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Binnoubah A, Hamdy R, G. Ragab O, M. El-Taher A, Abou El-Yazied A, A. Safhi F, A. Elzilal H, T. Althobaiti A, M. ALshamrani S, Abd El Moneim D, El-Banhawy A. Anatomical and Molecular Identification of Ornamental Plant Ficus L. Species. PHYTON 2023; 92:1329-1347. [DOI: 10.32604/phyton.2023.026888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/21/2022] [Indexed: 09/02/2023]
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Mahima K, Sunil Kumar KN, Rakhesh KV, Rajeswaran PS, Sharma A, Sathishkumar R. Advancements and future prospective of DNA barcodes in the herbal drug industry. Front Pharmacol 2022; 13:947512. [PMID: 36339543 PMCID: PMC9635000 DOI: 10.3389/fphar.2022.947512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/10/2022] [Indexed: 08/04/2023] Open
Abstract
Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
- Department of Pharmacognosy, Siddha Central Research Institute, Chennai, Tamil Nadu, India
| | | | | | | | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Santiago de Queretaro, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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Mahima K, Umapathy S, Sudhakar JV, Sathishkumar R. Systematic reinstatement of highly sacred Ficuskrishnae based on differences in morphology and DNA barcoding from Ficusbenghalensis (Moraceae). PHYTOKEYS 2021; 186:121-138. [PMID: 35002360 PMCID: PMC8677708 DOI: 10.3897/phytokeys.186.74086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/06/2021] [Indexed: 06/14/2023]
Abstract
Ficuskrishnae is considered as native to India and is well-known for the peculiarity in nature of its cup-shaped leaves where both the vernacular name (Krishna Fig) and specific epithet were derived. The taxonomic status of Ficuskrishnae is still unclear and currently treated as a subspecies or variety under Ficusbenghalensis. In the present study, morphological characters and molecular analysis were employed to address their species delimitation. The spacer markers ITS2 and trnH-psbA were used for constructing phylogenetic trees along with morphometric analysis. Ficuskrishnae distinctly differs from Ficusbenghalensis by having cup-forming leaves and the nature of the aerial roots, stipules, petioles, ostiolar bracts of the receptacle, DNA content, chromosome differences and nodal anatomy. The results showed that the highest divergence is observed in trnH-psbA (20.8 ± 12.2), followed by ITS2 (5.7 ± 3.2). The phylogenetic tree construction using Bayesian analysis showed a divergent boundary between the two species suggesting that F.krishnae could be an independent species, not a variety of F.benghalensis. The present study's findings support the view that these two floras can be treated as different species.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore–641 046, Tamil Nadu, IndiaBharathiar UniversityCoimbatoreIndia
| | - Senthilkumar Umapathy
- Department of Plant Biology and Plant Biotechnology, Madras Christian College, Chennai- 600 059, Tamil Nadu, IndiaMadras Christian CollegeChennaiIndia
| | - Jana Venkata Sudhakar
- Department of Botany, S.R.K Govt. Arts College, Pondicherry University–533 464, Tamil Nadu, India.Pondicherry UniversityPondicherryIndia
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore–641 046, Tamil Nadu, IndiaBharathiar UniversityCoimbatoreIndia
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Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume. DIVERSITY 2021. [DOI: 10.3390/d13120654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima.
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Liu Y, Zhang M, Chen X, Chen X, Hu Y, Gao J, Pan W, Xin Y, Wu J, Du Y, Zhang X. Developing an efficient DNA barcoding system to differentiate between Lilium species. BMC PLANT BIOLOGY 2021; 21:465. [PMID: 34645404 PMCID: PMC8513328 DOI: 10.1186/s12870-021-03229-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Lilium is an important ornamental bulb, possesses medicinal properties, and is also edible. Species within the Lilium genus share very similar morphology and macroscopic characteristics, thus they cannot be easily and clearly distinguished from one another. To date, no efficient species-specific markers have been developed for classifying wild lily species, which poses an issue with further characterizing its medicinal properties. RESULTS To develop a simple and reliable identification system for Lilium, 45 representative species from 6 sections were used to develop a DNA barcoding system, which was based on DNA sequence polymorphisms. In this study, we assessed five commonly used DNA barcode candidates (ITS, rbcL, ycf1b, matK and psbA-trnH) and five novel barcode candidates obtained from highly variable chloroplast genomic regions (trnL-trnF, trnS-trnG, trnF-ndhJ, trnP-psaJ-rpI33 and psbB-psbH). We showed that a set of three novel DNA barcodes (ITS + trnP-psaJ-rpI33 + psbB-psbH) could be efficiently used as a genetic marker to distinguish between lily species, as assessed by methods including DNAsp, BI and ML tree, and Pair Wise Group (PWG). CONCLUSIONS A rapid and reliable DNA barcoding method was developed for all 45 wild Lilium species by using ITS, trnP-psaJ-rpI33, and psbB-psbH as DNA barcoding markers. The method can be used in the classification of wild Lilium species, especially endangered species, and also provides an effective method for selective lily breeding.
