavonoids of GATE were identified by using UHPLC-DAD-MS/MS. Network pharmacology analysis indicated that the protection of GATE in treating NS might be associated with the regulation of oxidative stress and inflammation. In addition, the in vivo experiment validated that treatment with GATE markedly decreased reactive oxygen species production, malonaldehyde level, and increased superoxide dismutase activity both in plasma and renal tissues. TNF-α level in plasma and protein expression in kidney were significantly decreased in GATE treatment groups. Conclusions Combination of network pharmacology analysis and experimental verification revealed that GATE exerts anti-NS effect possibly through modulating oxidative stress and inflammation, suggesting the potential application of GATE or its derivatives in the prevention and treatment of NS and other related kidney diseases.
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Affiliation(s)
- Lihua Tan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078 Macao SAR China
| | - Yanbei Tu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078 Macao SAR China
| | - Kai Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078 Macao SAR China
| | - Bing Han
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078 Macao SAR China
| | - Hongquan Peng
- Renal Division, Kiang Wu Hospital, Macao, 999078 Macao SAR China
| | - Chengwei He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078 Macao SAR China
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Prieto JAF, Rodríguez JMA, Sanna M, Cires E. Phylogeographical patterns of Campanula gr. arvatica, an endemic group of the Cantabrian mountains (NW Iberian Peninsula), based on plastid and nuclear DNA polymorphisms. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1783715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- José Antonio Fernández Prieto
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Área de Botánica, C/Catedrático Rodrigo Uría s/n, Oviedo, 33071, Spain
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
| | - Jose M. Arjona Rodríguez
- Field Crops Program, IRTA (Institute for Food and Agricultural Research and Technology), Rovira Roure, Lleida, 191, 25198, Spain
| | - Mauro Sanna
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
| | - Eduardo Cires
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Área de Botánica, C/Catedrático Rodrigo Uría s/n, Oviedo, 33071, Spain
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
- Instituto Universitario de Biotecnología de Asturias, Campus El Cristo, Edificio Santiago Gascón 2a planta, Oviedo, 33006, Spain
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Grazina L, Amaral JS, Mafra I. Botanical origin authentication of dietary supplements by DNA‐based approaches. Compr Rev Food Sci Food Saf 2020; 19:1080-1109. [DOI: 10.1111/1541-4337.12551] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 01/22/2020] [Accepted: 02/06/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Liliana Grazina
- REQUIMTE‐LAQV, Faculdade de FarmáciaUniversidade do Porto Porto Portugal
| | - Joana S. Amaral
- Centro de Investigação de Montanha (CIMO)Instituto Politécnico de Bragança Bragança Portugal
| | - Isabel Mafra
- REQUIMTE‐LAQV, Faculdade de FarmáciaUniversidade do Porto Porto Portugal
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Mbareche H, Veillette M, Bilodeau G, Duchaine C. Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based sequencing of bioaerosols. PeerJ 2020; 8:e8523. [PMID: 32110484 PMCID: PMC7032056 DOI: 10.7717/peerj.8523] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/07/2020] [Indexed: 12/23/2022] Open
Abstract
This paper presents the performance of two eukaryotic genomic ribosomal regions, ITS1 and ITS2, in describing fungal diversity in aerosol samples using amplicon-based High-Throughput Sequencing (HTS). Composting sites, biomethanization facilities, and dairy farms, all affected by the presence of fungi, were visited to collect air samples. The amplicon-based HTS approach is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of amplification. For this reason, the authors of this paper used a shotgun metagenomic approach to compare its outcome with the amplicon-based method. Indeed, shotgun metagenomic does not rely on any amplification prior to sequencing, because all genes are sequenced without a specific target. In addition, culture methods were added to the analyses in biomethanization and dairy farms samples to validate their contribution to fungal diversity of aerosols. The results obtained are unequivocal towards ITS1 outperformance to ITS2 in terms of richness, and taxonomic coverage. The differential abundance analysis did demonstrate that some taxa were exclusively detected only by ITS2, and vice-versa for ITS1. However, the shotgun metagenomic approach showed a taxonomic profile more resembling to ITS1 than ITS2. Based on these results, neither of the barcodes evaluated is perfect in terms of distinguishing all species. Using both barcodes offers a broader view of the fungal aerosol population. However, with the actual knowledge, the authors strongly recommend using ITS1 as a universal fungal barcode for quick general analyses of diversity and when limited financial resources are available, primarily due its ability to capture taxonomic profiles similar to those obtained using the shotgun metagenomic. The culture comparison with amplicon-based sequencing showed the complementarity of both approaches in describing the most abundant taxa.
