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Wachananawat B, Kong BL, Shaw P, Bongcheewin B, Sangvirotjanapat S, Prombutara P, Pornputtapong N, Sukrong S. Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma comosa and C. latifolia. Heliyon 2024; 10:e31248. [PMID: 38813184 PMCID: PMC11133819 DOI: 10.1016/j.heliyon.2024.e31248] [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: 11/02/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
Members of the Curcuma genus, a crop in the Zingiberaceae, are widely utilized rhizomatous herbs globally. There are two distinct species, C. comosa Roxb. and C. latifolia Roscoe, referred to the same vernacular name "Wan Chak Motluk" in Thai. C. comosa holds economic importance and is extensively used as a Thai traditional medicine due to its phytoestrogenic properties. However, its morphology closely resembles that of C. latifolia, which contains zederone, a compound known for its hepatotoxic effects. They are often confused, which may affect the quality, efficacy and safety of the derived herbal materials. Thus, DNA markers were developed for discriminating C. comosa from C. latifolia. This study focused on analyzing core DNA barcode regions, including rbcL, matK, psbA-trnH spacer and ITS2, of the authentic C. comosa and C. latifolia species. As a result, no variable nucleotides in core DNA barcode regions were observed. The complete chloroplast (cp) genome was introduced to differentiate between the two species. The comparison revealed that the cp genomes of C. comosa and C. latifolia were 162,272 and 162,289 bp, respectively, with a total of 133 identified genes. The phylogenetic analysis revealed that C. comosa and C. latifolia exhibited a very close relationship with other Curcuma species. The cp genome of C. comosa and C. latifolia were identified for the first time, providing valuable insights for species identification and evolutionary research within the Zingiberaceae family.
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Affiliation(s)
- Bussarin Wachananawat
- Center of Excellence in DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Bobby Lim‐Ho Kong
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, N.T., China
| | - Pang‐Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, N.T., China
| | - Bhanubong Bongcheewin
- Department of Pharmaceutical Botany, Faculty of Pharmacy and Center of Excellence in Herbal Medicine and Natural Products, Faculty of Pharmacy, Mahidol University, Bangkok, 10400, Thailand
- Sireeruckhachati Nature Learning Park, Mahidol University, Nakhon Pathom, 73170, Thailand
| | | | - Pinidphon Prombutara
- Faculty of Science, Omics Science & Bioinformatics Center, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Natapol Pornputtapong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suchada Sukrong
- Center of Excellence in DNA Barcoding of Thai Medicinal Plants, Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
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Lonare N, Patil G, Waghmare S, Bhor R, Hardikar H, Tembe S. DNA Barcoding of Invasive Terrestrial Plant Species in India. Mol Biotechnol 2024:10.1007/s12033-024-01102-z. [PMID: 38430432 DOI: 10.1007/s12033-024-01102-z] [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: 09/02/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
Invasive plants are known to cause biodiversity loss and pose a major risk to human health and environment. Identification of invasive plants and distinguishing them from native species has been relied on morphological examination. Stringent requirement of floral characters and decreasing number of expert taxonomists are making conventional morphology-based identification system tedious and resource-intensive. DNA barcoding may help in quick identification of invasive species if distinct sequence divergence pattern at various taxonomic levels is observed. The present work evaluates the utility of four molecular markers; rbcL, matK, their combination (rbcL + matK), and psbA-trnH for identification of 37 invasive plant species from India and also in distinguishing them from 97 native species. A psbA-trnH locus was found to be of restricted utility in this work as it was represented by the members of a single family. A hierarchical increase in K2P mean divergence across different taxonomic levels was found to be the maximum for matK alone followed by rbcL + matK and rbcL alone, respectively. NJ clustering analysis, however, confirmed the suitability of combined locus (rbcL + matK) over individual rbcL and matK as the DNA barcode. RbcL showed the lowest resolution power among the three markers studied. MatK exhibited much better performance compared to rbcL alone in identifying most of the species accurately although it failed to show monophyly of genus Dinebra. Two families; Asteraceae and Poaceae, remained polyphyletic in the trees constructed by all three markers. Combined locus (rbcL + matK) was found to be the most suitable marker as it raised the resolution power of both the markers and could identify more than 90% of genera correctly. Phylogenetic tree constructed by Maximum-Parsimony method using combined locus as a molecular marker exhibited the best resolution, thus, supporting the significance of two-locus combination of rbcL + matK for barcoding invasive plant species from India. Present study contributes to the global barcode data of invasive plant species by adding fifty-one new sequences to it. Effective barcoding of additional number of native as well as invasive plant species from India is possible using this dual locus if it is combined with one or more new molecular plastid markers. Expansion of barcode database with a focus on barcode performance optimisation to improve discrimination ability at species level can be undertaken in future.
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Affiliation(s)
- Nayan Lonare
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Gayatri Patil
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Suprriya Waghmare
- IMT Technologies Pvt. Ltd, Kondhwa Khurd, Pune, Maharashtra, 411048, India
| | - Reshma Bhor
- IMT Technologies Pvt. Ltd, Kondhwa Khurd, Pune, Maharashtra, 411048, India
| | - Hrishikesh Hardikar
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Sanket Tembe
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India.
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Chen M, Sun J, Yao H, Gong F, Cai L, Wang C, Shao Q, Wang Z. Analysis of genetic and chemical variability of five Curcuma species based on DNA barcoding and HPLC fingerprints. FRONTIERS IN PLANT SCIENCE 2023; 14:1229041. [PMID: 37746000 PMCID: PMC10511903 DOI: 10.3389/fpls.2023.1229041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/04/2023] [Indexed: 09/26/2023]
Abstract
The rhizomes of Curcuma species have a long medicinal history in Asia. In China, Curcuma species mainly be utilized to make pharmaceutical products, including C. phaecocaulis, C. aromatica, C. wenyujin, C. kwangsiensis and C. longa. In this study, twenty-four samples were selected to study the genetic and chemical variability among five Curcuma species. The ITS2 and trnK intron gene fragment were used to identify the five Curcuma species, the differences in chemical composition were computed using the Euclidean distance based on the data of HPLC characteristic peak areas and the content of six key components, and agronomic characteristics were analyzed including morphological and volatile oil characteristics. The ITS2 and trnK intron gene fragment could distinguish the five Curcuma species clearly. The genetic distance between Curcuma species ranged from 0.0085 to 0.0767 based on the data of ITS2 gene sequences with 32 variation sites, and the genetic distance between Curcuma species ranged from 0.0003 to 0.0194 based on the data of trnK intron gene sequences with 39 variation sites. Five Curcuma species showed otherness chemical composition characteristics, with the Euclidean distance ranging from 3.373 to 6.998. The C. longa showed the biggest variation compared with other species, with the Euclidean distance above 6.239. Among the samples of the original plants of Ezhu, the volatile oil yield of W1 was the highest, reached to 105.75 mL per single plant. Among all the samples, J6 showed the highest yield of volatile oil, reached to 149.42 mL per single plant. The results showed that chemical composition similarity of the medicinal plants was the primary proof for the selection of the original plants of the Curcuma medicinal materials. The genetic distance and chemical variability were important references for discovering new medicinal plant resources.
