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Karbarz M, Szlachcikowska D, Zapał A, Leśko A. Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach. Genes (Basel) 2024; 15:689. [PMID: 38927625 PMCID: PMC11202981 DOI: 10.3390/genes15060689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.
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Affiliation(s)
| | - Dominika Szlachcikowska
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, 35-225 Rzeszów, Poland
| | - Angelika Zapał
- Institute of Biology, University of Rzeszow, 35-959 Rzeszów, Poland
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Jin DP, Sim S, Park JW, Choi JE, Yoon J, Lim CE, Kim MH. Identification of the Plant Family Caryophyllaceae in Korea Using DNA Barcoding. PLANTS (BASEL, SWITZERLAND) 2023; 12:2060. [PMID: 37653977 PMCID: PMC10222892 DOI: 10.3390/plants12102060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 09/02/2023]
Abstract
Caryophyllaceae is a large angiosperm family, with many species being utilized as ornamental or medicinal plants in Korea, in addition to several endangered species that are managed by the government. In this study, we used DNA barcoding for the accurate identification of Korean Caryophyllaceae. A total of 78 taxa (n = 215) were sequenced based on three chloroplast regions (rbcL, matK, and psbA-trnH) and nuclear ribosomal internal transcribed spacers (ITS). In the neighbor-joining tree, a higher accuracy of identification was generally observed when using ITS (>73%) rather than chloroplast regions (<62%). The highest resolution was found for rbcL + ITS (77.6%), although resolution varied according to the genus. Among the genera that included two and more species, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified. However, the species of five other genera (Cerastium, Gypsophila, Dianthus, Silene, and Spergularia) showed relatively low resolutions (0-61.1%). In the cases of Cerastium, Dianthus, and Silene, ambiguous taxonomic relationships among unidentified species may have been a factor contributing to such low resolutions. However, in contrast to these results, Gypsophila and Spergularia have been identified well in previous studies. Our findings indicate the need of taxonomic reconsideration in Korea.
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Affiliation(s)
- Dong-Pil Jin
- Urban Biodiversity Research Division, Sejong National Arboretum, Korean Arboretum and Gardens Institute, Sejong 30106, Republic of Korea
| | - Sunhee Sim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Jong-Won Park
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-Eun Choi
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Jiwon Yoon
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Chae Eun Lim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Min-Ha Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
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Safhi FA, Alshamrani SM, Fiteha YG, Abd El-Moneim D. DNA Barcoding of Endangered and Rarely Occurring Plants in Faifa Mountains (Jazan, Saudi Arabia). AGRICULTURE 2022; 12:1931. [DOI: 10.3390/agriculture12111931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Conservation of plant genetic resources, especially threatened species, is an important topic in biodiversity. It is a field that requires prior knowledge of the target species, in addition to correct identification and taxonomic description. In botany, the identification of plant species traditionally relies on key morphological descriptions and anatomical features. However, in complex species and tree plants, molecular identification can facilitate identification and increase species delimitation accuracy. In the Faifa mountains of Jazan province in Saudi Arabia, 12 rarely occurring plants were recorded and identified using two DNA barcoding regions (i.e., rbcL and ITS). All the samples were successfully amplified, sequenced, and analyzed using the standard DNA barcode protocol, and this resulted in the clear and accurate identification of 11 out of the 12 sampled species. A total of five species were in agreement in terms of both morpho- and molecular-based identification. Four and two species were identified based solely on ITS and rbcL phylogenetics, respectively. The geographic distribution records of the identified species showed that some species were distributed at a distance far from their usual region, while others were reported in proximate regions and localities. Some species were found to be medicinally important and required additional conservation plans.
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Wambugu PW, Henry R. Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies. Mol Ecol 2022; 31:2207-2222. [PMID: 35170117 PMCID: PMC9303585 DOI: 10.1111/mec.16402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/27/2022]
Abstract
The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.
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Affiliation(s)
- Peterson W Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, 00100, Nairobi, Kenya
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, 4072, Australia
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Diversity of Seahorse Species (Hippocampus spp.) in the International Aquarium Trade. DIVERSITY 2021. [DOI: 10.3390/d13050187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications.