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Affiliation(s)
- Hamza Mbareche
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, Canada
| | - Marc Veillette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, Quebec, Canada
| | - Guillaume Bilodeau
- Canadian Food Inspection Agency, Pathogen Identification Research Lab, Ottawa, Canada
| | - Caroline Duchaine
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, Canada
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Tu Y, Wang K, Wan JB, He C. Anti-inflammatory effects of Glycine tabacina extract in LPS-stimulated macrophages and collagen-induced arthritis mice. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.103528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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25
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Jia X, Zhang C, Bao J, Wang K, Tu Y, Wan JB, He C. Flavonoids from Rhynchosia minima root exerts anti-inflammatory activity in lipopolysaccharide-stimulated RAW 264.7 cells via MAPK/NF-κB signaling pathway. Inflammopharmacology 2019; 28:289-297. [DOI: 10.1007/s10787-019-00632-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/07/2019] [Indexed: 12/15/2022]
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26
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Robertson LJ, Clark CG, Debenham JJ, Dubey J, Kváč M, Li J, Ponce-Gordo F, Ryan U, Schares G, Su C, Tsaousis AD. Are molecular tools clarifying or confusing our understanding of the public health threat from zoonotic enteric protozoa in wildlife? Int J Parasitol Parasites Wildl 2019; 9:323-341. [PMID: 31338293 PMCID: PMC6626983 DOI: 10.1016/j.ijppaw.2019.01.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/13/2022]
Abstract
Emerging infectious diseases are frequently zoonotic, often originating in wildlife, but enteric protozoa are considered relatively minor contributors. Opinions regarding whether pathogenic enteric protozoa may be transmitted between wildlife and humans have been shaped by our investigation tools, and have led to oscillations regarding whether particular species are zoonotic or have host-adapted life cycles. When the only approach for identifying enteric protozoa was morphology, it was assumed that many enteric protozoa colonized multiple hosts and were probably zoonotic. When molecular tools revealed genetic differences in morphologically identical species colonizing humans and other animals, host specificity seemed more likely. Parasites from animals found to be genetically identical - at the few genes investigated - to morphologically indistinguishable parasites from human hosts, were described as having zoonotic potential. More discriminatory molecular tools have now sub-divided some protozoa again. Meanwhile, some infection events indicate that, circumstances permitting, some "host-specific" protozoa, can actually infect various hosts. These repeated changes in our understanding are linked intrinsically to the investigative tools available. Here we review how molecular tools have assisted, or sometimes confused, our understanding of the public health threat from nine enteric protozoa and example wildlife hosts (Balantoides coli - wild boar; Blastocystis sp. - wild rodents; Cryptosporidium spp. - wild fish; Encephalitozoon spp. - wild birds; Entamoeba spp. - non-human primates; Enterocytozoon bieneusi - wild cervids; Giardia duodenalis - red foxes; Sarcocystis nesbitti - snakes; Toxoplasma gondii - bobcats). Molecular tools have provided evidence that some enteric protozoa in wildlife may infect humans, but due to limited discriminatory power, often only the zoonotic potential of the parasite is indicated. Molecular analyses, which should be as discriminatory as possible, are one, but not the only, component of the toolbox for investigating potential public health impacts from pathogenic enteric protozoa in wildlife.
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Affiliation(s)
- Lucy J. Robertson
- Parasitology Laboratory, Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, PO Box 369 Sentrum, 0102, Oslo, Norway
| | - C. Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - John J. Debenham
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, PO Box 369 Sentrum, 0102, Oslo, Norway
| | - J.P. Dubey
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Building 1001, Beltsville, MD, 20705-2350, USA
| | - Martin Kváč
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05, Czech Republic
| | - Junqiang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Francisco Ponce-Gordo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University, Plaza Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Una Ryan
- Centre for Sustainable Aquatic Ecosystems, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
| | - Gereon Schares
- Institute of Epidemiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493, Greifswald, Insel Riems, Germany
| | - Chunlei Su
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996-1937, USA
| | - Anastasios D. Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, UK
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Galimberti A, Casiraghi M, Bruni I, Guzzetti L, Cortis P, Berterame NM, Labra M. From DNA barcoding to personalized nutrition: the evolution of food traceability. Curr Opin Food Sci 2019. [DOI: 10.1016/j.cofs.2019.07.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Tu Y, Wang K, Liang Y, Jia X, Wang L, Wan JB, Han J, He C. Glycine tabacina ethanol extract ameliorates collagen-induced arthritis in rats via inhibiting pro-inflammatory cytokines and oxidation. JOURNAL OF ETHNOPHARMACOLOGY 2019; 237:20-27. [PMID: 30880257 DOI: 10.1016/j.jep.2019.03.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/21/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The whole plant of Glycine tabacina (Labill.) Benth has been used as a traditional herbal medicine to treat rheumatism, ostealgia and nephritis in China. It is also one of the sources of the renowned native herbal medicine 'I-Tiao-Gung' in Taiwan. AIM OF THE STUDY This study aimed to investigate the anti-arthritic effect of ethanol extract of G. tabacina (GTE) in a collagen-induced arthritis (CIA) rat model. MATERIALS AND METHODS The chemical profile of GTE was analyzed by HPLC-UV. The CIA was induced in male Wistar rats by intradermal injection of bovine type II collagen at tail root, back and ankle joints. The rats were orally administrated daily with GTE (1.11, 2.22 and 4.44 g dry weight of herb powder per kg body weight) from day 0 and continued for 30 days. Swelling volume and thickness of paw, arthritis index, X-radiographs and histopathological changes were examined to assess the severity of arthritis. Furthermore, the levels of pro-inflammatory cytokines, such as interleukin1β (IL-1β), IL-6 and tumor necrosis factor α (TNF-α), total superoxide dismutase (T-SOD) activity and malonaldehyde (MDA) level were measured to preliminarily explore the possible mechanisms. RESULTS Oral administration of GTE significantly ameliorated the arthritic symptoms in CIA rat model, as indicated by the effects on paws swelling and arthritis index. X-radiographic analysis and histopathological examinations demonstrated that GTE effectively protected the bone and cartilage of joints from erosion, lesion and deformation. The efficacy of GTE treatment on CIA was comparable to that of indomethacin (positive drug). Besides, the overproduction of IL-1β, IL-6 and TNF-α was remarkably inhibited in the serum of all GTE treatment groups. The restoration of serum T-SOD activity and MDA level proved that GTE administration alleviated the oxidative stress in CIA rats. CONCLUSIONS GTE exhibited strong anti-CIA activity through inhibiting pro-inflammatory cytokines and oxidation in rats, suggesting its potential preventive and therapeutic effects on rheumatoid arthritis (RA).