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Affiliation(s)
- Mengying Chen
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Jian Sun
- Resource Center for Chinese Materia Medica, Zhejiang Research Institute of Traditional Chinese Medicine Co., Ltd., Hangzhou, China
| | - Hui Yao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Fuyu Gong
- Resource Center for Chinese Materia Medica, Zhejiang Research Institute of Traditional Chinese Medicine Co., Ltd., Hangzhou, China
| | - Long Cai
- Resource Center for Chinese Materia Medica, Zhejiang Research Institute of Traditional Chinese Medicine Co., Ltd., Hangzhou, China
| | - Chanyan Wang
- Resource Center for Chinese Materia Medica, Zhejiang Research Institute of Traditional Chinese Medicine Co., Ltd., Hangzhou, China
| | - Qingsong Shao
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Zhian Wang
- Resource Center for Chinese Materia Medica, Zhejiang Research Institute of Traditional Chinese Medicine Co., Ltd., Hangzhou, China
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Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese Curcuma (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera. FORESTS 2022. [DOI: 10.3390/f13020280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Curcuma is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of Curcuma (Chinese Curcuma, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese Curcuma species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese Curcuma with varying degrees of support using different methods and datasets.
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Abstract
Growing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2, matK, rbcL, trnH-psbA and their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matK exhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.
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Hu JL, Ci XQ, Liu ZF, Dormontt EE, Conran JG, Lowe AJ, Li J. Assessing candidate DNA barcodes for Chinese and internationally traded timber species. Mol Ecol Resour 2021; 22:1478-1492. [PMID: 34752673 DOI: 10.1111/1755-0998.13546] [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: 10/22/2020] [Revised: 10/22/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.
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Affiliation(s)
- Jian-Lin Hu
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Zhi-Fang Liu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Eleanor E Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - John G Conran
- Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and Sprigg Geobiology Centre (SGC), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew J Lowe
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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7
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Liu Q, Zhu S, Hayashi S, Anjiki N, Takano A, Kawahara N, Komatsu K. Genetic analysis of Curcuma species from Asia based on intron regions of genes encoding diketide-CoA synthase and curcumin synthase. J Nat Med 2021; 76:276-280. [PMID: 34495455 DOI: 10.1007/s11418-021-01563-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/01/2021] [Indexed: 11/27/2022]
Abstract
Intron length polymorphism (ILP) markers in genes encoding diketide-CoA synthase (DCS) and curcumin synthase (CURS) showed high identification rates in 13 Curcuma species from Asia. However, the sequences of the intron regions have not yet been analyzed. To elucidate the sequence differences in intron regions of the DCS and CURS genes and to search for specific sequences suitable for the identification of Curcuma species, a large number of sequences were determined through subcloning coupled with sequencing analysis of six Curcuma plant specimens belonging to five species that showed distinct ILP patterns. More than 30 sequences of each region from each specimen were grouped into genes DCS1, DCS2, or CURS1-3 and subsequently the sequences of the same genes were compared. Sequences belonging to the same gene showed inter-species similarity, and thus, these intron sequences were less informative within each single-gene region. The determined sequences from each specimen showed 3-5 kinds of sequence lengths in DCS intron I region, and 5-7 kinds of sequence lengths in CURS intron region. The length of determined sequences and the fragment number in each intron region were different among species, or specimens in C. longa, which were in accordance with the fragment lengths and numbers in their corresponding ILP patterns.
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Affiliation(s)
- Qundong Liu
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Shu Zhu
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.
| | - Shigeki Hayashi
- Tanegashima Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, 17007-2 Nakatane-cho, Kumage-Gun, Kagoshima, 891-3604, Japan
| | - Naoko Anjiki
- Tanegashima Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, 17007-2 Nakatane-cho, Kumage-Gun, Kagoshima, 891-3604, Japan
| | - Akihito Takano
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machidashi, Tokyo, 194-8543, Japan
| | - Nobuo Kawahara
- Tanegashima Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, 17007-2 Nakatane-cho, Kumage-Gun, Kagoshima, 891-3604, Japan
| | - Katsuko Komatsu
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.
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Liu Q, Zhu S, Hayashi S, Iida O, Takano A, Miyake K, Sukrong S, Agil M, Balachandran I, Nakamura N, Kawahara N, Komatsu K. Discrimination of Curcuma species from Asia using intron length polymorphism markers in genes encoding diketide-CoA synthase and curcumin synthase. J Nat Med 2021; 76:69-86. [PMID: 34482450 PMCID: PMC10050018 DOI: 10.1007/s11418-021-01558-2] [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: 05/18/2021] [Accepted: 07/20/2021] [Indexed: 01/20/2023]
Abstract
Recently, Curcuma rhizome-related foods with claimed health benefits have been used worldwide; however, correct identification and quality assessment have not been conducted. Due to the wide distribution and morphological similarities of Curcuma species, the classification of some species is debated and nomenclature is inconsistent among countries. In this study, to elucidate specific molecular markers of medicinally used Curcuma species in Asia, and to solve the confusion on the reported botanical origin of crude drugs, molecular analysis based on the intron length polymorphism (ILP) in genes encoding diketide-CoA synthase and curcumin synthase and the trnK intron sequences was performed using 59 plant specimens and 42 crude drug samples from 13 Curcuma species, obtained from Asian countries. The ILP patterns of the respective species from both plant specimens and crude drug samples revealed high consistency in C. aromatica, C. zedoaria, C. phaeocaulis, C. aeruginosa, C. wenyujin, and C. zanthorrhiza, but showed intraspecies polymorphism in C. longa, C. kwangsiensis, C. amada, C. mangga and C. comosa. The C. longa specimens and samples were separated into three subgroups which were highly consistent with their geographical origins. Based on the ILP markers and the trnK intron sequences, the botanical origins of "Khamin oi" from Thailand were correctly determined to be C. longa or a hybrid between C. longa and other species, and "Wan narn kum" from Thailand and "Kasturi manjal" from India were correctly determined to be C. zanthorrhiza.
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Affiliation(s)
- Qundong Liu
- Institute of Natural Medicine, University of Toyama, 2630, Sugitani, Toyama, 930-0194, Japan
| | - Shu Zhu
- Institute of Natural Medicine, University of Toyama, 2630, Sugitani, Toyama, 930-0194, Japan.
| | - Shigeki Hayashi
- Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, Kumage-Gun, 17007-2 Nakatane-cho, Kagoshima, 891-3604, Japan
| | - Osamu Iida
- Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, Kumage-Gun, 17007-2 Nakatane-cho, Kagoshima, 891-3604, Japan
| | - Akihito Takano
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machidashi, Tokyo, 194-8543, Japan
| | - Katsunori Miyake
- Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Suchada Sukrong
- Chulalongkorn University, 254 Phayathai Rd, Wang Mai, Pathum Wan District, Bangkok, 10330, Thailand
| | - Mangestuti Agil
- Airlangga University, Jl. Airlangga No.4 - 6, Airlangga, Kec. Gubeng, Kota SBY, Jawa Timur, 60115, Indonesia
| | - Indira Balachandran
- Center for Medicinal Plants Research, Arya Vaidya Sala, Kottakkal, Malappuram, Kerala, 676503, India
| | - Norio Nakamura
- Doshisha Women's College of Liberal Arts, Kodo, Kyotanabe City, Kyoto, 610-0395, Japan
| | - Nobuo Kawahara
- Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, Kumage-Gun, 17007-2 Nakatane-cho, Kagoshima, 891-3604, Japan
| | - Katsuko Komatsu
- Institute of Natural Medicine, University of Toyama, 2630, Sugitani, Toyama, 930-0194, Japan.