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Egydio Brandão APM, Yamaguchi LF, Tepe EJ, Salatino A, Kato MJ. Evaluation of DNA markers for molecular identification of three Piper species from Brazilian Atlantic Rainforest. PLoS One 2020; 15:e0239056. [PMID: 33075070 PMCID: PMC7571689 DOI: 10.1371/journal.pone.0239056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/28/2020] [Indexed: 01/08/2023] Open
Abstract
Piper is one of two large genera in the Piperaceae, and with ca. 2600 species, is one of the largest plant genera in the world. Species delimitation and evaluation of genetic diversity among populations are important requisites for conservation and adequate exploitation of economically important species. DNA barcoding has been used as a powerful tool and a practical method for species characterization and delimitation. The present work aims to evaluate molecular markers for barcoding three Piper species native to Brazil: P. gaudichaudianum (“jaborandi” or “pariparoba”), P. malacophyllum (“pariparoba-murta”) and P. regnellii (“caapeba” or “pariparoba”). A reference DNA barcode library was developed using sequences of three candidate regions: ITS2, trnH-psbA and rbcL. Transferability of the microsatellite (SSR) primers Psol 3, Psol 6 and Psol 10, designed originally for Piper solmsianum, to the three Piper species was also evaluated. The discriminatory power of the markers was based on the determination of inter- and intraspecific distances, phylogenetic reconstruction, and clustering analysis, as well as BLASTn comparison. Sequences of ITS2 enabled efficient species identification by means of the BLASTn procedure. Based on these sequences, intraspecific divergence was lower than interspecific variation. Maximum Parsimony analyses based on ITS2 sequences provided three resolved clades, each corresponding to one of the three analysed species. Sequences of trnH-psbA and rbcL had lower discriminatory value. Analyses combining sequences of these regions were less effective toward the attainment of resolved and strongly supported clades of all species. In summary, robustly supported clades of P. regnellii were obtained in most of the analyses, based either on isolated or combined sequences. The SSRs primers Psol 3, Psol 6 and Psol 10 were shown to be transferable to P. gaudichaudianum and P. regnellii, but not to P. malacophyllum. Preliminary cluster analyses based on the polymorphism of the amplified products suggested that Psol 3 has lower potential than Psol 6 and Psol 10 for discrimination of Piper species.
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Affiliation(s)
| | - Lydia F. Yamaguchi
- Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Eric J. Tepe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Antonio Salatino
- Department of Botany, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Massuo J. Kato
- Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil
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Hernández-León S, Little DP, Acevedo-Sandoval O, Gernandt DS, Rodríguez-Laguna R, Saucedo-García M, Arce-Cervantes O, Razo-Zárate R, Espitia-López J. Plant core DNA barcode performance at a local scale: identification of the conifers of the state of Hidalgo, Mexico. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2018.1546240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sergio Hernández-León
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, C.P. 43600, A.P. 32, México
| | - Damon P. Little
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, 10458-5126, USA
| | - Otilio Acevedo-Sandoval
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, C.P. 43600, A.P. 32, México
| | - David S. Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, AP 70-233, México
| | - Rodrigo Rodríguez-Laguna
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, C.P. 43600, A.P. 32, México
| | - Mariana Saucedo-García
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, C.P. 43600, A.P. 32, México
| | - Oscar Arce-Cervantes
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, C.P. 43600, A.P. 32, México
| | - Ramón Razo-Zárate
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, C.P. 43600, A.P. 32, México
| | - Josefa Espitia-López
- Área Académica de Ciencias Agrícolas y Forestales, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, C.P. 43600, A.P. 32, México
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Wu Y, Li M, Yang Y, Jiang L, Liu M, Wang B, Wang Y. Authentication of Small Berry Fruit in Fruit Products by DNA Barcoding Method. J Food Sci 2018; 83:1494-1504. [DOI: 10.1111/1750-3841.14177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/01/2018] [Accepted: 04/06/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Yajun Wu
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Meige Li
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Yange Yang
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Li Jiang
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Mingchang Liu
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Bin Wang
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
| | - Yingchun Wang
- Agro-product Safety Research Center; Chinese Academy of Inspection and Quarantine; No.11, Ronghua South Street, Yizhuang Economic Zone Beijing 100176 China
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van Zonneveld M, Loo J, Maselli S, Madrid JJ, Echeverria JL. Bridging molecular genetics and participatory research: how access and benefit-sharing stimulate interdisciplinary research for tropical biology and conservation. Biotropica 2018. [DOI: 10.1111/btp.12515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Judy Loo
- Bioversity International, HQ; Rome Italy
