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Chen W, Chen X, Xu J, Cai J, Wang X. Identification of Dendrobium officinale Using DNA Barcoding Method Combined with HRM and qPCR Technology. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-021-02194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants. Sci Rep 2021; 11:1424. [PMID: 33446865 PMCID: PMC7809279 DOI: 10.1038/s41598-021-81087-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/04/2021] [Indexed: 11/08/2022] Open
Abstract
DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.
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Tang X, Yuan Y, Zhang J. How Climate Change Will Alter the Distribution of Suitable Dendrobium Habitats. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.536339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wang Y, Huang HY, Wang YZ. Authentication of Dendrobium Officinale from Similar Species with Infrared and Ultraviolet-Visible Spectroscopies with Data Visualization and Mining. ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1719126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ye Wang
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, PR China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, PR China
| | - Heng-Yu Huang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, PR China
| | - Yuan-Zhong Wang
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, PR China
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Abstract
INTRODUCTION In Saudi Arabia, Rhazya stricta is a widely used folkloric plant because of its various therapeutic properties. It is sold in herbal markets as a dried powder; however, the absence of visible phenotypic traits in the powder can mask its authenticity. Potential misidentification of this substance threatens consumer health. DNA barcoding could accurately identify this plant regardless of its physical state, however barcoding presents the challenge of variations in marker loci. OBJECTIVES The objective of this work was to assess barcode markers from the chloroplast and nuclear regions to determine their taxonomic accuracy in R. stricta barcoding, and select the best marker for this species that could fulfill the authentication test for its fresh and dried samples. METHOD In this study, we assessed seven barcode markers from the chloroplast (psbA-trnH, matK, rbcL, rpoB, and rpoC1) and nuclear regions (ITS1and ITS2). We compared DNA sequences of R. stricta from 50 fresh locally collected samples and 10 dried ground samples from the herbal market with the database sequences of R. stricta, R. orientalis, and eight other related species as controls. We utilized three methods (BLAST, nearest distance, and neighbor-joining tree) in this analysis. RESULT With the exception of psbA-trnH, all the chloroplast markers determined high similarity with other taxa. However, nuclear ITS2 best distinguished between R. stricta, R. orientalis, and other related species because of its secondary structures, which allowed for more accurate distinctions. A two-locus marker of ITS1 + ITS2 sequences also showed promising results. A two-dimensional image of our proposed marker was generated to more easily handle DNA barcoding applications. CONCLUSION Our study indicates that ITS2 is a cost-effective barcoding marker capable of verifying the authenticity of R. stricta and other medicinal plants in order to protect consumer health.
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Nguyen NH, Vu HT, Le ND, Nguyen TD, Duong HX, Tran HD. Molecular Identification and Evaluation of the Genetic Diversity of Dendrobium Species Collected in Southern Vietnam. BIOLOGY 2020; 9:E76. [PMID: 32290139 PMCID: PMC7236015 DOI: 10.3390/biology9040076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 01/12/2023]
Abstract
Dendrobium has been widely used not only as ornamental plants but also as food and medicines. The identification and evaluation of the genetic diversity of Dendrobium species support the conservation of genetic resources of endemic Dendrobium species. Uniquely identifying Dendrobium species used as medicines helps avoid misuse of medicinal herbs. However, it is challenging to identify Dendrobium species morphologically during their immature stage. Based on the DNA barcoding method, it is now possible to efficiently identify species in a shorter time. In this study, the genetic diversity of 76 Dendrobium samples from Southern Vietnam was investigated based on the ITS (Internal transcribed spacer), ITS2, matK (Maturase_K), rbcL (ribulose-bisphosphate carboxylase large subunit) and trnH-psbA (the internal space of the gene coding histidine transfer RNA (trnH) and gene coding protein D1, a polypeptide of the photosystem I reaction center (psaB)) regions. The ITS region was found to have the best identification potential. Nineteen out of 24 Dendrobium species were identified based on phylogenetic tree and Indel information of this region. Among these, seven identified species were used as medicinal herbs. The results of this research contributed to the conservation, propagation, and hybridization of indigenous Dendrobium species in Southern Vietnam.
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Affiliation(s)
- Nhu-Hoa Nguyen
- Faculty of Biology, Ho Chi Minh City University of Education, 280 An Duong Vuong Street, Ward 4, District 5, Ho Chi Minh 72711, Vietnam
| | - Huyen-Trang Vu
- Faculty of Biotechnology, Nguyen Tat Thanh University, 298A-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh 72820, Vietnam; (H.-T.V.); (N.-D.L.); (T.-D.N.)
| | - Ngoc-Diep Le
- Faculty of Biotechnology, Nguyen Tat Thanh University, 298A-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh 72820, Vietnam; (H.-T.V.); (N.-D.L.); (T.-D.N.)
| | - Thanh-Diem Nguyen
- Faculty of Biotechnology, Nguyen Tat Thanh University, 298A-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh 72820, Vietnam; (H.-T.V.); (N.-D.L.); (T.-D.N.)
| | - Hoa-Xo Duong
- Biotechnology Center of Ho Chi Minh City, 2374 Highway 1, Quarter 2, Ward Trung My Tay, District 12, Ho Chi Minh 71507, Vietnam;
| | - Hoang-Dung Tran
- Faculty of Biotechnology, Nguyen Tat Thanh University, 298A-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh 72820, Vietnam; (H.-T.V.); (N.-D.L.); (T.-D.N.)