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Bhatt P, Thaker V. A comparative study on 193 plastomes of Poaceae for validity and implications of individual barcode genes and concatenated protein coding sequences with selected plastomes of grasses from the desert of India. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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10
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Chandrasekara CHWMRB, Naranpanawa DNU, Bandusekara BS, Pushpakumara DKNG, Wijesundera DSA, Bandaranayake PCG. Universal barcoding regions, rbcL, matK and trnH-psbA do not discriminate Cinnamomum species in Sri Lanka. PLoS One 2021; 16:e0245592. [PMID: 33566825 PMCID: PMC7875411 DOI: 10.1371/journal.pone.0245592] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
The genus Cinnamomum consists of about 250 species spread globally. Out of these, C. verum (C. zeylanicum), also known as true cinnamon or Ceylon cinnamon, has gained worldwide attention due to its culinary uses and medicinal values. Sri Lanka is the largest true cinnamon producer in the world and accounts for about 80-90% of global production. Other than the cultivated species, Sri Lankan natural vegetation is home to seven endemic wild species of the genus Cinnamomum. While these are underutilized, proper identification and characterization are essential steps in any sustainable conservation and utilization strategies. Currently, species identification is purely based on morphological traits, and intraspecific diversity has made it more challenging. In this study, all the eight Cinnamomum species found in Sri Lanka, C. capparu-coronde, C. citriodorum C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum, C. sinharajaense, and C. verum were collected in triplicates and identified using typical morphological traits. DNA extracted with the same collection was assessed with universal barcoding regions, rbcL, matK, and trnH-psbA. While no intraspecific sequence differences were observed in C. citriodorum, C. rivulorum, and C. verum, the others had polymorphic sites in one, two, or all regions assessed. Interestingly, two individuals of C. sinharajaense had identical barcodes to the cultivated species C. verum, while the other one had one variable cite in matK region and three cites in trnH-psbA reigon. Further, one C. dubium and one C. capparu-coronde accession each had identical, rbcL, and trnH-psbA sequences while those had only a single nucleotide variation observed in matK region. Overall, the phylogeny of Cinnamomum species found in Sri Lanka could not be completely resolved with DNA barcoding regions studied.
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Affiliation(s)
| | - D. Nathasha U. Naranpanawa
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - B. Supun Bandusekara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - D. K. N. G. Pushpakumara
- Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
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Li L, Jiang Y, Liu Y, Niu Z, Xue Q, Liu W, Ding X. The large single-copy (LSC) region functions as a highly effective and efficient molecular marker for accurate authentication of medicinal Dendrobium species. Acta Pharm Sin B 2020; 10:1989-2001. [PMID: 33163349 PMCID: PMC7606094 DOI: 10.1016/j.apsb.2020.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/19/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Having great medicinal values, Dendrobium species of "Fengdou" (DSFs) are a taxonomically complex group in Dendrobium genus including many closely related and recently diverged species. Traditionally used DNA markers have been proved to be insufficient in authenticating many species of this group. Here, we investigated 101 complete plastomes from 23 DSFs, comprising 72 newly sequenced and 29 documented, which all exhibited well-conserved genomic organization and gene order. Plastome-wide comparison showed the co-occurrence of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), which can be explained by both the repeat-associated and indel-associated mutation hypotheses. Moreover, guanine-cytosine (GC) content was found to be negatively correlated with the three divergence variables (SNPs, indels and repeats), indicating that GC content may reflect the level of the local sequence divergence. Our species authentication analyses revealed that the relaxed filtering strategies of sequence alignment had no negative impact on species identification. By assessing the maximum likelihood (ML) trees inferred from different datasets, we found that the complete plastome and large single-copy (LSC) datasets both successfully identified all 23 DSFs with the maximum bootstrap values. However, owing to the high efficiency of LSC in species identification, we recommend using LSC for accurate authentication of DSFs.
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Affiliation(s)
- Ludan Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yu Jiang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuanyuan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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12
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Tan WH, Chai LC, Chin CF. Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular Malaysia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1889-1896. [PMID: 32943824 PMCID: PMC7468033 DOI: 10.1007/s12298-020-00868-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 08/01/2020] [Accepted: 08/14/2020] [Indexed: 05/20/2023]
Abstract
Alpinia belongs to a large genus with many species found in Peninsular Malaysia. Several species of Alpinia exhibit important medicinal potential. However, progressive studies on the genus Alpinia were hampered by difficulties encountered in species identification. With the advancement achieved in genomic technology, more sensitive tools such as DNA barcoding were developed, which can be used for species identification. Internal Transcribe Spacer 2 (ITS2) is a DNA barcode which has proven to be a promising tool for species identification. The criterions of ITS2 efficacy namely universality and efficacy for species identification were tested on Alpinia species collected from Peninsular Malaysia. The results showed that a success rate of 96.97% was achieved using ITS2 for screening 11 species of Alpinia and an outgroup sample (Zingiber specatabile). Combined with 15 additional sequences from the Genbank for five Alpinia species, ITS2 demonstrated high species identification efficacy with 88.2% of species identified using phylogenetic and distance analysis. The analysis was further improved with the use of ITS2 secondary structure. The results of both criterions demonstrated the ability of ITS2 to successfully discriminate Alpinia species, which will help to improve species identification of Alpinia species in Peninsular Malaysia.
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Affiliation(s)
- Wei Harn Tan
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
| | - Li Chin Chai
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, Semenyih, Malaysia
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13
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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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Oyebanji OO, Chukwuma EC, Bolarinwa KA, Adejobi OI, Adeyemi SB, Ayoola AO. Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers. J Biosci 2020. [DOI: 10.1007/s12038-020-00061-2] [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]
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Song F, Li T, Burgess KS, Feng Y, Ge XJ. Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China. BMC PLANT BIOLOGY 2020; 20:261. [PMID: 32513105 PMCID: PMC7282103 DOI: 10.1186/s12870-020-02466-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/26/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group. RESULTS The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution, where ndhF and trnS-G were able to distinguish the highest proportion of Calligonum species (56%). CONCLUSIONS The entire plastid genome was the most effective barcode for the genus Calligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum.
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Affiliation(s)
- Feng Song
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 83011, China
| | - Ting Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Kevin S Burgess
- Department of Biology, Columbus State University, University System of Georgia, Columbus, GA, 31907-5645, USA
| | - Ying Feng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 83011, China.
- The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 83011, China.