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Affiliation(s)
- Yanbei Tu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, 999078, China
| | - Kai Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, 999078, China
| | - Yeer Liang
- Zhuhai Livzon Cynvenio Diagnostics Ltd., Zhuhai, Guangdong, 519060, China
| | - Xuejing Jia
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, 999078, China
| | - Lili Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jian-Bo Wan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, 999078, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Chengwei He
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, 999078, China.
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29
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Gesto-Borroto R, Cardoso-Taketa A, Yactayo-Chang JP, Medina-Jiménez K, Hornung-Leoni C, Lorence A, Villarreal ML. DNA barcoding and TLC as tools to properly identify natural populations of the Mexican medicinal species Galphimia glauca Cav. PLoS One 2019; 14:e0217313. [PMID: 31136619 PMCID: PMC6538163 DOI: 10.1371/journal.pone.0217313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/08/2019] [Indexed: 01/30/2023] Open
Abstract
Galphimia glauca is a plant that is endemic to Mexico and has been commonly used since pre-Hispanic times to treat various illnesses, including central nervous system disorders and inflammation. The first studies investigating a natural population of G. glauca in Mexico showed that the plant has anxiolytic and sedative activities in mice and humans. The plant's bioactive compounds were isolated and identified, and they belong to a family of nor-secofriedelanes called galphimines. The integration of DNA barcoding and thin-layer chromatography analysis was performed to clarify whether the botanical classification of the populations in the study, which were collected in different regions of Mexico, as G. glauca was correct or if the populations consist of more than one species of the genus Galphimia. We employed six DNA barcodes (matK, rbcL, rpoC1, psbA-trnH, ITS1 and ITS2) that were analyzed individually and in combination and then compared each other, to indicate differences among the studied populations. In the phylogenetic analysis, ITS1 and ITS2 markers as well as the combination of all DNA regions were the most efficient for discriminating the population studied. The thin-layer chromatography analysis exhibited four principal chemical profiles, one of which corresponded to the populations that produced galphimines. DNA barcoding was consistent and enabled us to differentiate the populations that produce galphimines from those that do not. The results of this investigation suggest that the studied populations belong to at least four different species of the genus Galphimia. The phylogenetic analysis and the thin-layer chromatography chemical profiles were convenient tools for establishing a strong relationship between the genotype and phenotype of the studied populations and could be used for quality control purposes to prepare herbal medicines from plants of the genus Galphimia.
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Affiliation(s)
- Reinier Gesto-Borroto
- Doctorado en Ciencias, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos, México
- Laboratorio de Investigación en Plantas Medicinales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Morelos, México
| | - Alexandre Cardoso-Taketa
- Laboratorio de Investigación en Plantas Medicinales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Morelos, México
| | - Jessica P. Yactayo-Chang
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Karina Medina-Jiménez
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Claudia Hornung-Leoni
- Centro de Investigaciones Biológicas, Instituto de Ciencias Básicas e Ingeniería Universidad Autónoma del Estado de Hidalgo, Hidalgo, México
| | - Argelia Lorence
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Maria Luisa Villarreal
- Laboratorio de Investigación en Plantas Medicinales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Morelos, México
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He T, Jiao L, Wiedenhoeft AC, Yin Y. Machine learning approaches outperform distance- and tree-based methods for DNA barcoding of Pterocarpus wood. PLANTA 2019; 249:1617-1625. [PMID: 30825008 DOI: 10.1007/s00425-019-03116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/20/2019] [Indexed: 05/10/2023]
Abstract
Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal logging and associated trade, and the development of reliable and efficient analytical methods is essential for its extensive application in the trade of wood and in the forensics of natural materials more broadly. In this study, 120 DNA sequences of four barcodes (ITS2, matK, ndhF-rpl32, and rbcL) generated in our previous study and 85 downloaded from National Center for Biotechnology Information (NCBI) were collected to establish a reference data set for six commercial Pterocarpus woods. MLAs (BLOG, BP-neural network, SMO and J48) were compared with distance- (TaxonDNA) and tree-based (NJ tree) methods based on identification accuracy and cost-effectiveness across these six species, and also were applied to discriminate the CITES-listed species Pterocarpus santalinus from its anatomically similar species P. tinctorius for forensic identification. MLAs provided higher identification accuracy (30.8-100%) than distance- (15.1-97.4%) and tree-based methods (11.1-87.5%), with SMO performing the best among the machine learning classifiers. The two-locus combination ITS2 + matK when using SMO classifier exhibited the highest resolution (100%) with the fewest barcodes for discriminating the six Pterocarpus species. The CITES-listed species P. santalinus was discriminated successfully from P. tinctorius using MLAs with a single barcode, ndhF-rpl32. This study shows that MLAs provided higher identification accuracy and cost-effectiveness for forensic application over other analytical methods in DNA barcoding of Pterocarpus wood.