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Barcaccia G, Palumbo F, Scariolo F, Vannozzi A, Borin M, Bona S. Potentials and Challenges of Genomics for Breeding Cannabis Cultivars. FRONTIERS IN PLANT SCIENCE 2020; 11:573299. [PMID: 33101342 PMCID: PMC7546024 DOI: 10.3389/fpls.2020.573299] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/07/2020] [Indexed: 05/12/2023]
Abstract
Cannabis (Cannabis sativa L.) is an influential yet controversial agricultural plant with a very long and prominent history of recreational, medicinal, and industrial usages. Given the importance of this species, we deepened some of the main challenges-along with potential solutions-behind the breeding of new cannabis cultivars. One of the main issues that should be fixed before starting new breeding programs is the uncertain taxonomic classification of the two main taxa (e.g., indica and sativa) of the Cannabis genus. We tried therefore to examine this topic from a molecular perspective through the use of DNA barcoding. Our findings seem to support a unique species system (C. sativa) based on two subspecies: C. sativa subsp. sativa and C. sativa subsp. indica. The second key issue in a breeding program is related to the dioecy behavior of this species and to the comprehension of those molecular mechanisms underlying flower development, the main cannabis product. Given the role of MADS box genes in flower identity, we analyzed and reorganized all the genomic and transcriptomic data available for homeotic genes, trying to decipher the applicability of the ABCDE model in Cannabis. Finally, reviewing the limits of the conventional breeding methods traditionally applied for developing new varieties, we proposed a new breeding scheme for the constitution of F1 hybrids, without ignoring the indisputable contribution offered by genomics. In this sense, in parallel, we resumed the main advances in the genomic field of this species and, ascertained the lack of a robust set of SNP markers, provided a discriminant and polymorphic panel of SSR markers as a valuable tool for future marker assisted breeding programs.
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Vu HT, Vu QL, Nguyen TD, Tran N, Nguyen TC, Luu PN, Tran DD, Nguyen TK, Le L. Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences. BIOLOGY 2019; 9:E9. [PMID: 31906128 PMCID: PMC7168009 DOI: 10.3390/biology9010009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022]
Abstract
Paphiopedilum is among the most popular ornamental orchid genera due to its unique slipper flowers and attractive leaf coloration. Most of the Paphiopedilum species are in critical danger due to over-exploitation. They were listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents their being traded across borders. While most Paphiopedilum species are distinctive, owing to their respective flowers, their vegetative features are more similar and undistinguished. Hence, the conservation of these species is challenging, as most traded specimins are immature and non-flowered. An urgent need exists for effective identification methods to prevent further illegal trading of Paphiopedilum species. DNA barcoding is a rapid and sensitive method for species identification, at any developmental stage, using short DNA sequences. In this study, eight loci, i.e., ITS, LEAFY, ACO, matK, trnL, rpoB, rpoC1, and trnH-psbA, were screened for potential barcode sequences on the Vietnamese Paphiopedilum species. In total, 17 out of 22 Paphiopedilum species were well identified. The studied DNA sequences were deposited to GenBank, in which Paphiopedilum dalatense accessions were introduced for the first time. ACO, LEAFY, and trnH-psbA were limited in amplification rate for Paphiopedilum. ITS was the best single barcode. Single ITS could be used along with nucleotide polymorphism characteristics for species discrimination. The combination of ITS + matK was the most efficient identification barcode for Vietnamese Paphiopedilum species. This barcode also succeeded in recognizing misidentified or wrongly-named traded samples. Different bioinformatics programs and algorithms for establishing phylogenetic trees were also compared in the study to propose quick, simple, and effective tools for practical use. It was proved that both the Bayesian Inference method in the MRBAYES program and the neighbor-joining method in the MEGA software met the criteria. Our study provides a barcoding database of Vietnamese Paphiopedilum which may significantly contribute to the control and conservation of these valuable species.
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Affiliation(s)
- Huyen-Trang Vu
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Hochiminh City 700000, Vietnam; (H.-T.V.); (T.-D.N.); (T.-C.N.)
- Faculty of Biotechnology, International University—Vietnam National University, Linh Trung Ward, Thu Duc District, Hochiminh City 700000, Vietnam;
| | - Quoc-Luan Vu
- Tay Nguyen Institute for Scientific Research, Vietnam Academy of Science and Technology, 116 Xo Viet Nghe Tinh, Ward 7, Da Lat City, Lam Dong province 66000, Vietnam;
| | - Thanh-Diem Nguyen
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Hochiminh City 700000, Vietnam; (H.-T.V.); (T.-D.N.); (T.-C.N.)
| | - Ngan Tran
- Faculty of Biotechnology, International University—Vietnam National University, Linh Trung Ward, Thu Duc District, Hochiminh City 700000, Vietnam;
| | - Thanh-Cong Nguyen
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Hochiminh City 700000, Vietnam; (H.-T.V.); (T.-D.N.); (T.-C.N.)
| | - Phuong-Nam Luu
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Hochiminh City 700000, Vietnam; (H.-T.V.); (T.-D.N.); (T.-C.N.)
| | - Duy-Duong Tran
- Agricultural Genetics Institute, Pham Van Dong Street, Hanoi 100000, Vietnam; (D.-D.T.); (T.-K.N.)
| | - Truong-Khoa Nguyen
- Agricultural Genetics Institute, Pham Van Dong Street, Hanoi 100000, Vietnam; (D.-D.T.); (T.-K.N.)