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Bratzel F, Heller S, Cyrannek N, Paule J, Leme EMC, Loreth A, Nowotny A, Kiefer M, Till W, Barfuss MHJ, Lexer C, Koch MA, Zizka G. The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae. BMC PLANT BIOLOGY 2020; 20:111. [PMID: 32164546 PMCID: PMC7068990 DOI: 10.1186/s12870-020-2326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND The angiosperm family Bromeliaceae comprises over 3.500 species characterized by exceptionally high morphological and ecological diversity, but a very low genetic variation. In many genera, plants are vegetatively very similar which makes determination of non flowering bromeliads difficult. This is particularly problematic with living collections where plants are often cultivated over decades without flowering. DNA barcoding is therefore a very promising approach to provide reliable and convenient assistance in species determination. However, the observed low genetic variation of canonical barcoding markers in bromeliads causes problems. RESULT In this study the low-copy nuclear gene Agt1 is identified as a novel DNA barcoding marker suitable for molecular identification of closely related bromeliad species. Combining a comparatively slowly evolving exon sequence with an adjacent, genetically highly variable intron, correctly matching MegaBLAST based species identification rate was found to be approximately double the highest rate yet reported for bromeliads using other barcode markers. CONCLUSION In the present work, we characterize Agt1 as a novel plant DNA barcoding marker to be used for barcoding of bromeliads, a plant group with low genetic variation. Moreover, we provide a comprehensive marker sequence dataset for further use in the bromeliad research community.
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Affiliation(s)
- Fabian Bratzel
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Centre for Organismal Studies (COS) Heidelberg, Department for Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.
| | - Sascha Heller
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Nadine Cyrannek
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Elton M C Leme
- Marie Selby Botanical Gardens, 811 South Palm Avenue, Sarasota, FL, 34236, USA
| | - Anna Loreth
- Centre for Organismal Studies (COS) Heidelberg, Department for Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Annika Nowotny
- Centre for Organismal Studies (COS) Heidelberg, Department for Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Markus Kiefer
- Centre for Organismal Studies (COS) Heidelberg, Department for Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Walter Till
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Christian Lexer
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Department for Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
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Whitehurst LE, Cunard CE, Reed JN, Worthy SJ, Marsico TD, Lucardi RD, Burgess KS. Preliminary application of DNA barcoding toward the detection of viable plant propagules at an initial, international point-of-entry in Georgia, USA. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02204-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution. Gene 2020; 732:144355. [PMID: 31935501 DOI: 10.1016/j.gene.2020.144355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/13/2023]
Abstract
Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.
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Jiao L, Lu Y, He T, Li J, Yin Y. A strategy for developing high-resolution DNA barcodes for species discrimination of wood specimens using the complete chloroplast genome of three Pterocarpus species. PLANTA 2019; 250:95-104. [PMID: 30923906 DOI: 10.1007/s00425-019-03150-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/23/2019] [Indexed: 05/25/2023]
Abstract
A method for extraction of wood DNA and a strategy for designing high-resolution barcodes for wood were developed. Ycf1b was the prioritized barcode to resolve the Pterocarpus wood species studied. DNA barcoding, an effective tool for wood species identification, mainly focuses on universal barcodes and often lacks high resolution to differentiate species, especially for closely related taxa within the same genus. Therefore, more highly informative DNA barcodes need to be identified. This study is the first to report a strategy for developing specific DNA barcodes of wood tissues. The complete chloroplast genomes of leaf samples of three Pterocarpus species, i.e., P. indicus, P. santalinus, and P. tinctorius, were sequenced, and thereafter, the most variable DNA regions were identified on the scale of the complete chloroplast genomes. Finally, wood DNA was extracted from 30 wood specimens of the three Pterocarpus species, and DNA recovery rates of the selected regions were tested for applicability to verification on the wood specimens studied. The seven regions with the most variation (rpl32-ccsA, rpl20-clpP, trnC-rpoB, ycf1b, accD-ycf4, ycf1a, and psbK-accD) were identified from the chloroplast genome by quantifying nucleotide diversity (Pi > 0.02), which was remarkably higher than that of the plant universal barcodes (rbcL, matK, and trnH-psbA) and the previously reported barcodes (ndhF-rpl32 and trnL-F) used for phylogenetic analysis in Pterocarpus. After comprehensive evaluation of species discrimination ability and applicability, the ycf1b region performed well in terms of the recovery success rate (76.7%) and species identification (100%) for wood specimens of the three Pterocarpus species, and was identified as the preferred high-resolution chloroplast barcode for selected Pterocarpus species. It will offer technical support for curbing illegal timber harvesting activities and for conserving endangered and valuable wood species.
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Affiliation(s)
- 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
| | - Yang Lu
- 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
| | - 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
| | - Jianing Li
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Hainan, 571737, 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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20
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Basak S, Aadi Moolam R, Parida A, Mitra S, Rangan L. Evaluation of rapid molecular diagnostics for differentiating medicinal Kaempferia species from its adulterants. PLANT DIVERSITY 2019; 41:206-211. [PMID: 31453420 PMCID: PMC6704042 DOI: 10.1016/j.pld.2019.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 06/10/2023]
Abstract
Accurate detection of unique herbs is crucial for herbal medicine preparation. Zingiberaceae species, which are important in Ayurvedic medicine of India, are often misidentified in Northeast (NE) Indian herbal markets. Kaempferia galanga (Zingiberaceae) is one of the major components of popular Ayurvedic drugs used for rheumatic diseases (i.e., "Gandha Thailam" and "Rasnairandadi Kashayam"), contusions, fractures, and sprains. In NE India, herbal healers often misidentify plants from the Marantaceae family (e.g., Calathea bachemiana and Maranta leuconeura) as Kaempferia, which leads to adulteration of the medicinal herb. This misidentification of herbs occurs in NE India because Zingiberaceae plant barcoding information is inadequate. As a consequence, herbal medicine is not only therapeutically less effective but may also cause adverse reactions that range from mild to life-threatening. In this study, we used eight barcoding loci to develop "fingerprints" for four Kaempferia species and two species frequently mistaken for Kaempferia. The PCR and sequencing success of the loci matK, rbcL and trnH-psbA were found to be 100%; the combination of matK, rbcL, and trnH-psbA proved to be the ideal locus for discriminating the Kaempferia species from their adulterants because the combined loci showed greater variability than individual loci. This reliable tool was therefore developed in the current study for accurate identification of Kaempferia plants which can effectively resolve identification issues for herbal healers.