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Affiliation(s)
- Yixin Liu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Mingfang Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xuqing Chen
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xi Chen
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yue Hu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Junlian Gao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wenqiang Pan
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China
| | - Yin Xin
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China
| | - Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China.
| | - Yunpeng Du
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Xiuhai Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Mustafa AA, Derise MR, Yong WTL, Rodrigues KF. A Concise Review of Dendrocalamus asper and Related Bamboos: Germplasm Conservation, Propagation and Molecular Biology. PLANTS 2021; 10:plants10091897. [PMID: 34579429 PMCID: PMC8468032 DOI: 10.3390/plants10091897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Bamboos represent an emerging forest resource of economic significance and provide an avenue for sustainable development of forest resources. The development of the commercial bamboo industry is founded upon efficient molecular and technical approaches for the selection and rapid multiplication of elite germplasm for its subsequent propagation via commercial agro-forestry business enterprises. This review will delve into the micropropagation of Dendrocalamus asper, one of the most widely cultivated commercial varieties of bamboo, and will encompass the selection of germplasm, establishment of explants in vitro and micropropagation techniques. The currently available information pertaining to molecular biology, DNA barcoding and breeding, has been included, and potential areas for future research in the area of genetic engineering and gene regulation have been highlighted. This information will be of relevance to both commercial breeders and molecular biologists who have an interest in establishing bamboo as a crop of the future.
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Suriani C, Prasetya E, Harsono T, Manurung J, Prakasa H, Handayani D, Jannah M, Rachmawati Y. DNA Barcoding of Andaliman ( Zanthoxylum acanthopodium DC) from North Sumatra Province of Indonesia Using Maturase K Gene. Trop Life Sci Res 2021; 32:15-28. [PMID: 34367512 PMCID: PMC8300946 DOI: 10.21315/tlsr2021.32.2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Andaliman (Zanthoxylum acanthopodium DC) is a native plant of North Sumatra province. Zanthoxylum acanthopodium is a member of Rutaceae family widely found in northern Sumatra, Indonesia. The aim of this study was to barcode Z. acanthopodium in North Sumatra province, Indonesia based on cpDNA maturase K (matK). Samples were collected in seven localities across six regions of North Sumatra province. Phylogenetic analysis was conducted using Maximum Likelihood method. The results of phylogenetic analysis indicate that Z. acanthopodium is a monophyletic group that is derived from a common ancestor. The results of the phylogenetic tree construction show that there is a grouping of accession between Z. acanthopodium species separate from other species in the Zanthoxylum genus as well as those of the Rutaceae family. The results showed that cpDNA matK marker can effectively be used as DNA barcoding to identify Z. acanthopodium.