| | - Ly Le
- Faculty of Biotechnology, International University—Vietnam National University, Linh Trung Ward, Thu Duc District, Hochiminh City 700000, Vietnam;
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Duan H, Wang W, Zeng Y, Guo M, Zhou Y. The screening and identification of DNA barcode sequences for Rehmannia. Sci Rep 2019; 9:17295. [PMID: 31754140 PMCID: PMC6872558 DOI: 10.1038/s41598-019-53752-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022] Open
Abstract
In this study, ITS, ITS2, matK, rbcL and psbA-trnH in Rehmannia were successfully amplified and sequenced, but some ITS sequences need to be proofread according to ITS2 sequences. Compared with rbcL, matK and psbA-trnH, ITS and ITS2 had higher mutation rate and more information sites, and ITS2 had higher interspecific diversity and lower intraspecific variation in Rehmannia, but the interspecific genetic variation of rbcL and matK was lower. Furthermore, the obvious barcoding gap was found in psbA-trnH or ITS2 + psbA-trnH, and the overlap between interspecific and intraspecific variation of ITS, ITS2 or matK was less. In addition, the phylogenetic tree based on ITS or ITS2 indicated that R. glutinosa, R. chingii or R. henryi with obvious monophyly could be successfully identified, but R. piasezkii and R. elata were clustered into one branch, R. solanifolia could not be distinguished from R. glutinosa, and R. chingii was closer to R. henryi. In phylogenetic tree based on psbA-trnH or ITS2 + psbA-trnH, cultivars and wild varieties of R. glutinosa could be distinguished, were clearly separated from other Rehmannia species, and cultivars or wild varieties of R. glutinosa could be also distinguished by matK. Taken together, ITS2 has great potential in systematic study and species identification of Rehmannia, the combination of ITS2 and psbA-trnH might be the most suitable DNA barcode for Rehmannia species.
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Affiliation(s)
- Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Wanshen Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yunpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Mengmeng Guo
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yanqing Zhou
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.
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Wang Y, Zuo ZT, Shen T, Huang HY, Wang YZ. Authentication of Dendrobium Species Using Near-Infrared and Ultraviolet–Visible Spectroscopy with Chemometrics and Data Fusion. ANAL LETT 2018. [DOI: 10.1080/00032719.2018.1451874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ye Wang
- College of Traditional Chinese Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, China
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Zhi-Tian Zuo
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Tao Shen
- College of Resources and Environment, Yuxi Normal University, Yuxi, RP China
| | - Heng-Yu Huang
- College of Traditional Chinese Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Yuan-Zhong Wang
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, China
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Gao YX, Zhou YY, Xie Y, Feng L, Shen SG. The complete chloroplast genome sequence of an endangered Orchidaceae species Dendrobium monilforme and its phylogenetic implications. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0834-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Shinozaki J, Kazuma K, Satake M, Kondo K, Konno K. [PCR-RFLP Method for Rapid Discrimination of Toxic Plants Involved in Food Poisoning]. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2018; 59:134-140. [PMID: 30033990 DOI: 10.3358/shokueishi.59.134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Food poisoning caused by natural toxins, especially poisonous plants, is characterized by severe symptoms and a relatively high mortality rate. Therefore, rapid and accurate identification of the causative agent is extremely important. From plant toxin food poisoning data published by the Ministry of Health, Labour and Welfare of Japan from 1989 to 2015, we selected five plants (Veratrum spp., Datura spp., Aconitum spp., Narcissus spp. and Colchicum spp.) that are frequently involved in poisoning outbreaks, and developed a PCR-RFLP assay to discriminate them. Separation of the PCR-RFLP products by electrophoresis resulted in detection of two fragments from poisonous plants and one from edible plants. The PCR-RFLP method is rapid and straightforward and does not require expensive analytical devices. This assay was also confirmed to be applicable to cooked samples.
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Affiliation(s)
| | - Kohei Kazuma
- Institute of Natural Medicine, University of Toyama
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Population authentication of the traditional medicinal plant Cassia tora L. based on ISSR markers and FTIR analysis. Sci Rep 2018; 8:10714. [PMID: 30013159 PMCID: PMC6048050 DOI: 10.1038/s41598-018-29114-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/20/2018] [Indexed: 01/05/2023] Open
Abstract
Cassia tora is a plant of medicinal importance. Medicinal plants from different localities are believed to differ in their therapeutic potency. In this study, six populations of C. tora with different eco-geographical origins were investigated genotypically (ISSR) and phytochemically (FTIR) to establish an integrated approach for population discrimination and authentication of the origin of this medicinal herb. CHS gene expression analysis and determination of flavonoid content were carried out to substantiate the study. A total of 19 population-specific authentication bands were observed in 11 ISSR fingerprints. Authentication codes were generated using six highly polymorphic bands, including three authentication bands. FTIR spectra revealed that the peaks at wavenumber 1623 cm−1 (carbonyl group) and 1034 cm−1 (>CO- group) were powerful in separating the populations. These peaks are assigned to flavonoids and carbohydrates, respectively, were more intense for Ranchi (highland) population. Variation in the transcript level of CHS gene was observed. The findings of FTIR and RT-PCR analyses were in agreement with the TFC analysis, where, the lowest amount of flavonoids observed for Lucknow (lowland) population. All the populations of C. tora have been authenticated accurately by ISSR analyses and FTIR fingerprinting, and the Ranchi site was observed to be more suitable for the potential harvesting of therapeutic bioactive compounds.