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Affiliation(s)
- Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and National Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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Sundaresan N, Jagan EG, Kathamuthu G, Pandi M. Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia. PLoS One 2019; 14:e0215024. [PMID: 30964914 PMCID: PMC6456209 DOI: 10.1371/journal.pone.0215024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/25/2019] [Indexed: 11/19/2022] Open
Abstract
Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal (FEF) assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence-secondary structural features based phylogenetic analysis, also known as molecular morphometrics. A total of 392 FEF isolates were obtained from the Aglaia elaeagnoidea, Flacourtia inermis, and Premna serratifolia leaves and grouped into 98 morphotypes. Among these host plants, P. serratifolia showed the maximum percentage of colonization frequency. Representatives of each morphotype was sequenced and subjected to further molecular characterization. The results revealed that morphotypes were belonged to the phylum of Ascomycota, distributed over two classes (Sordariomycetes (68.59%) and Dothideomycetes (31.41%)), 6 orders and 19 genera. Based on compensatory base changes (CBC) analysis and absolute identity of ITS2 structure, 21, 20 and 23 species were recognized from A. elaeagnoidea, F. inermis, and P. serratifolia respectively. Diversity indices were higher in A. elaeagnoidea, despite it accounted for a modest 16.8% of total isolates recorded in this study. The genus Colletotrichum was predominant in A. elaeagnoidea (39%) and P. serratifolia (48%). Similarly, Diaporthe (43%) was dominant in F. inermis. Several host-specific species were also observed. This study concludes that these plants host diverse species of Ascomycota. To the best of our knowledge, this is the first detailed report on FEF diversity from these plants. Also, the inclusion of ITS2 secondary structure information along with the sequence provides a further dimension to resolve the inherent problems in identification of fungal species.
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Affiliation(s)
- Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Enthai Ganeshan Jagan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - GokulRaj Kathamuthu
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
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Ren F, Wang Y, Xu Z, Li Y, Xin T, Zhou J, Qi Y, Wei X, Yao H, Song J. DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae. Ecol Evol 2019; 9:1934-1945. [PMID: 30847083 PMCID: PMC6392370 DOI: 10.1002/ece3.4886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/02/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya-Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA-trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P-distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia-recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well-supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.
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Affiliation(s)
- Feng‐Ming Ren
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Chongqing Institute of Medicinal Plant Cultivation, Research and Utilization on Characteristic Biological Resources of Sichuan and Chongqing Co‐construction LabChinese Medicine Breeding and Evaluation Engineering Technology Research Center of ChongqingChongqingChina
| | - Ying‐Wei Wang
- Beijing Botanical Garden, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Zhi‐Chao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Tian‐Yi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jian‐Guo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yao‐Dong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Xue‐Ping Wei
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jing‐Yuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
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Quirós-Guerrero L, Albertazzi F, Araya-Valverde E, Romero RM, Villalobos H, Poveda L, Chavarría M, Tamayo-Castillo G. Phenolic variation among Chamaecrista nictitans subspecies and varieties revealed through UPLC-ESI(-)-MS/MS chemical fingerprinting. Metabolomics 2019; 15:14. [PMID: 30830463 DOI: 10.1007/s11306-019-1475-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Comparative analysis of metabolic features of plants has a high potential for determination of quality control of active ingredients, ecological or chemotaxonomic purposes. Specifically, the development of efficient and rapid analytical tools that allow the differentiation among species, subspecies and varieties of plants is a relevant issue. Here we describe a multivariate model based on LC-MS/MS fingerprinting capable of discriminating between subspecies and varieties of the medicinal plant Chamaecrista nictitans, a rare distributed species in Costa Rica. METHODS Determination of the chemical fingerprint was carried out on a LC-MS (ESI-QTOF) in negative ionization mode, main detected and putatively identified compounds included proanthocyanidin oligomers, several flavonoid C- and O-glycosides, and flavonoid acetates. Principal component analysis (PCA), partial least square-discriminant analysis (PLS-DA) and cluster analysis of chemical profiles were performed. RESULTS Our method showed a clear discrimination between the subspecies and varieties of Chamaecrista nictitans, separating the samples into four fair differentiated groups: M1 = C. nictitans ssp. patellaria; M2 = C. nictitans ssp. disadena; M3 = C. nictitans ssp. nictitans var. jaliscensis and M4 = C. nictitans ssp. disadena var. pilosa. LC-MS/MS fingerprint data was validated using both morphological characters and DNA barcoding with ITS2 region. The comparison of the morphological characters against the chemical profiles and DNA barcoding shows a 63% coincidence, evidencing the morphological similarity in C. nictitans. On the other hand, genetic data and chemical profiles grouped all samples in a similar pattern, validating the functionality of our metabolomic approach. CONCLUSION The metabolomic method described in this study allows a reliably differentiation between subspecies and varieties of C. nictitans using a straightforward protocol that lacks extensive purification steps.
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Affiliation(s)
- Luis Quirós-Guerrero
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica
| | - Federico Albertazzi
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
| | - Emanuel Araya-Valverde
- Centro Nacional de Innovaciones Biotecnológicas (CENiBiot), CeNAT-CONARE, San Jose, 1174-1200, Costa Rica
- Escuela de Biología, Instituto Tecnológico de Costa Rica, Cartago, 159-7050, Costa Rica
| | - Rosaura M Romero
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica
| | - Heidy Villalobos
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
| | - Luis Poveda
- Herbario Juvenal Valerio Rodríguez, Universidad Nacional, Heredia, Costa Rica
| | - Max Chavarría
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica
- Centro Nacional de Innovaciones Biotecnológicas (CENiBiot), CeNAT-CONARE, San Jose, 1174-1200, Costa Rica
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica.
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San Jose, 11501-2060, Costa Rica.