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Affiliation(s)
- Supriyo Basak
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781 039, India
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ramesh Aadi Moolam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781 039, India
| | - Ajay Parida
- Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India
| | - Sudip Mitra
- Centre for Rural Technology, Indian Institute of Technology Guwahati, Assam, 781 039, India
| | - Latha Rangan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781 039, India
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Li QJ, Wang X, Wang JR, Su N, Zhang L, Ma YP, Chang ZY, Zhao L, Potter D. Efficient Identification of Pulsatilla (Ranunculaceae) Using DNA Barcodes and Micro-Morphological Characters. FRONTIERS IN PLANT SCIENCE 2019; 10:1196. [PMID: 31649688 PMCID: PMC6794950 DOI: 10.3389/fpls.2019.01196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/30/2019] [Indexed: 05/04/2023]
Abstract
Pulsatilla (Ranunculaceae) comprises about 40 species, many of which have horticultural and/or medicinal importance. However, the recognition and identification of wild Pulsatilla species is difficult due to the presence of complex morphological characters. DNA barcoding is a powerful molecular tool capable of rapidly and accurately distinguishing between species. Here, we assessed the effectiveness of four commonly used DNA barcoding loci-rbcL (R), trnH-psbA ( T ), matK (M), and ITS (I)-to identify species of Pulsatilla from a comprehensive sampling group. Among the four barcoding single loci, the nuclear ITS marker showed the highest interspecific distances and the highest rate of correct identification. Among the eleven combinations, the chloroplast multi-locus R+T and R+M+T combinations were found to have the best species discrimination rate, followed by R+M. Overall, we propose that the R+M+T combination and the ITS marker on its own are, respectively, the best multi- and single-locus barcodes for discriminating among species of Pulsatilla. The phylogenetic analysis was able to distinguish species of Pulsatilla to the subgenus level, but the analysis also showed relatively low species resolution. This may be caused by incomplete lineage sorting and/or hybridization events in the evolutionary history of the genus, or by the resolution limit of the candidate barcodes. We also investigated the leaf epidermis of eight representative species using scanning electronic microscopy. The resulting micro-morphological characters were valuable for identification of related species. Using additional genome fragments, or even whole chloroplast genomes combined with micro-morphological data may permit even higher resolution of species in Pulsatilla.
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Affiliation(s)
- Qiu-jie Li
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Xi Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Jun-ru Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Na Su
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Ling Zhang
- College of Life Sciences, Tarim University, Alaer, China
| | - Yue-ping Ma
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Zhao-yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
- *Correspondence: Liang Zhao,
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, Davis, CA, United States
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Jiao J, Huang W, Bai Z, Liu F, Ma C, Liang Z. DNA barcoding for the efficient and accurate identification of medicinal polygonati rhizoma in China. PLoS One 2018; 13:e0201015. [PMID: 30021015 PMCID: PMC6051646 DOI: 10.1371/journal.pone.0201015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/06/2018] [Indexed: 12/23/2022] Open
Abstract
Polygonati rhizoma (PR), a traditional medicinal and edible product with various bioactive components (Polygonatum polysaccharides, saponins, phenols, and flavonoids), is widely consumed in China. However, other species with morphological characteristics similar to those of the actual components are being used to replace or adulterate PR, causing issues with quality control and product safety. The morphological similarity of PR and its substitutes makes classic morphological identification challenging. To address this issue, DNA barcoding-based identification using ITS2 and psbA-trnH sequences was applied in this study to evaluate the efficiency and accuracy of this approach in identifying PR samples collected from 39 different regions in China. The identification of PR by this method was confirmed by other methods (phylogeny-based and character-based methods), and all the samples were clearly and accurately distinguished. This study highlights the efficient and accurate nature of DNA barcoding in PR identification. Applying this technique will provide a means to differentiate PR from other altered formulations, thus improving product quality and safety for consumers of PR and its products.
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Affiliation(s)
- Jie Jiao
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenli Huang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Zhenqing Bai
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Feng Liu
- Research Department, Buchang Pharma, Xi’an, Shaanxi, China
| | - Cunde Ma
- Research Department, Buchang Pharma, Xi’an, Shaanxi, China
| | - Zongsuo Liang
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Science, Zhejiang SCI-TECH University, Hangzhou, Zhejiang, China
- * E-mail:
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23
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Yan M, Xiong Y, Liu R, Deng M, Song J. The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks. FRONTIERS IN PLANT SCIENCE 2018; 9:569. [PMID: 29868047 PMCID: PMC5952231 DOI: 10.3389/fpls.2018.00569] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 05/10/2023]
Abstract
The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia - Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiaojiao Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shangrao Normal University, Shangrao, China
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Xu SZ, Li ZY, Jin XH. DNA barcoding of invasive plants in China: A resource for identifying invasive plants. Mol Ecol Resour 2017; 18:128-136. [PMID: 28865184 DOI: 10.1111/1755-0998.12715] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 01/05/2023]
Abstract
Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China. In this study, five common single markers (ITS, ITS2, matK, rbcL and trnH-psbA) were evaluated using 634 species (including 469 invasive plant species in China, 10 new records to China, 16 potentially invasive plant species around the world but not introduced into China yet and 139 plant species native to China) based on three different methods. Our results indicated that ITS2 displayed largest intra- and interspecific divergence (1.72% and 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH-psbA provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates, respectively. The combination of ITS + matK performed best and provided 91.03% discriminatory power, followed by ITS2 + matK (85.78%). For identifying unknown individuals, ITS + matK had 100% correct identification rate based on our database, followed by ITS/ITS2 (both 93.33%) and ITS2 + matK (91.67%). Thus, we propose ITS/ITS2 + matK as the most suitable barcode for invasive plants in China. This study also demonstrated that DNA barcoding is an efficient tool for identifying invasive species.
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Affiliation(s)
- Song-Zhi Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhen-Yu Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Mishra P, Kumar A, Nagireddy A, Shukla AK, Sundaresan V. Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia. PLoS One 2017; 12:e0182836. [PMID: 28829803 PMCID: PMC5567895 DOI: 10.1371/journal.pone.0182836] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is used as a universal tool for delimiting species boundaries in taxonomically challenging groups, with different plastid and nuclear regions (rbcL, matK, ITS and psbA-trnH) being recommended as primary DNA barcodes for plants. We evaluated the feasibility of using these regions in the species-rich genus Terminalia, which exhibits various overlapping morphotypes with pantropical distribution, owing to its complex taxonomy. Terminalia bellerica and T. chebula are ingredients of the famous Ayurvedic Rasayana formulation Triphala, used for detoxification and rejuvenation. High demand for extracted phytochemicals as well as the high trade value of several species renders mandatory the need for the correct identification of traded plant material. Three different analytical methods with single and multilocus barcoding regions were tested to develop a DNA barcode reference library from 222 individuals representing 41 Terminalia species. All the single barcodes tested had a lower discriminatory power than the multilocus regions, and the combination of matK+ITS had the highest resolution rate (94.44%). The average intra-specific variations (0.0188±0.0019) were less than the distance to the nearest neighbour (0.106±0.009) with matK and ITS. Distance-based Neighbour Joining analysis outperformed the character-based Maximum Parsimony method in the identification of traded species such as T. arjuna, T. chebula and T. tomentosa, which are prone to adulteration. rbcL was shown to be a highly conservative region with only 3.45% variability between all of the sequences. The recommended barcode combination, rbcL+matK, failed to perform in the genus Terminalia. Considering the complexity of resolution observed with single regions, the present study proposes the combination of matK+ITS as the most successful barcode in Terminalia.