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14
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Chloroplast genome sequence of the endangered Orchidaceae species Dendrobium hancockii. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0788-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Vu HT, Huynh P, Tran HD, Le L. In Silico Study on Molecular Sequences for Identification of Paphiopedilum Species. Evol Bioinform Online 2018; 14:1176934318774542. [PMID: 29899659 PMCID: PMC5993066 DOI: 10.1177/1176934318774542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/09/2018] [Indexed: 12/02/2022] Open
Abstract
Our study searched all available sequences of Paphiopedilum from NCBI (National Center for Biotechnology Information) and tested for their species resolution capability in single as well as in combination forms. A total of 28 loci were applied for analyses in the study. From the nuclear genome, the highest resolution was of LFY, followed by ACO, DEF4, and RAD51. These 4 loci were found to be even better than the popular region ITS for Paphiopedilum identification. Among the chloroplast regions, the intergenic spacer atpB-rbcL gave the highest species resolution (76.7%), followed by matK, trnL, rpoC2, and ycf1. The divergence of CHS, XDH, 18S, Nad1, ccsA, rbcL, and ycf2 was very low and should not be used as identifying markers for Paphiopedilum. In addition, 2-locus combinations could improve significantly the resolving capability for the genus, in which 14/36 data sets could be resolved completely (100%) with interspecies relationships. The indel information was also effective supporting data for molecular discrimination of species.
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Affiliation(s)
- Huyen-Trang Vu
- Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.,International University - Vietnam National University, Ho Chi Minh City, Vietnam
| | - Phuong Huynh
- Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | | | - Ly Le
- International University - Vietnam National University, Ho Chi Minh City, Vietnam
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Niu Z, Pan J, Xue Q, Zhu S, Liu W, Ding X. Plastome-wide comparison reveals new SNV resources for the authentication of Dendrobium huoshanense and its corresponding medicinal slice (Huoshan Fengdou). Acta Pharm Sin B 2018; 8:466-477. [PMID: 29881686 PMCID: PMC5989833 DOI: 10.1016/j.apsb.2017.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/24/2017] [Accepted: 11/08/2017] [Indexed: 11/06/2022] Open
Abstract
Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine (TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants (SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3'trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices (Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system (ARMS).
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Affiliation(s)
| | | | | | | | | | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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Zhang YJ, Ma C, Feng Y, Cheng X, Song J. The complete chloroplast genome sequence of an Endangered orchid species Dendrobium bellatulum (Orchidaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:233-234. [PMID: 33474127 PMCID: PMC7800090 DOI: 10.1080/23802359.2018.1437811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Dendrobium bellatulum Rolfe is an Endangered orchid species that is distributed in the subtropical regions of Yunnan Province, China. It was listed in the category of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Here, we reported the complete chloroplast (cp) genome sequence and the cp genomic features of D. bellatulum. The genome was 152,107 bp long with 129 genes comprising 83 protein-coding genes, 40 tRNA genes, and 6 rRNA genes. Phylogenetic analysis of a data set of cp genomes indicated that D. bellatulum is clustered with other species in Dendrobium.
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Affiliation(s)
- Yun-Jiao Zhang
- Haiyuan College, Kunming Medical University, Kunming, China
| | - Cong Ma
- Yunnan Science Research Institute of Communication & Transportation, Kunming, China
| | - Yang Feng
- Yunnan Science Research Institute of Communication & Transportation, Kunming, China.,College of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Xing Cheng
- Haiyuan College, Kunming Medical University, Kunming, China
| | - Ji Song
- Haiyuan College, Kunming Medical University, Kunming, China
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18
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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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Zhitao N, Shuying Z, Jiajia P, Ludan L, Jing S, Xiaoyu D. Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots. Sci Rep 2017. [PMID: 28522861 DOI: 10.1038/s41598-017-02252-2258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotspots-trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ-should be used in the phylogenetic and identification studies of Dendrobium.
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Affiliation(s)
- Niu Zhitao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhu Shuying
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Pan Jiajia
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Li Ludan
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Sun Jing
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ding Xiaoyu
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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20
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Zhitao N, Shuying Z, Jiajia P, Ludan L, Jing S, Xiaoyu D. Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots. Sci Rep 2017; 7:2073. [PMID: 28522861 PMCID: PMC5437043 DOI: 10.1038/s41598-017-02252-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/07/2017] [Indexed: 11/10/2022] Open
Abstract
Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotspots-trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ-should be used in the phylogenetic and identification studies of Dendrobium.
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Affiliation(s)
- Niu Zhitao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhu Shuying
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Pan Jiajia
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Li Ludan
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Sun Jing
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ding Xiaoyu
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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21
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Zhang YJ, Song J, Cheng X. The complete chloroplast genome sequence of an endangered traditional Chinese medicine plant Dendrobium candidum (Orchidaceae). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0750-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Dendrobium officinale Kimura et Migo: A Review on Its Ethnopharmacology, Phytochemistry, Pharmacology, and Industrialization. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:7436259. [PMID: 28386292 PMCID: PMC5366227 DOI: 10.1155/2017/7436259] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/23/2016] [Indexed: 12/04/2022]
Abstract
Ethnopharmacological Relevance. Dendrobii Officinalis Caulis, the stems of Dendrobium officinale Kimura et Migo, as a tonic herb in Chinese materia medica and health food in folk, has been utilized for the treatment of yin-deficiency diseases for decades. Methods. Information for analysis of Dendrobium officinale Kimura et Migo was obtained from libraries and Internet scientific databases such as PubMed, Web of Science, Google Scholar, ScienceDirect, Wiley InterScience, Ingenta, Embase, CNKI, and PubChem. Results. Over the past decades, about 190 compounds have been isolated from Dendrobium officinale Kimura et Migo. Its wide modern pharmacological actions in hepatoprotective effect, anticancer effect, hypoglycemic effect, antifatigue effect, gastric ulcer protective effect, and so on were reported. This may mainly attribute to the major and bioactive components: polysaccharides. However, other small molecule components require further study. Conclusions. Due to the lack of systematic data of Dendrobium officinale, it is important to explore its ingredient-function relationships with modern pharmacology. Recently, studies on the chemical constituents of Dendrobium officinale concentrated in crude polysaccharides and its structure-activity relationships remain scant. Further research is required to determine the Dendrobium officinale toxicological action and pharmacological mechanisms of other pure ingredients and crude extracts. In addition, investigation is needed for better quality control and novel drug or product development.