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Sheth BP, Punia S, Dheer M, Rakhashiya PM, Patel PP, Thaker VS. Phylogenetic implications and secondary structure analyses of Vigna mungo (L.) Hepper genotypes based on nrDNA ITS2 sequences. Comput Biol Chem 2019; 78:389-397. [PMID: 30606693 DOI: 10.1016/j.compbiolchem.2018.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/25/2018] [Indexed: 01/07/2023]
Abstract
The internal transcribed spacers are highly preferred nuclear markers for the phylogenetic assessment of most eukaryotes, including plants. More recently, ITS2 has shown to possess equivalent phylogenetic significance as the entire ITS region. Vigna mungo L. Hepper is comparatively less explored from the molecular aspects as compared to the other species of the Vigna genus. The study presents the intra-individual characterization of 24 distinct genotypes Vigna mungo L. Hepper, using morphological as well as nrDNA ITS2 sequences and secondary structural data. The morphological characterization has been carried out using nine important agro-morphological traits. The molecular phylogeny of the sequence data, using the maximum parsimony and neighbor joining methods, shows the significant distinction based on the haplotypic variations amongst blackgram genotypes. The ITS2 secondary structures predicted using the homology modeling approach were compatible with the eukaryote-universal ITS2 secondary structure. The sequence-structure phylogeny reconstructed using the profile neighbour joining approach, also showed the presence of haplotypic variations in form of clusters on the phylogenetic tree. Further, the high GC content in the sequence data and highly negative ΔG values of the folded secondary structures ruled out the possibilities of the presence of any pseudogenes in the data set. Our analysis recommends the use of ITS2 sequence and secondary structure data at the intraspecific levels of plant taxonomical classification. Moreover, this study for the very first time reports the combined use morphological, and molecular data (using ITS2 sequence and secondary structural information) for the characterization of plants at the varietal level of taxonomical classification.
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Affiliation(s)
- Bhavisha P Sheth
- DST-Centre for Policy Research, Entrepreneurship Development Institute of India, P.O. Bhat 382428. Gandhinagar, Gujarat, India.
| | - Sumer Punia
- College of Agriculture, Sri Karan Narendra Agriculture University, Jobner, Jaipur, Rajasthan, India
| | - Meenakshi Dheer
- Agricultural Research Station, Ummedganj, Kota 324001. Rajasthan, India
| | - Purvi M Rakhashiya
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Pooja P Patel
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Vrinda S Thaker
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India.
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Makiola A, Dickie IA, Holdaway RJ, Wood JR, Orwin KH, Lee CK, Glare TR. Biases in the metabarcoding of plant pathogens using rust fungi as a model system. Microbiologyopen 2018; 8:e00780. [PMID: 30585441 PMCID: PMC6612544 DOI: 10.1002/mbo3.780] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost-effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next-generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large-scale detection and quantification of rust fungi, but not for confirming the absence of species.
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Affiliation(s)
- Andreas Makiola
- Agroécologie, AgroSup Dijon, INRAUniversité Bourgogne, Université Bourgogne Franche‐ComtéDijonFrance,Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
| | - Ian A. Dickie
- Bio‐Protection Research Centre, School of Biological SciencesUniversity of CanterburyNew Zealand
| | | | - Jamie R. Wood
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Kate H. Orwin
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Charles K. Lee
- Waikato DNA Sequencing Facility, School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Travis R. Glare
- Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
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Mbareche H, Veillette M, Bilodeau GJ, Duchaine C. An amplicon-based sequencing approach for the study of aeromycology. J Xenobiot 2018; 8:7810. [PMID: 30701064 PMCID: PMC6343103 DOI: 10.4081/xeno.2018.7810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/17/2018] [Indexed: 11/22/2022] Open
Abstract
Not available.
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Affiliation(s)
- Hamza Mbareche
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City (QC)
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City (QC)
| | - Marc Veillette
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City (QC)
| | - Guillaume J. Bilodeau
- Pathogen Identification Research Lab, Canadian Food Inspection Agency (CFIA), Ottawa, Canada
| | - Caroline Duchaine
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City (QC)
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City (QC)
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Gong L, Qiu XH, Huang J, Xu W, Bai JQ, Zhang J, Su H, Xu CM, Huang ZH. Constructing a DNA barcode reference library for southern herbs in China: A resource for authentication of southern Chinese medicine. PLoS One 2018; 13:e0201240. [PMID: 30044868 PMCID: PMC6059470 DOI: 10.1371/journal.pone.0201240] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022] Open
Abstract
Southern Chinese Medicine (SCM) is an important sect of Traditional Chinese Medicine (TCM) with its own special cultural style. Species identification is essential for TCM quality control because authentic herbs are possibly substituted with adulterants that would threaten the health of the public or even cause death. Here, we provided the first local reference DNA barcode library based on the second internal transcribed spacer (ITS2) for the molecular identification of SCM. A total of 1512 specimens of southern herbs representing 359 species were collected under the instructions and identification of taxonomic experts. Genomic DNA was extracted, and the PCR reaction proceeded according to standard procedures. After Sanger sequencing, sequence assembling and annotation, a reliable ITS2 barcode library with 1276 sequences from 309 species of Southern herbs was constructed. The PCR efficiency of the whole samples was 84.39%. Characteristics of the ITS2 barcode were analyzed, including sequence lengths and GC contents in different taxa. Neighbor-joining trees based on Kimura 2-Parameter (K2P) genetic distances showed a 67.56% successful rate of species identification with ITS2 barcode. In addition, 96.57% of species could be successfully identified at the genus level by the BLAST method. Eleven plant species were discovered to be cryptic. In addition, we found that there is an incorrect sequence existing in the public database, making a reliable local DNA barcode reference more meaningful. ITS2 barcodes exhibit advantages in TCM identification. This DNA barcode reference library could be used in Southern Chinese Medicine quality control, thus contributing to protecting public health.