| | - Silvana Maselli
- University del Valle en Guatemala (UVG); Ciudad de Guatemala Guatemala
| | - Julio Javier Madrid
- The Association of Community Forestry Organizations in the Petén (ACOFOP); Santa Elena Guatemala
| | - José Luis Echeverria
- National Council of Protected Areas (CONAP); Oficina Técnica de Biodiversidad; Ciudad de Guatemala Guatemala
- ABS National Focal Point; Ciudad de Guatemala Guatemala
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Mishra P, Kumar A, Sivaraman G, Shukla AK, Kaliamoorthy R, Slater A, Velusamy S. Character-based DNA barcoding for authentication and conservation of IUCN Red listed threatened species of genus Decalepis (Apocynaceae). Sci Rep 2017; 7:14910. [PMID: 29097709 PMCID: PMC5668324 DOI: 10.1038/s41598-017-14887-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 10/09/2017] [Indexed: 11/09/2022] Open
Abstract
The steno-endemic species of genus Decalepis are highly threatened by destructive wild harvesting. The medicinally important fleshy tuberous roots of Decalepis hamiltonii are traded as substitute, to meet the international market demand of Hemidesmus indicus. In addition, the tuberous roots of all three species of Decalepis possess similar exudates and texture, which challenges the ability of conventional techniques alone to perform accurate species authentication. This study was undertaken to generate DNA barcodes that could be utilized in monitoring and curtailing the illegal trade of these endangered species. The DNA barcode reference library was developed in BOLD database platform for candidate barcodes rbcL, matK, psbA-trnH, ITS and ITS2. The average intra-specific variations (0-0.27%) were less than the distance to nearest neighbour (0.4-11.67%) with matK and ITS. Anchoring the coding region rbcL in multigene tiered approach, the combination rbcL + matK + ITS yielded 100% species resolution, using the least number of loci combinations either with PAUP or BLOG methods to support a character-based approach. Species-specific SNP position (230 bp) in the matK region that is characteristic of D. hamiltonii could be used to design specific assays, enhancing its applicability for direct use in CITES enforcement for distinguishing it from H. indicus.
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Affiliation(s)
- Priyanka Mishra
- Plant Biology and Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Center, Allalsandra, GKVK Post, Bengaluru, 560065, Karnataka, India
| | - Amit Kumar
- Plant Biology and Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Center, Allalsandra, GKVK Post, Bengaluru, 560065, Karnataka, India
| | - Gokul Sivaraman
- Plant Biology and Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Center, Allalsandra, GKVK Post, Bengaluru, 560065, Karnataka, India
| | - Ashutosh K Shukla
- Biotechnology Division, CSIR - Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, Uttar Pradesh, India
| | - Ravikumar Kaliamoorthy
- School of Conservation, TransDisciplinary University, 74/2, Jarakabande Kaval, Post Attur, Via Yelahanka, Bangalore, 560064, Karnataka, India
| | - Adrian Slater
- Biomolecular Technology Group, Faculty of Health and Life Sciences, De Montfort University, Leicester, LE1 9BH, UK
| | - Sundaresan Velusamy
- Plant Biology and Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Center, Allalsandra, GKVK Post, Bengaluru, 560065, Karnataka, India.
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Yao PC, Gao HY, Wei YN, Zhang JH, Chen XY, Li HQ. Evaluating sampling strategy for DNA barcoding study of coastal and inland halo-tolerant Poaceae and Chenopodiaceae: A case study for increased sample size. PLoS One 2017; 12:e0185311. [PMID: 28934362 PMCID: PMC5608404 DOI: 10.1371/journal.pone.0185311] [Citation(s) in RCA: 14] [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: 06/14/2017] [Accepted: 09/11/2017] [Indexed: 12/11/2022] Open
Abstract
Environmental conditions in coastal salt marsh habitats have led to the development of specialist genetic adaptations. We evaluated six DNA barcode loci of the 53 species of Poaceae and 15 species of Chenopodiaceae from China's coastal salt marsh area and inland area. Our results indicate that the optimum DNA barcode was ITS for coastal salt-tolerant Poaceae and matK for the Chenopodiaceae. Sampling strategies for ten common species of Poaceae and Chenopodiaceae were analyzed according to optimum barcode. We found that by increasing the number of samples collected from the coastal salt marsh area on the basis of inland samples, the number of haplotypes of Arundinella hirta, Digitaria ciliaris, Eleusine indica, Imperata cylindrica, Setaria viridis, and Chenopodium glaucum increased, with a principal coordinate plot clearly showing increased distribution points. The results of a Mann-Whitney test showed that for Digitaria ciliaris, Eleusine indica, Imperata cylindrica, and Setaria viridis, the distribution of intraspecific genetic distances was significantly different when samples from the coastal salt marsh area were included (P < 0.01). These results suggest that increasing the sample size in specialist habitats can improve measurements of intraspecific genetic diversity, and will have a positive effect on the application of the DNA barcodes in widely distributed species. The results of random sampling showed that when sample size reached 11 for Chloris virgata, Chenopodium glaucum, and Dysphania ambrosioides, 13 for Setaria viridis, and 15 for Eleusine indica, Imperata cylindrica and Chenopodium album, average intraspecific distance tended to reach stability. These results indicate that the sample size for DNA barcode of globally distributed species should be increased to 11–15.