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Teixeira da Silva JA, Jin X, Dobránszki J, Lu J, Wang H, Zotz G, Cardoso JC, Zeng S. Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding. Mol Phylogenet Evol 2016; 95:196-216. [DOI: 10.1016/j.ympev.2015.10.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
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Ngo Ngwe MFS, Omokolo DN, Joly S. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices. PLoS One 2015; 10:e0145364. [PMID: 26691919 PMCID: PMC4686806 DOI: 10.1371/journal.pone.0145364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022] Open
Abstract
Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.
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Affiliation(s)
- Marie Florence Sandrine Ngo Ngwe
- Laboratory of Plant Physiology, Higher Teacher’s Training College, University of Yaoundé 1, P. O. Box 47, Yaounde, Cameroon
- Institute of Agricultural Research for Development-CEREFEN, BP 167, Meyomessala, Cameroon
- * E-mail:
| | - Denis Ndoumou Omokolo
- Laboratory of Plant Physiology, Higher Teacher’s Training College, University of Yaoundé 1, P. O. Box 47, Yaounde, Cameroon
| | - Simon Joly
- Institut de recherche en biologie végétale, Montreal Botanical Garden and Université de Montréal, 4101 Sherbrooke East, Montréal, QC, H1X 2B2, Canada
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25
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Yan L, Wang X, Liu H, Tian Y, Lian J, Yang R, Hao S, Wang X, Yang S, Li Q, Qi S, Kui L, Okpekum M, Ma X, Zhang J, Ding Z, Zhang G, Wang W, Dong Y, Sheng J. The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb. MOLECULAR PLANT 2015; 8:922-34. [PMID: 25825286 DOI: 10.1016/j.molp.2014.12.011] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 05/05/2023]
Abstract
Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome sequences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16-epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe.
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Affiliation(s)
- Liang Yan
- College of Life Science, Jilin University, Changchun 130012, China; Pu'er Institute of Pu-er Tea, Pu'er 665000, China
| | - Xiao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Hui Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Yang Tian
- College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jinmin Lian
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Ruijuan Yang
- Pu'er Institute of Pu-er Tea, Pu'er 665000, China
| | - Shumei Hao
- Yunnan University, Kunming 650091, China
| | - Xuanjun Wang
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shengchao Yang
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Qiye Li
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuai Qi
- Agri-Biotech Lab, Kunming 650502, China
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Moses Okpekum
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Xiao Ma
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajin Zhang
- School of Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China
| | - Zhaoli Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Guojie Zhang
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Yang Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China; Laboratory of Applied Genomics and Synthetic Biology, College of Life Science, Kunming University of Science and Technology, Kunming 650500, China.
| | - Jun Sheng
- College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
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26
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Evaluation of the DNA barcodes in Dendrobium (Orchidaceae) from mainland Asia. PLoS One 2015; 10:e0115168. [PMID: 25602282 PMCID: PMC4300225 DOI: 10.1371/journal.pone.0115168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 11/19/2014] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding has been proposed to be one of the most promising tools for accurate and rapid identification of taxa. However, few publications have evaluated the efficiency of DNA barcoding for the large genera of flowering plants. Dendrobium, one of the largest genera of flowering plants, contains many species that are important in horticulture, medicine and biodiversity conservation. Besides, Dendrobium is a notoriously difficult group to identify. DNA barcoding was expected to be a supplementary means for species identification, conservation and future studies in Dendrobium. We assessed the power of 11 candidate barcodes on the basis of 1,698 accessions of 184 Dendrobium species obtained primarily from mainland Asia. Our results indicated that five single barcodes, i.e., ITS, ITS2, matK, rbcL and trnH-psbA, can be easily amplified and sequenced with the currently established primers. Four barcodes, ITS, ITS2, ITS+matK, and ITS2+matK, have distinct barcoding gaps. ITS+matK was the optimal barcode based on all evaluation methods. Furthermore, the efficiency of ITS+matK was verified in four other large genera including Ficus, Lysimachia, Paphiopedilum, and Pedicularis in this study. Therefore, we tentatively recommend the combination of ITS+matK as a core DNA barcode for large flowering plant genera.
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27
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Abstract
DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.