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Affiliation(s)
- Lu Gong
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Xiao Hui Qiu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China
| | - Juan Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Wen Xu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Jun Qi Bai
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Jing Zhang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - He Su
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Chu Mei Xu
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
| | - Zhi Hai Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou, China
- * E-mail:
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Vu HT, Huynh P, Tran HD, Le L. In Silico Study on Molecular Sequences for Identification of Paphiopedilum Species. Evol Bioinform Online 2018; 14:1176934318774542. [PMID: 29899659 PMCID: PMC5993066 DOI: 10.1177/1176934318774542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/09/2018] [Indexed: 12/02/2022] Open
Abstract
Our study searched all available sequences of Paphiopedilum from NCBI (National Center for Biotechnology Information) and tested for their species resolution capability in single as well as in combination forms. A total of 28 loci were applied for analyses in the study. From the nuclear genome, the highest resolution was of LFY, followed by ACO, DEF4, and RAD51. These 4 loci were found to be even better than the popular region ITS for Paphiopedilum identification. Among the chloroplast regions, the intergenic spacer atpB-rbcL gave the highest species resolution (76.7%), followed by matK, trnL, rpoC2, and ycf1. The divergence of CHS, XDH, 18S, Nad1, ccsA, rbcL, and ycf2 was very low and should not be used as identifying markers for Paphiopedilum. In addition, 2-locus combinations could improve significantly the resolving capability for the genus, in which 14/36 data sets could be resolved completely (100%) with interspecies relationships. The indel information was also effective supporting data for molecular discrimination of species.
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Affiliation(s)
- Huyen-Trang Vu
- Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.,International University - Vietnam National University, Ho Chi Minh City, Vietnam
| | - Phuong Huynh
- Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | | | - Ly Le
- International University - Vietnam National University, Ho Chi Minh City, Vietnam
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Tahir A, Hussain F, Ahmed N, Ghorbani A, Jamil A. Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae. PeerJ 2018; 6:e4499. [PMID: 29576968 PMCID: PMC5855882 DOI: 10.7717/peerj.4499] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/21/2018] [Indexed: 01/14/2023] Open
Abstract
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.
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Affiliation(s)
- Aisha Tahir
- Department of Biochemistry, Faculty of Science, University of Agriculture, Faisalabad, Pakistan
| | - Fatma Hussain
- Department of Biochemistry, Faculty of Science, University of Agriculture, Faisalabad, Pakistan
| | - Nisar Ahmed
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | | | - Amer Jamil
- Department of Biochemistry, Faculty of Science, University of Agriculture, Faisalabad, Pakistan
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Yu X, Zhang Y, Wang D, Jiang L, Xu X. Identification of Three Kinds of Citri Reticulatae Pericarpium Based on Deoxyribonucleic Acid Barcoding and High-performance Liquid Chromatography-diode Array Detection-electrospray Ionization/Mass Spectrometry/Mass Spectrometry Combined with Chemometric Analysis. Pharmacogn Mag 2018; 14:64-69. [PMID: 29576703 PMCID: PMC5858244 DOI: 10.4103/pm.pm_581_16] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 02/01/2017] [Indexed: 11/16/2022] Open
Abstract
Background: Citri Reticulatae Pericarpium is the dried mature pericarp of Citrus reticulata Blanco which can be divided into “Chenpi” and “Guangchenpi.” “Guangchenpi” is the genuine Chinese medicinal material in Xinhui, Guangdong province; based on the greatest quality and least amount, it is most expensive among others. Hesperidin is used as the marker to identify Citri Reticulatae Pericarpium described in the Chinese Pharmacopoeia 2010. However, both “Chenpi” and “Guangchenpi” contain hesperidin so that it is impossible to differentiate them by measuring hesperidin. Objective: Our study aims to develop an efficient and accurate method to separate and identify “Guangchenpi” from other Citri Reticulatae Pericarpium. Materials and Methods: The genomic deoxyribonucleic acid (DNA) of all the materials was extracted and then the internal transcribed spacer 2 was amplified, sequenced, aligned, and analyzed. The secondary structures were created in terms of the database and website established by Jörg Schultz et al. High-performance liquid chromatography-diode array detection-electrospray Ionization/mass spectrometry (HPLC-DAD-ESI-MS)/MS coupled with chemometric analysis was applied to compare the differences in chemical profiles of the three kinds of Citri Reticulatae Pericarpium. Results: A total of 22 samples were classified into three groups. The results of DNA barcoding were in accordance with principal component analysis and hierarchical cluster analysis. Eight compounds were deduced from HPLC-DAD-ESI-MS/MS. Conclusions: This method is a reliable and effective tool to differentiate the three Citri Reticulatae Pericarpium. SUMMARY The internal transcribed spacer 2 regions and the secondary structure among three kinds of Citri Reticulatae Pericarpium varied considerably All the 22 samples were analyzed by high-performance liquid chromatography (HPLC) to obtain the chemical profiles Principal component analysis and hierarchical cluster analysis were used in the chemometric analysis deoxyribonucleic acid barcoding and HPLC-diode array detection-electrospray ionization/mass spectrometry/MS coupled with chemometric analysis provided an accurate and strong proof to identify these three herbs.
Abbreviations used: CTAB: Hexadecyltrimethylammonium bromide, DNA: Deoxyribonucleic acid, ITS2: Internal transcribed spacer 2, PCR: Polymerase chain reaction.