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Affiliation(s)
- Peng-Cheng Yao
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Hai-Yan Gao
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Ya-Nan Wei
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Jian-Hang Zhang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiao-Yong Chen
- School of Ecological and Environmental Sciences, Tiantong National Station of Forest Ecosystem, East China Normal University, Shanghai, China
- * E-mail: (HQL); (XYC)
| | - Hong-Qing Li
- School of Life Sciences, East China Normal University, Shanghai, China
- * E-mail: (HQL); (XYC)
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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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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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14
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Ghorbani A, Gravendeel B, Selliah S, Zarré S, de Boer H. DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep. Mol Ecol Resour 2016; 17:342-352. [DOI: 10.1111/1755-0998.12615] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/26/2016] [Accepted: 09/06/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Abdolbaset Ghorbani
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
- Traditional Medicine and Materia Medica Research Center; Shahid Beheshti University of Medical Sciences; No 19, Tavanir Street, Hemmat Highway P.O. Box 14155-6153 Tehran Iran
| | - Barbara Gravendeel
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- University of Applied Sciences Leiden; Zernikedreef 11 2333 CK Leiden The Netherlands
| | - Sugirthini Selliah
- The Natural History Museum; University of Oslo; P.O. Box 1172 Blindern 0318 Oslo Norway
| | - Shahin Zarré
- Department of Plant Sciences; School of Biology; College of Science; University of Tehran; 14155-6455 Tehran Iran
| | - Hugo de Boer
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- The Natural History Museum; University of Oslo; P.O. Box 1172 Blindern 0318 Oslo Norway
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15
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Hollingsworth PM, Li DZ, van der Bank M, Twyford AD. Telling plant species apart with DNA: from barcodes to genomes. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150338. [PMID: 27481790 PMCID: PMC4971190 DOI: 10.1098/rstb.2015.0338] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 12/17/2022] Open
Abstract
Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, Yunnan 650201, People's Republic of China
| | - Michelle van der Bank
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland park, Johannesburg PO Box 524, South Africa
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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16
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Hassold S, Lowry PP, Bauert MR, Razafintsalama A, Ramamonjisoa L, Widmer A. DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species. PLoS One 2016; 11:e0157881. [PMID: 27362258 PMCID: PMC4928830 DOI: 10.1371/journal.pone.0157881] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/05/2016] [Indexed: 12/01/2022] Open
Abstract
Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world’s most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods.
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Affiliation(s)
- Sonja Hassold
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, Missouri, United States of America
- ISYEB (UMR 7205), Département Systématique et Evolution, Muséum National d’Histoire Naturelle, Paris, France
| | | | | | | | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- * E-mail:
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17
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Hartvig I, Czako M, Kjær ED, Nielsen LR, Theilade I. The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.). PLoS One 2015; 10:e0138231. [PMID: 26375850 PMCID: PMC4573973 DOI: 10.1371/journal.pone.0138231] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/26/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions.
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Affiliation(s)
- Ida Hartvig
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Mihaly Czako
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Erik Dahl Kjær
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Lene Rostgaard Nielsen
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Ida Theilade
- Global Development, Department of Food and Resource Economics, University of Copenhagen, Frederiksberg, Denmark
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18
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Larranaga N, Hormaza JI. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae). FRONTIERS IN PLANT SCIENCE 2015; 6:589. [PMID: 26284104 PMCID: PMC4519677 DOI: 10.3389/fpls.2015.00589] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/16/2015] [Indexed: 05/23/2023]
Abstract
The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL) Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra, and A. purpurea) and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD) data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia) and in an interspecific hybrid (A. cherimola x A. squamosa). The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management.