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Affiliation(s)
- Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, Carmarthenshire, SA32 8HG, UK,
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28
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SNP typing for germplasm identification of Amomum villosum Lour. Based on DNA barcoding markers. PLoS One 2014; 9:e114940. [PMID: 25531885 PMCID: PMC4274006 DOI: 10.1371/journal.pone.0114940] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 11/16/2014] [Indexed: 12/02/2022] Open
Abstract
Amomum villosum Lour., produced from Yangchun, Guangdong Province, China, is a Daodi medicinal material of Amomi Fructus in traditional Chinese medicine. This herb germplasm should be accurately identified and collected to ensure its quality and safety in medication. In the present study, single nucleotide polymorphism typing method was evaluated on the basis of DNA barcoding markers to identify the germplasm of Amomi Fructus. Genomic DNA was extracted from the leaves of 29 landraces representing three Amomum species (A. villosum Lour., A. xanthioides Wall. ex Baker and A. longiligulare T. L. Wu) by using the CTAB method. Six barcoding markers (ITS, ITS2, LSU D1–D3, matK, rbcL and trnH-psbA) were PCR amplified and sequenced; SNP typing and phylogenetic analysis were performed to differentiate the landraces. Results showed that high-quality bidirectional sequences were acquired for five candidate regions (ITS, ITS2, LSU D1–D3, matK, and rbcL) except trnH-psbA. Three ribosomal regions, namely, ITS, ITS2, and LSU D1–D3, contained more SNP genotypes (STs) than the plastid genes rbcL and matK. In the 29 specimens, 19 STs were detected from the combination of four regions (ITS, LSU D1–D3, rbcL, and matK). Phylogenetic analysis results further revealed two clades. Minimum-spanning tree demonstrated the existence of two main groups: group I was consisting of 9 STs (ST1–8 and ST11) of A. villosum Lour., and group II was composed of 3 STs (ST16–18) of A. longiligulare T.L. Wu. Our results suggested that ITS and LSU D1–D3 should be incorporated with the core barcodes rbcL and matK. The four combined regions could be used as a multiregional DNA barcode to precisely differentiate the Amomi Fructus landraces in different producing areas.
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29
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Ajmal Ali M, Gyulai G, Hidvégi N, Kerti B, Al Hemaid FM, Pandey AK, Lee J. The changing epitome of species identification - DNA barcoding. Saudi J Biol Sci 2014; 21:204-31. [PMID: 24955007 PMCID: PMC4061418 DOI: 10.1016/j.sjbs.2014.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/22/2014] [Accepted: 03/23/2014] [Indexed: 01/11/2023] Open
Abstract
The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.
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Affiliation(s)
- M. Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Gábor Gyulai
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Norbert Hidvégi
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Balázs Kerti
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Fahad M.A. Al Hemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Arun K. Pandey
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Joongku Lee
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305 806, South Korea
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Techen N, Parveen I, Pan Z, Khan IA. DNA barcoding of medicinal plant material for identification. Curr Opin Biotechnol 2013; 25:103-10. [PMID: 24484887 DOI: 10.1016/j.copbio.2013.09.010] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/27/2013] [Indexed: 01/13/2023]
Abstract
Because of the increasing demand for herbal remedies and for authentication of the source material, it is vital to provide a single database containing information about authentic plant materials and their potential adulterants. The database should provide DNA barcodes for data retrieval and similarity search. In order to obtain such barcodes, several molecular methods have been applied to develop markers that aid with the authentication and identification of medicinal plant materials. In this review, we discuss the genomic regions and molecular methods selected to provide barcodes, available databases and the potential future of barcoding using next generation sequencing.
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Affiliation(s)
- Natascha Techen
- National Center for Natural Products Research and Research Institute of Pharmaceutical Sciences, Department of Pharmacognosy, School of Pharmacy, University of Mississippi, P.O. Box 1848, MS 38677, USA
| | - Iffat Parveen
- National Center for Natural Products Research and Research Institute of Pharmaceutical Sciences, Department of Pharmacognosy, School of Pharmacy, University of Mississippi, P.O. Box 1848, MS 38677, USA
| | - Zhiqiang Pan
- USDA-ARS-NPURU, P.O. Box 8048, University, MS 38677, USA
| | - Ikhlas A Khan
- National Center for Natural Products Research and Research Institute of Pharmaceutical Sciences, Department of Pharmacognosy, School of Pharmacy, University of Mississippi, P.O. Box 1848, MS 38677, USA; School of Pharmacy, King Saud University, Saudi Arabia.
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31
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Mahadani P, Sharma GD, Ghosh SK. Identification of ethnomedicinal plants (Rauvolfioideae: Apocynaceae) through DNA barcoding from northeast India. Pharmacogn Mag 2013; 9:255-63. [PMID: 23930011 PMCID: PMC3732430 DOI: 10.4103/0973-1296.113284] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/28/2012] [Accepted: 06/11/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND DNA barcode-based molecular characterization is in practice for plants, but yet lacks total agreement considering the selection of marker. Plant species of subfamily Rauvolfioideae have long been used as herbal medicine by the majority of tribal people in Northeast (NE) India and at present holds mass effect on the society. Hence, there is an urgent need of correct taxonomic inventorization vis-à-vis species level molecular characterization of important medicinal plants. OBJECTIVE To test the efficiency of matK in species delineation like DNA barcoding in Rauvolfiadae (Apocynaceae). MATERIALS AND METHODS In this study, the core DNA barcode matK and trnH-psbA sequences are examined for differentiation of selected ethnomedicinal plants of Apocynaceae. DNA from young leaves of selected species was isolated, and matK gene (~800 bp) and trnH-psbA spacer (~450 bp) of Chloroplast DNA was amplified for species level identification. RESULTS The ~758 bp matK sequence in comparison to the trnH-psbA showed easy amplification, alignment, and high level of discrimination value among the medicinal Rauvolfioidae species. Intergenic spacer trnH-psbA is also exhibited persistent problem in obtaining constant bidirectional sequences. Partial matK sequences exhibited 3 indels in multiple of 3 at 5 end. Evidently, generated matK sequences are clustered cohesively, with their conspecific Genbank sequences. However, repeat structures with AT-rich regions, possessing indels in multiple of 3, could be utilized as qualitative molecular markers in further studies both at the intra-specific and shallow inter-specific levels like the intergenic spacers of CpDNA. CONCLUSION matK sequence information could help in correct species identification for medicinal plants of Rauvolfioideae.