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Affiliation(s)
- Xiaoxue Yu
- Laboratory of Pharmaceutical Analysis and Quality Assessment, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | | | - Dongmei Wang
- Laboratory of Pharmaceutical Analysis and Quality Assessment, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Lin Jiang
- Laboratory of Pharmaceutical Analysis and Quality Assessment, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xinjun Xu
- Laboratory of Pharmaceutical Analysis and Quality Assessment, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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Yan DH, Gao Q, Sun X, Song X, Li H. ITS2 sequence-structure phylogeny reveals diverse endophytic Pseudocercospora fungi on poplars. Genetica 2018; 146:187-198. [PMID: 29397500 DOI: 10.1007/s10709-018-0011-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 01/31/2018] [Indexed: 01/13/2023]
Abstract
For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s. str. genus using RNAshape program. The model has a typical eukaryotic four-helix ITS2 secondary structure. But a single U base occurred in conserved motif of U-U mismatch in Helix 2, and a UG emerged in UGGU motif in Helix 3 to Pseudocercospora fungi. The phylogeny analyses based on the ITS2 sequence-secondary structures with compensatory base change characterizations are able to delimit more species for Pseudocercospora s. str. than phylogenic inferences of traditional multi-loci alignments do. The model was employed to explore the diversity of endophytic Pseudocercospora fungi in poplar trees. The analysis results also showed that endophytic Pseudocercospora fungi were diverse in species and evolved a specific lineage in poplar trees. This work suggested that ITS2 sequence-structures could become as additionally significant loci for species phylogenetic and taxonomic studies on Pseudocerospora fungi, and that Pseudocercospora endophytes could be important roles to Pseudocercospora fungi's evolution and function in ecology.
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Affiliation(s)
- Dong-Hui Yan
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Hai Dian District, Beijing, 100091, People's Republic of China.
| | - Qian Gao
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Hai Dian District, Beijing, 100091, People's Republic of China
| | - Xiaoming Sun
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Hai Dian District, Beijing, 100091, People's Republic of China
| | - Xiaoyu Song
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Hai Dian District, Beijing, 100091, People's Republic of China
| | - Hongchang Li
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Hai Dian District, Beijing, 100091, People's Republic of China
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Lo YT, Shaw PC. DNA-based techniques for authentication of processed food and food supplements. Food Chem 2018; 240:767-774. [DOI: 10.1016/j.foodchem.2017.08.022] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/07/2017] [Accepted: 08/03/2017] [Indexed: 12/31/2022]
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Yu M, Jiao L, Guo J, Wiedenhoeft AC, He T, Jiang X, Yin Y. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. PLANTA 2017; 246:1165-1176. [PMID: 28825134 DOI: 10.1007/s00425-017-2758-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.
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Affiliation(s)
- Min Yu
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Juan Guo
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Center for Wood Anatomy Research, USDA Forest Service, Forest Products Laboratory, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaomei Jiang
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2734960. [PMID: 29181391 PMCID: PMC5664236 DOI: 10.1155/2017/2734960] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/17/2017] [Accepted: 09/13/2017] [Indexed: 11/17/2022]
Abstract
Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.
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Derivative Technology of DNA Barcoding (Nucleotide Signature and SNP Double Peak Methods) Detects Adulterants and Substitution in Chinese Patent Medicines. Sci Rep 2017; 7:5858. [PMID: 28724933 PMCID: PMC5517575 DOI: 10.1038/s41598-017-05892-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/05/2017] [Indexed: 11/21/2022] Open
Abstract
Lonicerae japonicae Flos has been used to produce hundred kinds of Chinese patent medicines (CPMs) in China. Economically motivated adulterants have been documented, leading to market instability and a decline in consumer confidence. ITS2 has been used to identify raw medicinal materials, but it’s not suitable for the identification of botanical extracts and complex CPMs. Therefore, a short barcode for the identification of processed CPMs would be profitable. A 34 bp nucleotide signature (5′ CTAGCGGTGGTCGTACGATAGCCAATGCATGAGT 3′) was developed derived from ITS2 region of Eucommiae Folium based on unique motifs. Mixtures of powdered Lonicerae japonicae Flos and Lonicerae Flos resulted in double peaks at the expected SNP (Single Nucleotide Polymorphisms) positions, of which the height of the peaks were roughly indicative of the species’ ratio in the mixed powder. Subsequently we tested 20 extracts and 47 CPMs labelled as containing some species of Lonicera. The results revealed only 17% of the extracts and 22% of the CPMs were authentic, others exist substitution or adulterant; 7% were shown to contain both of two adulterants Eucommiae Folium and Lonicerae Flos. The methods developed in this study will widely broaden the application of DNA barcode in quality assurance of natural health products.
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Yu N, Wei YL, Zhang X, Zhu N, Wang YL, Zhu Y, Zhang HP, Li FM, Yang L, Sun JQ, Sun AD. Barcode ITS2: a useful tool for identifying Trachelospermum jasminoides and a good monitor for medicine market. Sci Rep 2017; 7:5037. [PMID: 28698616 PMCID: PMC5506054 DOI: 10.1038/s41598-017-04674-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/18/2017] [Indexed: 01/31/2023] Open
Abstract
Trachelospermum jasminoides is commonly used in traditional Chinese medicine. However, the use of the plant's local alternatives is frequent, causing potential clinical problems. The T. jasminoides sold in the medicine market is commonly dried and sliced, making traditional identification methods difficult. In this study, the ITS2 region was evaluated on 127 sequences representing T. jasminoides and its local alternatives according to PCR and sequencing rates, intra- and inter-specific divergences, secondary structure, and discrimination capacity. Results indicated the 100% success rates of PCR and sequencing and the obvious presence of a barcoding gap. Results of BLAST 1, nearest distance and neighbor-joining tree methods showed that barcode ITS2 could successfully identify all the texted samples. The secondary structures of the ITS2 region provided another dimensionality for species identification. Two-dimensional images were obtained for better and easier identification. Previous studies on DNA barcoding concentrated more on the same family, genus, or species. However, an ideal barcode should be variable enough to identify closely related species. Meanwhile, the barcodes should also be conservative in identifying distantly related species. This study highlights the application of barcode ITS2 in solving practical problems in the distantly related local alternatives of medical plants.