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Affiliation(s)
- Priyanka Mishra
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Amit Kumar
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Akshitha Nagireddy
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Ashutosh K. Shukla
- Biotechnology Division, CSIR—Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Velusamy Sundaresan
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
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Saddhe AA, Jamdade RA, Kumar K. Evaluation of multilocus marker efficacy for delineating mangrove species of West Coast India. PLoS One 2017; 12:e0183245. [PMID: 28817640 PMCID: PMC5560660 DOI: 10.1371/journal.pone.0183245] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 08/01/2017] [Indexed: 01/31/2023] Open
Abstract
The plant DNA barcoding is a complex and requires more than one marker(s) as compared to animal barcoding. Mangroves are diverse estuarine ecosystem prevalent in the tropical and subtropical zone, but anthropogenic activity turned them into the vulnerable ecosystem. There is a need to build a molecular reference library of mangrove plant species based on molecular barcode marker along with morphological characteristics. In this study, we tested the core plant barcode (rbcL and matK) and four promising complementary barcodes (ITS2, psbK-psbI, rpoC1 and atpF-atpH) in 14 mangroves species belonging to 5 families from West Coast India. Data analysis was performed based on barcode gap analysis, intra- and inter-specific genetic distance, Automated Barcode Gap Discovery (ABGD), TaxonDNA (BM, BCM), Poisson Tree Processes (PTP) and General Mixed Yule-coalescent (GMYC). matK+ITS2 marker based on GMYC method resolved 57.14% of mangroves species and TaxonDNA, ABGD, and PTP discriminated 42.85% of mangrove species. With a single locus analysis, ITS2 exhibited the higher discriminatory power (87.82%) and combinations of matK + ITS2 provided the highest discrimination success (89.74%) rate except for Avicennia genus. Further, we explored 3 additional markers (psbK-psbI, rpoC1, and atpF-atpH) for Avicennia genera (A. alba, A. officinalis and A. marina) and atpF-atpH locus was able to discriminate three species of Avicennia genera. Our analysis underscored the efficacy of matK + ITS2 markers along with atpF-atpH as the best combination for mangrove identification in West Coast India regions.
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Affiliation(s)
- Ankush Ashok Saddhe
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, India
| | | | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, India
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Duan Z, Song W, Chen K, Qiao X, Ye M. Assessment of Genetic and Chemical Variability in Curcumae Longae Rhizoma (Curcuma longa) Based on DNA Barcoding Markers and HPLC Fingerprints. Biol Pharm Bull 2017; 40:1638-1645. [PMID: 28747591 DOI: 10.1248/bpb.b17-00020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Curcumae Longae Rhizoma (Curcuma longa L.) is an important traditional Chinese medicine with multiple beneficial effects. To elucidate the genetic and chemical differences among Curcumae Longae Rhizoma samples, three DNA barcoding markers (rbcL, matK, and ITS-LSU D1/D3) and HPLC fingerprinting were employed in this study. The discriminatory power of rbcL and matK was low, as they only detected one sequence type that showed 100% similarity with more than 20 congeneric species in the Barcode of Life Data Systems (BOLD) database. In contrast, ITS-LSU D1/D3 showed sufficient discriminatory power to precisely identify all of the market samples as C. longa L. in a BLAST search as well as differentiate each sample based on 2-10 ITS-LSU D1/D3 haplotypes with intragenomic variability (mean p-distance: 0.7%, range: 0-2.6%; mean number of differences: 9.6 sites, range: 0-38 sites). HPLC fingerprinting of 13 commercial samples showed a similarity that ranged from 0.769 to 0.996, indicating that the sample quality varied. A cluster analysis based on 5 common peak areas from the HPLC chromatogram resulted in two groups. Group I included 9 samples with a relatively high chemical content, and group II contained 4 samples with a low chemical content. A Mantel test revealed a low correlation (r=0.1721, p=0.047) between genetic and chemical differences. Our findings suggest that the integrated approach of ITS-LSU D1/D3 DNA barcoding and HPLC fingerprinting provides a comprehensive, precise, and convenient method to clarify the genetic and chemical differences in Curcumae Longae Rhizoma.
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Affiliation(s)
- Zhonggang Duan
- School of Life Science, Huizhou University.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University
| | - Wei Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University
| | - Kuan Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University
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28
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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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29
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Yang J, Vázquez L, Chen X, Li H, Zhang H, Liu Z, Zhao G. Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks ( Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes. FRONTIERS IN PLANT SCIENCE 2017; 8:816. [PMID: 28579999 PMCID: PMC5437370 DOI: 10.3389/fpls.2017.00816] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/01/2017] [Indexed: 05/04/2023]
Abstract
Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species (Quercus rubra and Castanea mollissima) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in Quercus subgenus Quercus, a diverse species group without sufficient molecular differentiation. With the comparison, nine and 14 plastid markers were selected as barcoding and phylogeographic candidates for the Chinese oaks. Five (psbA-trnH, matK-trnK, ycf3-trnS, matK, and ycf1) of the nine plastid candidate barcodes, with the addition of newly designed ITS and a single-copy nuclear gene (SAP), were then tested on 35 Chinese oak species employing four different barcoding approaches (genetic distance-, BLAST-, character-, and tree-based methods). The four methods showed different species identification powers with character-based method performing the best. Of the seven barcodes tested, a barcoding gap was absent in all of them across the Chinese oaks, while ITS and psbA-trnH provided the highest species resolution (30.30%) with the character- and BLAST-based methods, respectively. The six-marker combination (psbA-trnH + matK-trnK + matK + ycf1 + ITS + SAP) showed the best species resolution (84.85%) using the character-based method for barcoding the Chinese oaks. The barcoding results provided additional implications for taxonomy of the Chinese oaks in subg. Quercus, basically identifying three major infrageneric clades of the Chinese oaks (corresponding to Groups Quercus, Cerris, and Ilex) referenced to previous phylogenetic classification of Quercus. While the morphology-based allocations proposed for the Chinese oaks in subg. Quercus were challenged. A low variation rate of the chloroplast genome, and complex speciation patterns involving incomplete lineage sorting, interspecific hybridization and introgression, possibly have negative impacts on the species assignment and phylogeny of oak species.
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Affiliation(s)
- Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Lucía Vázquez
- Biology Department, University of Illinois at SpringfieldSpringfield, IL, United States
| | - Xiaodan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Huimin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Hao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Zhanlin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
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30
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Liu ZF, Ci XQ, Li L, Li HW, Conran JG, Li J. DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China. PLoS One 2017; 12:e0175788. [PMID: 28414813 PMCID: PMC5393608 DOI: 10.1371/journal.pone.0175788] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/01/2017] [Indexed: 11/18/2022] Open
Abstract
Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH–psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China. We tested the ability of DNA barcoding to distinguish species and as an alternative tool for correcting species misidentification. We also used the rbcL+matK+trnH–psbA+ITS loci to investigate the phylogenetic relationships of the species examined. Among the gene regions and their combinations, ITS was the most efficient for identifying species (57.5%) and genera (70%). DNA barcoding also had a positive role for correcting species misidentification (10.8%). Furthermore, based on the results of the phylogenetic analyses, Chinese Lauraceae species formed three supported monophyletic clades, with the Cryptocarya group strongly supported (PP = 1.00, BS = 100%) and the clade including the Persea group, Laureae and Cinnamomum also receiving strong support (PP = 1.00, BS = 98%), whereas the Caryodaphnopsis–Neocinnamomum received only moderate support (PP = 1.00 and BS = 85%). This study indicates that molecular barcoding can assist in screening difficult to identify families like Lauraceae, detecting errors of species identification, as well as helping to reconstruct phylogenetic relationships. DNA barcoding can thus help with large-scale biodiversity inventories and rare species conservation by improving accuracy, as well as reducing time and costs associated with species identification.