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Affiliation(s)
- Pradosh Mahadani
- Department of Biotechnology, Assam University, Silchar - 788 011, Assam, India
| | - Gouri Dutta Sharma
- Life Science and Bioinformatics, Assam University, Silchar - 788 011, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar - 788 011, Assam, India
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Bafeel SO, Arif IA, Bakir MA, Al Homaidan AA, Al Farhan AH, Khan HA. DNA barcoding of arid wild plants using rbcL gene sequences. GENETICS AND MOLECULAR RESEARCH 2012; 11:1934-41. [PMID: 22869548 DOI: 10.4238/2012.july.19.12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life (CBOL) plant working group needs to be evaluated for a wide range of plant species. We therefore tested the potential of the rbcL marker for the identification of wild plants belonging to diverse families of arid regions. Maximum likelihood tree analysis was performed to evaluate the discriminatory power of the rbcL gene. Our findings showed that using rbcL gene sequences enabled identification of the majority of the samples (92%) to genus level and only 17% to species level.
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Affiliation(s)
- S O Bafeel
- Department of Biology, College of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Boonsom T, Waranuch N, Ingkaninan K, Denduangboripant J, Sukrong S. Molecular analysis of the genus Asparagus based on matK sequences and its application to identify A. racemosus, a medicinally phytoestrogenic species. Fitoterapia 2012; 83:947-53. [DOI: 10.1016/j.fitote.2012.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/11/2012] [Accepted: 04/15/2012] [Indexed: 11/16/2022]
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Kool A, de Boer HJ, Krüger A, Rydberg A, Abbad A, Björk L, Martin G. Molecular identification of commercialized medicinal plants in southern Morocco. PLoS One 2012; 7:e39459. [PMID: 22761800 PMCID: PMC3384669 DOI: 10.1371/journal.pone.0039459] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/21/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Medicinal plant trade is important for local livelihoods. However, many medicinal plants are difficult to identify when they are sold as roots, powders or bark. DNA barcoding involves using a short, agreed-upon region of a genome as a unique identifier for species- ideally, as a global standard. RESEARCH QUESTION What is the functionality, efficacy and accuracy of the use of barcoding for identifying root material, using medicinal plant roots sold by herbalists in Marrakech, Morocco, as a test dataset. METHODOLOGY In total, 111 root samples were sequenced for four proposed barcode regions rpoC1, psbA-trnH, matK and ITS. Sequences were searched against a tailored reference database of Moroccan medicinal plants and their closest relatives using BLAST and Blastclust, and through inference of RAxML phylograms of the aligned market and reference samples. PRINCIPAL FINDINGS Sequencing success was high for rpoC1, psbA-trnH, and ITS, but low for matK. Searches using rpoC1 alone resulted in a number of ambiguous identifications, indicating insufficient DNA variation for accurate species-level identification. Combining rpoC1, psbA-trnH and ITS allowed the majority of the market samples to be identified to genus level. For a minority of the market samples, the barcoding identification differed significantly from previous hypotheses based on the vernacular names. CONCLUSIONS/SIGNIFICANCE Endemic plant species are commercialized in Marrakech. Adulteration is common and this may indicate that the products are becoming locally endangered. Nevertheless the majority of the traded roots belong to species that are common and not known to be endangered. A significant conclusion from our results is that unknown samples are more difficult to identify than earlier suggested, especially if the reference sequences were obtained from different populations. A global barcoding database should therefore contain sequences from different populations of the same species to assure the reference sequences characterize the species throughout its distributional range.
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Affiliation(s)
- Anneleen Kool
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
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de Vere N, Rich TCG, Ford CR, Trinder SA, Long C, Moore CW, Satterthwaite D, Davies H, Allainguillaume J, Ronca S, Tatarinova T, Garbett H, Walker K, Wilkinson MJ. DNA barcoding the native flowering plants and conifers of Wales. PLoS One 2012; 7:e37945. [PMID: 22701588 PMCID: PMC3368937 DOI: 10.1371/journal.pone.0037945] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 04/26/2012] [Indexed: 11/19/2022] Open
Abstract
We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.
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Affiliation(s)
- Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, United Kingdom.