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Affiliation(s)
- Ning Yu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yu-Long Wei
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Xin Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Ning Zhu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yan-Li Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Yue Zhu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Hai-Ping Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Fen-Mei Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Lan Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Jia-Qi Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China
| | - Ai-Dong Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, 100083, China.
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DNA barcode and identification of the varieties and provenances of Taiwan's domestic and imported made teas using ribosomal internal transcribed spacer 2 sequences. J Food Drug Anal 2017; 25:260-274. [PMID: 28911667 PMCID: PMC9332525 DOI: 10.1016/j.jfda.2016.06.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 01/17/2023] Open
Abstract
The major aim of made tea identification is to identify the variety and provenance of the tea plant. The present experiment used 113 tea plants [Camellia sinensis (L.) O. Kuntze] housed at the Tea Research and Extension Substation, from which 113 internal transcribed spacer 2 (ITS2) fragments, 104 trnL intron, and 98 trnL-trnF intergenic sequence region DNA sequences were successfully sequenced. The similarity of the ITS2 nucleotide sequences between tea plants housed at the Tea Research and Extension Substation was 0.379–0.994. In this polymerase chain reaction-amplified noncoding region, no varieties possessed identical sequences. Compared with the trnL intron and trnL-trnF intergenic sequence fragments of chloroplast cpDNA, the proportion of ITS2 nucleotide sequence variation was large and is more suitable for establishing a DNA barcode database to identify tea plant varieties. After establishing the database, 30 imported teas and 35 domestic made teas were used in this model system to explore the feasibility of using ITS2 sequences to identify the varieties and provenances of made teas. A phylogenetic tree was constructed using ITS2 sequences with the unweighted pair group method with arithmetic mean, which indicated that the same variety of tea plant is likely to be successfully categorized into one cluster, but contamination from other tea plants was also detected. This result provides molecular evidence that the similarity between important tea varieties in Taiwan remains high. We suggest a direct, wide collection of made tea and original samples of tea plants to establish an ITS2 sequence molecular barcode identification database to identify the varieties and provenances of tea plants. The DNA barcode comparison method can satisfy the need for a rapid, low-cost, frontline differentiation of the large amount of made teas from Taiwan and abroad, and can provide molecular evidence of their varieties and provenances.
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Mishra P, Kumar A, Rodrigues V, Shukla AK, Sundaresan V. Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae). PeerJ 2016; 4:e2638. [PMID: 27994958 PMCID: PMC5162394 DOI: 10.7717/peerj.2638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/30/2016] [Indexed: 12/13/2022] Open
Abstract
PREMISE OF THE STUDY The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. METHODOLOGY A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. PRINCIPAL FINDINGS Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. CONCLUSION The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.
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Affiliation(s)
- Priyanka Mishra
- Department of Plant Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatics Plants, Research Center , Bangalore , Karnataka , India
| | - Amit Kumar
- Department of Plant Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatics Plants, Research Center , Bangalore , Karnataka , India
| | - Vereena Rodrigues
- Department of Plant Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatics Plants, Research Center , Bangalore , Karnataka , India
| | - Ashutosh K Shukla
- Biotechnology Division, CSIR - Central Institute of Medicinal and Aromatic Plants , Lucknow , Uttar Pradesh , India
| | - Velusamy Sundaresan
- Department of Plant Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatics Plants, Research Center , Bangalore , Karnataka , India
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A Nucleotide Signature for the Identification of Angelicae Sinensis Radix (Danggui) and Its Products. Sci Rep 2016; 6:34940. [PMID: 27713564 PMCID: PMC5054691 DOI: 10.1038/srep34940] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 09/20/2016] [Indexed: 02/07/2023] Open
Abstract
It is very difficult to identify Angelicae sinensis radix (Danggui) when it is processed into Chinese patent medicines. The proposed internal transcribed spacer 2 (ITS2) is not sufficient to resolve heavily processed materials. Therefore, a short barcode for the identification of processed materials is urgently needed. In this study, 265 samples of Angelicae sinensis radix and adulterants were collected. The ITS2 region was sequenced, and based on one single nucleotide polymorphism(SNP) site unique to Angelica sinensis, a nucleotide signature consisting of 37-bp (5′-aatccgcgtc atcttagtga gctcaaggac ccttagg-3′) was developed. It is highly conserved and specific within Angelica sinensis while divergent among other species. Then, we designed primers (DG01F/DG01R) to amplify the nucleotide signature region from processed materials. 15 samples procured online were analysed. By seeking the signature, we found that 7 of them were counterfeits. 28 batches of Chinese patent medicines containing Danggui were amplified. 19 of them were found to contain the signature, and adulterants such as Ligusticum sinense, Notopterygium incisum, Angelica decursiva and Angelica gigas were detected in other batches. Thus, this nucleotide signature, with only 37-bp, will broaden the application of DNA barcoding to identify the components in decoctions, Chinese patent medicines and other products with degraded DNA.
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Feng S, Jiang M, Shi Y, Jiao K, Shen C, Lu J, Ying Q, Wang H. Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study. FRONTIERS IN PLANT SCIENCE 2016; 7:1047. [PMID: 27486467 PMCID: PMC4949264 DOI: 10.3389/fpls.2016.01047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/04/2016] [Indexed: 05/15/2023]
Abstract
Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources.
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Affiliation(s)
- Shangguo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Mengying Jiang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yujun Shi
- School of Foreign Languages, Zhejiang Gongshang UniversityHangzhou, China
| | - Kaili Jiao
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Chenjia Shen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Qicai Ying
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
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