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Affiliation(s)
| | - José I. Hormaza
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-Universidad de Málaga, Consejo Superior de Investigaciones Científicas)Málaga, Spain
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19
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Efficiency of ITS sequences for DNA barcoding in Passiflora (Passifloraceae). Int J Mol Sci 2015; 16:7289-303. [PMID: 25837628 PMCID: PMC4425017 DOI: 10.3390/ijms16047289] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/21/2015] [Accepted: 03/25/2015] [Indexed: 01/20/2023] Open
Abstract
DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.
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20
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Chen J, Zhao J, Erickson DL, Xia N, Kress WJ. Testing DNA barcodes in closely related species ofCurcuma(Zingiberaceae) from Myanmar and China. Mol Ecol Resour 2014; 15:337-48. [DOI: 10.1111/1755-0998.12319] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; the Chinese Academy of Sciences; No 723 Xingke Road Tianhe District Guangzhou 510650 China
| | - Jietang Zhao
- College of Horticulture; South China Agricultural University; Guangzhou 510642 China
| | - David L. Erickson
- Department of Botany; MRC-166; National Museum of Natural History; Smithsonian Institution; P.O. Box 37012 Washington DC 20013-7012 USA
| | - Nianhe Xia
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; the Chinese Academy of Sciences; No 723 Xingke Road Tianhe District Guangzhou 510650 China
| | - W. John Kress
- Department of Botany; MRC-166; National Museum of Natural History; Smithsonian Institution; P.O. Box 37012 Washington DC 20013-7012 USA
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21
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DNA barcode authentication of saw palmetto herbal dietary supplements. Sci Rep 2013; 3:3518. [PMID: 24343362 PMCID: PMC3865462 DOI: 10.1038/srep03518] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 11/28/2013] [Indexed: 11/09/2022] Open
Abstract
Herbal dietary supplements made from saw palmetto (Serenoa repens; Arecaceae) fruit are commonly consumed to ameliorate benign prostate hyperplasia. A novel DNA mini-barcode assay to accurately identify [specificity = 1.00 (95% confidence interval = 0.74-1.00); sensitivity = 1.00 (95% confidence interval = 0.66-1.00); n = 31] saw palmetto dietary supplements was designed from a DNA barcode reference library created for this purpose. The mini-barcodes were used to estimate the frequency of mislabeled saw palmetto herbal dietary supplements on the market in the United States of America. Of the 37 supplements examined, amplifiable DNA could be extracted from 34 (92%). Mini-barcode analysis of these supplements demonstrated that 29 (85%) contain saw palmetto and that 2 (6%) supplements contain related species that cannot be legally sold as herbal dietary supplements in the United States of America. The identity of 3 (9%) supplements could not be conclusively determined.
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22
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Little DP. A DNA mini-barcode for land plants. Mol Ecol Resour 2013; 14:437-46. [PMID: 24286499 DOI: 10.1111/1755-0998.12194] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/11/2013] [Accepted: 10/18/2013] [Indexed: 11/27/2022]
Abstract
Small portions of the barcode region - mini-barcodes - may be used in place of full-length barcodes to overcome DNA degradation for samples with poor DNA preservation. 591,491,286 rbcL mini-barcode primer combinations were electronically evaluated for PCR universality, and two novel highly universal sets of priming sites were identified. Novel and published rbcL mini-barcode primers were evaluated for PCR amplification [determined with a validated electronic simulation (n = 2765) and empirically (n = 188)], Sanger sequence quality [determined empirically (n = 188)], and taxonomic discrimination [determined empirically (n = 30,472)]. PCR amplification for all mini-barcodes, as estimated by validated electronic simulation, was successful for 90.2-99.8% of species. Overall Sanger sequence quality for mini-barcodes was very low - the best mini-barcode tested produced sequences of adequate quality (B20 ≥ 0.5) for 74.5% of samples. The majority of mini-barcodes provide correct identifications of families in excess of 70.1% of the time. Discriminatory power noticeably decreased at lower taxonomic levels. At the species level, the discriminatory power of the best mini-barcode was less than 38.2%. For samples believed to contain DNA from only one species, an investigator should attempt to sequence, in decreasing order of utility and probability of success, mini-barcodes F (rbcL1/rbcLB), D (F52/R193) and K (F517/R604). For samples believed to contain DNA from more than one species, an investigator should amplify and sequence mini-barcode D (F52/R193).