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Establishment of DNA barcodes for the identification of the botanical sources of the Chinese ‘cooling’ beverage. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.12.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Singh HK, Parveen I, Raghuvanshi S, Babbar SB. The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species. BMC Res Notes 2012; 5:42. [PMID: 22260646 PMCID: PMC3292824 DOI: 10.1186/1756-0500-5-42] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/19/2012] [Indexed: 11/27/2022] Open
Abstract
Background Based on the testing of several loci, predominantly against floristic backgrounds, individual or different combinations of loci have been suggested as possible universal DNA barcodes for plants. The present investigation was undertaken to check the applicability of the recommended locus/loci for congeneric species with Dendrobium species as an illustrative example. Results Six loci, matK, rbcL, rpoB, rpoC1, trnH-psbA spacer from the chloroplast genome and ITS, from the nuclear genome, were compared for their amplification, sequencing and species discrimination success rates among multiple accessions of 36 Dendrobium species. The trnH-psbA spacer could not be considered for analysis as good quality sequences were not obtained with its forward primer. Among the tested loci, ITS, recommended by some as a possible barcode for plants, provided 100% species identification. Another locus, matK, also recommended as a universal barcode for plants, resolved 80.56% species. ITS remained the best even when sequences of investigated loci of additional Dendrobium species available on the NCBI GenBank (93, 33, 20, 18 and 17 of ITS, matK, rbcL, rpoB and rpoC1, respectively) were also considered for calculating the percent species resolution capabilities. The species discrimination of various combinations of the loci was also compared based on the 36 investigated species and additional 16 for which sequences of all the five loci were available on GenBank. Two-locus combination of matK+rbcL recommended by the Plant Working Group of Consortium for Barcoding of Life (CBOL) could discriminate 86.11% of 36 species. The species discriminating ability of this barcode was reduced to 80.77% when additional sequences available on NCBI were included in the analysis. Among the recommended combinations, the barcode based on three loci - matK, rpoB and rpoC1- resolved maximum number of species. Conclusions Any recommended barcode based on the loci tested so far, is not likely to provide 100% species identification across the plant kingdom and thus is not likely to act as a universal barcode. It appears that barcodes, if based on single or limited locus(i), would be taxa specific as is exemplified by the success of ITS among Dendrobium species, though it may not be suitable for other plants because of the problems that are discussed.
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Takamiya T, Wongsawad P, Tajima N, Shioda N, Lu JF, Wen CL, Wu JB, Handa T, Iijima H, Kitanaka S, Yukawa T. Identification of dendrobium species used for herbal medicines based on ribosomal DNA internal transcribed spacer sequence. Biol Pharm Bull 2011; 34:779-82. [PMID: 21532173 DOI: 10.1248/bpb.34.779] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Stems of genus Dendrobium (Orchidaceae) have been traditionally used as an herbal medicine (Dendrobii Herba) in Eastern Asia. Although demand for Dendrobium is increasing rapidly, wild resources are decreasing due to over-collection. This study aimed to identify plant sources of Dendrobii Herba on the market based on sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. We constructed an ITS1-5.8S-ITS2 sequence database of 196 Dendrobium species, and the database was employed to identify 21 herbal samples. We found that 13 Dendrobium species (D. catenatum, D. cucullatum, D. denudans, D. devonianum, D. eriiflorum, D. hancockii, D. linawianum, D. lituiflorum, D. loddigesii, D. polyanthum, D. primulinum, D. regium, and D. transparens) were possibly used as plant sources of Dendrobii Herba, and unidentified species allied to D. denudans, D. eriiflorum, D. gregulus, or D. hemimelanoglossum were also used as sources. Furthermore, it is clear that D. catenatum is one of the most important sources of Dendrobii Herba (5 out of 21 samples).
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Wang W, Wu Y, Yan Y, Ermakova M, Kerstetter R, Messing J. DNA barcoding of the Lemnaceae, a family of aquatic monocots. BMC PLANT BIOLOGY 2010; 10:205. [PMID: 20846439 PMCID: PMC2956554 DOI: 10.1186/1471-2229-10-205] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 09/16/2010] [Indexed: 05/21/2023]
Abstract
BACKGROUND Members of the aquatic monocot family Lemnaceae (commonly called duckweeds) represent the smallest and fastest growing flowering plants. Their highly reduced morphology and infrequent flowering result in a dearth of characters for distinguishing between the nearly 38 species that exhibit these tiny, closely-related and often morphologically similar features within the same family of plants. RESULTS We developed a simple and rapid DNA-based molecular identification system for the Lemnaceae based on sequence polymorphisms. We compared the barcoding potential of the seven plastid-markers proposed by the CBOL (Consortium for the Barcode of Life) plant-working group to discriminate species within the land plants in 97 accessions representing 31 species from the family of Lemnaceae. A Lemnaceae-specific set of PCR and sequencing primers were designed for four plastid coding genes (rpoB, rpoC1, rbcL and matK) and three noncoding spacers (atpF-atpH, psbK-psbI and trnH-psbA) based on the Lemna minor chloroplast genome sequence. We assessed the ease of amplification and sequencing for these markers, examined the extent of the barcoding gap between intra- and inter-specific variation by pairwise distances, evaluated successful identifications based on direct sequence comparison of the "best close match" and the construction of a phylogenetic tree. CONCLUSIONS Based on its reliable amplification, straightforward sequence alignment, and rates of DNA variation between species and within species, we propose that the atpF-atpH noncoding spacer could serve as a universal DNA barcoding marker for species-level identification of duckweeds.
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Affiliation(s)
- Wenqin Wang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Yongrui Wu
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Yiheng Yan
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Marina Ermakova
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Randall Kerstetter
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
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Lou SK, Wong KL, Li M, But PPH, Tsui SKW, Shaw PC. An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database). BMC Genomics 2010; 11:402. [PMID: 20576098 PMCID: PMC2996930 DOI: 10.1186/1471-2164-11-402] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 06/24/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database. DESCRIPTION We have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD) for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed at http://www.cuhk.edu.hk/icm/mmdbd.htm. CONCLUSIONS This work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry.
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Affiliation(s)
- Shao-Ke Lou
- Department of Biochemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ka-Lok Wong
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ming Li
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Paul Pui-Hay But
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Stephen Kwok-Wing Tsui
- Department of Biochemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Pang-Chui Shaw
- Department of Biochemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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