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Affiliation(s)
- Zhi-Fang Liu
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Lang Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
| | - Hsi-Wen Li
- Herbarium (KUN), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
- * E-mail:
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31
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Zhang N, Erickson DL, Ramachandran P, Ottesen AR, Timme RE, Funk VA, Luo Y, Handy SM. An analysis of Echinacea chloroplast genomes: Implications for future botanical identification. Sci Rep 2017; 7:216. [PMID: 28303008 PMCID: PMC5428300 DOI: 10.1038/s41598-017-00321-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/21/2017] [Indexed: 12/14/2022] Open
Abstract
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field. We used Next Generation Sequencing (NGS) and CLC Genomics Workbench to assemble complete chloroplast genomes for all nine species. Full chloroplasts unambiguously differentiated all nine species, compared with the very few single nucleotide polymorphisms (SNPs) available with core DNA barcoding markers. SNPs for any two Echinacea chloroplast genomes ranged from 181 to 910, and provided robust data for unambiguous species delimitation. Implications for DNA-based species identification assays derived from chloroplast genome sequences are discussed in light of product safety, adulteration and quality issues.
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Affiliation(s)
- Ning Zhang
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
| | - David L Erickson
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Andrea R Ottesen
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Ruth E Timme
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-0166, USA
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
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32
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Baker TR, Pennington RT, Dexter KG, Fine PVA, Fortune-Hopkins H, Honorio EN, Huamantupa-Chuquimaco I, Klitgård BB, Lewis GP, de Lima HC, Ashton P, Baraloto C, Davies S, Donoghue MJ, Kaye M, Kress WJ, Lehmann CER, Monteagudo A, Phillips OL, Vasquez R. Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists. Trends Ecol Evol 2017; 32:258-267. [PMID: 28214038 DOI: 10.1016/j.tree.2017.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 11/26/2022]
Abstract
Closer collaboration among ecologists, systematists, and evolutionary biologists working in tropical forests, centred on studies within long-term permanent plots, would be highly beneficial for their respective fields. With a key unifying theme of the importance of vouchered collection and precise identification of species, especially rare ones, we identify four priority areas where improving links between these communities could achieve significant progress in biodiversity and conservation science: (i) increasing the pace of species discovery; (ii) documenting species turnover across space and time; (iii) improving models of ecosystem change; and (iv) understanding the evolutionary assembly of communities and biomes.
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Affiliation(s)
| | | | - Kyle G Dexter
- Royal Botanic Garden Edinburgh, Edinburgh, UK; School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Paul V A Fine
- Department of Integrative Biology and University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | | | | | - Isau Huamantupa-Chuquimaco
- Programa de Pós-Graduação em Botânica, Escola Nacional de Botânica Tropical, Instituto de Pesquisas Jardim Botânico de Rio de Janeiro (ENBT/JBRJ). Rua Pacheco Leão, 2040. RJ, Brazil
| | - Bente B Klitgård
- Department for Identification and Naming, Royal Botanic Gardens, Kew, UK
| | - Gwilym P Lewis
- Department for Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, UK
| | - Haroldo C de Lima
- Programa de Pós-Graduação em Botânica, Escola Nacional de Botânica Tropical, Instituto de Pesquisas Jardim Botânico de Rio de Janeiro (ENBT/JBRJ). Rua Pacheco Leão, 2040. RJ, Brazil
| | | | - Christopher Baraloto
- International Center for Tropical Botany, Florida International University, Miami, USA
| | - Stuart Davies
- Center for Tropical Forest Science - Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Washington, DC, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Maria Kaye
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - W John Kress
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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33
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Poovitha S, Stalin N, Balaji R, Parani M. Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L. Genome 2016; 59:1150-1156. [DOI: 10.1139/gen-2015-0205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%–9.6% with individual markers, which increased to 0%–12.5% and 0.8%–20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.
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Affiliation(s)
- Sundar Poovitha
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Nithaniyal Stalin
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Raju Balaji
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Madasamy Parani
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
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Nithaniyal S, Vassou SL, Poovitha S, Raju B, Parani M. Identification of species adulteration in traded medicinal plant raw drugs using DNA barcoding. Genome 2016; 60:139-146. [PMID: 28067539 DOI: 10.1139/gen-2015-0225] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Plants are the major source of therapeutic ingredients in complementary and alternative medicine (CAM). However, species adulteration in traded medicinal plant raw drugs threatens the reliability and safety of CAM. Since morphological features of medicinal plants are often not intact in the raw drugs, DNA barcoding was employed for species identification. Adulteration in 112 traded raw drugs was tested after creating a reference DNA barcode library consisting of 1452 rbcL and matK barcodes from 521 medicinal plant species. Species resolution of this library was 74.4%, 90.2%, and 93.0% for rbcL, matK, and rbcL + matK, respectively. DNA barcoding revealed adulteration in about 20% of the raw drugs, and at least 6% of them were derived from plants with completely different medicinal or toxic properties. Raw drugs in the form of dried roots, powders, and whole plants were found to be more prone to adulteration than rhizomes, fruits, and seeds. Morphological resemblance, co-occurrence, mislabeling, confusing vernacular names, and unauthorized or fraudulent substitutions might have contributed to species adulteration in the raw drugs. Therefore, this library can be routinely used to authenticate traded raw drugs for the benefit of all stakeholders: traders, consumers, and regulatory agencies.
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Affiliation(s)
- Stalin Nithaniyal
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
| | - Sophie Lorraine Vassou
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
| | - Sundar Poovitha
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
| | - Balaji Raju
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
| | - Madasamy Parani
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India.,Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Kattankulathur 603203, India
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Saddhe AA, Jamdade RA, Kumar K. Assessment of mangroves from Goa, west coast India using DNA barcode. SPRINGERPLUS 2016; 5:1554. [PMID: 27652127 PMCID: PMC5021661 DOI: 10.1186/s40064-016-3191-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 09/01/2016] [Indexed: 11/16/2022]
Abstract
Mangroves are salt-tolerant forest ecosystems of tropical and subtropical intertidal regions. They are among most productive, diverse, biologically important ecosystem and inclined toward threatened system. Identification of mangrove species is of critical importance in conserving and utilizing biodiversity, which apparently hindered by a lack of taxonomic expertise. In recent years, DNA barcoding using plastid markers rbcL and matK has been suggested as an effective method to enrich traditional taxonomic expertise for rapid species identification and biodiversity inventories. In the present study, we performed assessment of available 14 mangrove species of Goa, west coast India based on core DNA barcode markers, rbcL and matK. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in rbcL (97.7 %) and matK (95.5 %) region. The two candidate chloroplast barcoding regions (rbcL, matK) yielded barcode gaps. Our results clearly demonstrated that matK locus assigned highest correct identification rates (72.09 %) based on TaxonDNA Best Match criteria. The concatenated rbcL + matK loci were able to adequately discriminate all mangrove genera and species to some extent except those in Rhizophora, Sonneratia and Avicennia. Our study provides the first endorsement of the species resolution among mangroves using plastid genes with few exceptions. Our future work will be focused on evaluation of other barcode markers to delineate complete resolution of mangrove species and identification of putative hybrids.