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Affiliation(s)
- Damon P Little
- Cullman Program for Molecular Systematics, The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY, 10458, USA
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23
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Little DP, Knopf P, Schulz C. DNA barcode identification of Podocarpaceae--the second largest conifer family. PLoS One 2013; 8:e81008. [PMID: 24312258 PMCID: PMC3842326 DOI: 10.1371/journal.pone.0081008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 10/09/2013] [Indexed: 11/28/2022] Open
Abstract
We have generated matK, rbcL, and nrITS2 DNA barcodes for 320 specimens representing all 18 extant genera of the conifer family Podocarpaceae. The sample includes 145 of the 198 recognized species. Comparative analyses of sequence quality and species discrimination were conducted on the 159 individuals from which all three markers were recovered (representing 15 genera and 97 species). The vast majority of sequences were of high quality (B 30 = 0.596-0.989). Even the lowest quality sequences exceeded the minimum requirements of the BARCODE data standard. In the few instances that low quality sequences were generated, the responsible mechanism could not be discerned. There were no statistically significant differences in the discriminatory power of markers or marker combinations (p = 0.05). The discriminatory power of the barcode markers individually and in combination is low (56.7% of species at maximum). In some instances, species discrimination failed in spite of ostensibly useful variation being present (genotypes were shared among species), but in many cases there was simply an absence of sequence variation. Barcode gaps (maximum intraspecific p-distance > minimum interspecific p-distance) were observed in 50.5% of species when all three markers were considered simultaneously. The presence of a barcode gap was not predictive of discrimination success (p = 0.02) and there was no statistically significant difference in the frequency of barcode gaps among markers (p = 0.05). In addition, there was no correlation between number of individuals sampled per species and the presence of a barcode gap (p = 0.27).
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Affiliation(s)
- Damon P. Little
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, United States of America
| | - Patrick Knopf
- Lehrstuhl für Evolution und Biodiversität der Pflanzen, Ruhr–Universität Bochum, Bochum, Nordrhein–Westfalen, Bundesrepublik Deutschland
| | - Christian Schulz
- Lehrstuhl für Evolution und Biodiversität der Pflanzen, Ruhr–Universität Bochum, Bochum, Nordrhein–Westfalen, Bundesrepublik Deutschland
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Dong W, Cheng T, Li C, Xu C, Long P, Chen C, Zhou S. Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set. Mol Ecol Resour 2013; 14:336-43. [PMID: 24119263 DOI: 10.1111/1755-0998.12185] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 09/11/2013] [Accepted: 10/01/2013] [Indexed: 11/26/2022]
Abstract
The ideal DNA barcode for plants remains to be discovered, and the candidate barcode rbcL has been met with considerable skepticism since its proposal. In fact, the variability within this gene has never been fully explored across all plant groups from algae to flowering plants, and its performance as a barcode has not been adequately tested. By analysing all of the rbcL sequences currently available in GenBank, we attempted to determine how well a region of rbcL performs as a barcode in species discrimination. We found that the rbcLb region was more variable than the frequently used rbcLa region. Both universal and plant group-specific primers were designed to amplify rbcLb, and the performance of rbcLa and rbcLb was tested in several ways. Using blast, both regions successfully identified all families and nearly all genera; however, the successful species identification rates varied significantly among plant groups, ranging from 24.58% to 85.50% for rbcLa and from 36.67% to 90.89% for rbcLb. Successful species discrimination ranged from 5.19% to 96.33% for rbcLa and from 22.09% to 98.43% for rbcLb in species-rich families, and from 0 to 88.73% for rbcLa and from 2.04% to 100% for rbcLb in species-rich genera. Both regions performed better for lower plants than for higher plants, although rbcLb performed significantly better than rbcLa overall, particularly for angiosperms. Considering the applicability across plants, easy and unambiguous alignment, high primer universality, high sequence quality and high species discrimination power for lower plants, we suggest rbcLb as a universal plant barcode.
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Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
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