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Affiliation(s)
- Ankush Ashok Saddhe
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa Campus, Sancoale, Goa 403726 India
| | - Rahul Arvind Jamdade
- Department of Zoology, Yashwantrao Chavan Institute of Science, Satara, Maharashtra 415001 India
| | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa Campus, Sancoale, Goa 403726 India
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Yao X, Tan YH, Liu YY, Song Y, Yang JB, Corlett RT. Chloroplast genome structure in Ilex (Aquifoliaceae). Sci Rep 2016; 6:28559. [PMID: 27378489 PMCID: PMC4932625 DOI: 10.1038/srep28559] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/06/2016] [Indexed: 01/25/2023] Open
Abstract
Aquifoliaceae is the largest family in the campanulid order Aquifoliales. It consists of a single genus, Ilex, the hollies, which is the largest woody dioecious genus in the angiosperms. Most species are in East Asia or South America. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. We produced the first complete chloroplast genomes in this family, including seven Ilex species, by Illumina sequencing of long-range PCR products and subsequent reference-guided de novo assembly. These genomes have a typical bicyclic structure with a conserved genome arrangement and moderate divergence. The total length is 157,741 bp and there is one large single-copy region (LSC) with 87,109 bp, one small single-copy with 18,436 bp, and a pair of inverted repeat regions (IR) with 52,196 bp. A total of 144 genes were identified, including 96 protein-coding genes, 40 tRNA and 8 rRNA. Thirty-four repetitive sequences were identified in Ilex pubescens, with lengths >14 bp and identity >90%, and 11 divergence hotspot regions that could be targeted for phylogenetic markers. This study will contribute to improved resolution of deep branches of the Ilex phylogeny and facilitate identification of Ilex species.
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Affiliation(s)
- Xin Yao
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun-Hong Tan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Ying-Ying Liu
- Key Laboratory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, Yunnan, 666100, China
| | - Yu Song
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Richard T Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
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Osathanunkul M, Suwannapoom C, Osathanunkul K, Madesis P, de Boer H. Evaluation of DNA barcoding coupled high resolution melting for discrimination of closely related species in phytopharmaceuticals. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2016; 23:156-65. [PMID: 26926177 DOI: 10.1016/j.phymed.2015.11.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/11/2015] [Accepted: 11/12/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Phytopharmaceuticals are increasingly popular as alternative medicines, but poorly regulated in many countries. The manufacturers of these products should be subject to strict controls regarding each product's quality and constituents. Routine testing and identification of raw materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. HYPOTHESIS/PURPOSE We have applied DNA Barcoding - High Resolution Melting (Bar-HRM), an emerging method for identifying of medicinal plant species based on DNA dissociation kinetics and DNA barcoding, for the authentication of medicinal plant species. STUDY DESIGN Commonly commercialized Thai medicinal plants that are widely used for medicinal purposes were used in this study. Publicly available sequences of four plastid markers were used for universal primer design. Species discrimination efficiency of the designed primers was evaluated as single and multi-locus analyses by using the primers sets. METHODS HRM analysis was performed in triplicate on each of the 26 taxa to establish the Tm for each primer set (matK, rbcLA, rbcLB, rbcLC, rpoC1, and trnL). The shapes of the melting curves were analyzed to distinguish the different plant species. Bar-HRM species identification success rates were assessed for each single-locus as well as for multi-locus combinations to establish the optimal combination of primer sets. RESULTS In single locus analysis the rpoC1 primer set gave the highest discrimination (58%), and in multi locus analysis this could be increased from 87% to 99% depending on the total number of regions included. Different combinations proved to be more or less effective at discrimination, depending on the genus or family examined. CONCLUSIONS Bar-HRM has proven to be a cost-effective and reliable method for the identification of species in this study of Thai medicinal plants, and results show an identification success rate of 99% among species in the test set.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, 239 Huay Kaew Rd., Suthep, Muang, Chiang Mai 50200, Thailand.
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution State, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Kitisak Osathanunkul
- Department of Computer Science, Faculty of Science, Maejo University, Chiang Mai 50290, Thailand
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Hugo de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden; The Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
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Li Y, Tong Y, Xing F. DNA Barcoding Evaluation and Its Taxonomic Implications in the Recently Evolved Genus Oberonia Lindl. (Orchidaceae) in China. FRONTIERS IN PLANT SCIENCE 2016; 7:1791. [PMID: 27994608 PMCID: PMC5136562 DOI: 10.3389/fpls.2016.01791] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/14/2016] [Indexed: 05/20/2023]
Abstract
The orchid genus Oberonia Lindl., is a taxonomically complex genus characterized by recent species radiations and many closely related species. All Oberonia species are under conservation as listed in the CITES and the IUCN Red List Categories and Criteria. Given its difficulties in taxonomy and conservation status, Oberonia is an excellent model for developing DNA barcodes. Three analytical methods and five DNA barcoding regions (rbcL, matK, trnH-psbA, ITS, and ITS2) were evaluated on 127 individuals representing 40 species and 1 variety of Oberonia from China. All the three plastid candidates tested (rbcL, matK, and trnH-psbA) have a lower discriminatory power than the nuclear regions (ITS and ITS2), and ITS had the highest resolution rate (82.14%). Two to four combinations of these gene sets were not better than the ITS alone, but when considering modes of inheritance, rbcL+ITS and matK+ITS were the best barcodes for identifying Oberonia species. Furthermore, the present barcoding system has many new insights in the current Oberonia taxonomy, such as correcting species identification, resolving taxonomic uncertainties, and the underlying presence of new or cryptic species in a genus with a complex speciation history.
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Affiliation(s)
- Yuling Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Yi Tong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
| | - Fuwu Xing
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Fuwu Xing
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Curci PL, De Paola D, Sonnante G. Development of chloroplast genomic resources for Cynara. Mol Ecol Resour 2015; 16:562-73. [PMID: 26354522 DOI: 10.1111/1755-0998.12457] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/31/2015] [Accepted: 08/14/2015] [Indexed: 12/17/2022]
Abstract
In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole-genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference-based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes ('Brindisino' artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short 'variable' cp regions. The evaluation of the molecular resources obtained from this study led us to support the 'super-barcode' theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level.
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Affiliation(s)
- Pasquale L Curci
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
| | - Domenico De Paola
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
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40
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Cheng T, Xu C, Lei L, Li C, Zhang Y, Zhou S. Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Mol Ecol Resour 2015; 16:138-49. [PMID: 26084789 DOI: 10.1111/1755-0998.12438] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 04/20/2015] [Accepted: 06/09/2015] [Indexed: 01/22/2023]
Abstract
The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.
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Affiliation(s)
- Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Lei
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Changhao Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yu Zhang
- Beijing Botanic Gardens, Beijing, 100093, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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