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Affiliation(s)
- Cicik Suriani
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan, Jl. Willem Iskandar, Pasar V, Medan Estate, Medan, 20221, North Sumatra, Indonesia
| | - Eko Prasetya
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan, Jl. Willem Iskandar, Pasar V, Medan Estate, Medan, 20221, North Sumatra, Indonesia
| | - Tri Harsono
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan, Jl. Willem Iskandar, Pasar V, Medan Estate, Medan, 20221, North Sumatra, Indonesia
| | - Johannes Manurung
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan, Jl. Willem Iskandar, Pasar V, Medan Estate, Medan, 20221, North Sumatra, Indonesia
| | - Hary Prakasa
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan, Jl. Willem Iskandar, Pasar V, Medan Estate, Medan, 20221, North Sumatra, Indonesia
| | - Dina Handayani
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Medan, Jl. Willem Iskandar, Pasar V, Medan Estate, Medan, 20221, North Sumatra, Indonesia
| | - Miftahul Jannah
- Department of Biology, Faculty of Sciences and Technology, Islamic University of Assyafiiyah, Jl. Jatiwaringin Raya, No 12, East Jakarta,17411 Indonesia
| | - Yuanita Rachmawati
- Department of Biology, Faculty of Sciences and Technology, Islamic State University Sunan Ampel Surabaya, Jl. Ahmad Yani 117 Surabaya, East Java, 60237, Indonesia
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Mahima K, Sudhakar JV, Sathishkumar R. Molecular phylogeny of the Ficus virens complex (Moraceae). Genome 2020; 63:597-606. [PMID: 32822559 DOI: 10.1139/gen-2019-0210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The closely related species present in the subgenera of Urostigma are challenging to classify due to the existence of overlapping morphological characteristics, which makes identification habitually problematic. It is still unresolved whether the species of the Ficus virens complex, which includes F. virens, F. middletonii, F. caulocarpa, F. concinna, and F. superba, are the same or distinct species due to the complexities in classification. To clarify the circumscription between the species and re-evaluate the taxonomical status, morphological characteristics were extensively examined; further, a phylogenetic reconstruction based on two DNA markers (ITS2 and trnH-psbA) in combination with morphological traits was carried out. The phylogenetic tree constructed using the combined morphology and DNA markers revealed that the five species should be demarcated as independent species. This study supports the importance of using both molecular and morphological data for efficient discrimination of species having high similarities. Further investigation into the species present in the subgenera Urostigma may provide additional information regarding the ancestral traits and its evolutionary history.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Jana Venkata Sudhakar
- Department of Botany, S.R.K. Govt. Arts College, Affiliated to Pondicherry University, Yanam 533 464, UT of Puducherry, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
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Oyebanji OO, Chukwuma EC, Bolarinwa KA, Adejobi OI, Adeyemi SB, Ayoola AO. Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers. J Biosci 2020. [DOI: 10.1007/s12038-020-00061-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Volf M, Klimeš P, Lamarre GPA, Redmond CM, Seifert CL, Abe T, Auga J, Anderson-Teixeira K, Basset Y, Beckett S, Butterill PT, Drozd P, Gonzalez-Akre E, Kaman O, Kamata N, Laird-Hopkins B, Libra M, Manumbor M, Miller SE, Molem K, Mottl O, Murakami M, Nakaji T, Plowman NS, Pyszko P, Šigut M, Šipoš J, Tropek R, Weiblen GD, Novotny V. Quantitative assessment of plant-arthropod interactions in forest canopies: A plot-based approach. PLoS One 2019; 14:e0222119. [PMID: 31644586 PMCID: PMC6808442 DOI: 10.1371/journal.pone.0222119] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/21/2019] [Indexed: 11/19/2022] Open
Abstract
Research on canopy arthropods has progressed from species inventories to the study of their interactions and networks, enhancing our understanding of how hyper-diverse communities are maintained. Previous studies often focused on sampling individual tree species, individual trees or their parts. We argue that such selective sampling is not ideal when analyzing interaction network structure, and may lead to erroneous conclusions. We developed practical and reproducible sampling guidelines for the plot-based analysis of arthropod interaction networks in forest canopies. Our sampling protocol focused on insect herbivores (leaf-chewing insect larvae, miners and gallers) and non-flying invertebrate predators (spiders and ants). We quantitatively sampled the focal arthropods from felled trees, or from trees accessed by canopy cranes or cherry pickers in 53 0.1 ha forest plots in five biogeographic regions, comprising 6,280 trees in total. All three methods required a similar sampling effort and provided good foliage accessibility. Furthermore, we compared interaction networks derived from plot-based data to interaction networks derived from simulated non-plot-based data focusing either on common tree species or a representative selection of tree families. All types of non-plot-based data showed highly biased network structure towards higher connectance, higher web asymmetry, and higher nestedness temperature when compared with plot-based data. Furthermore, some types of non-plot-based data showed biased diversity of the associated herbivore species and specificity of their interactions. Plot-based sampling thus appears to be the most rigorous approach for reconstructing realistic, quantitative plant-arthropod interaction networks that are comparable across sites and regions. Studies of plant interactions have greatly benefited from a plot-based approach and we argue that studies of arthropod interactions would benefit in the same way. We conclude that plot-based studies on canopy arthropods would yield important insights into the processes of interaction network assembly and dynamics, which could be maximised via a coordinated network of plot-based study sites.
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Affiliation(s)
- Martin Volf
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- * E-mail:
| | - Petr Klimeš
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Greg P. A. Lamarre
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Conor M. Redmond
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Carlo L. Seifert
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Tomokazu Abe
- Faculty of Science, Chiba University, Chiba, Japan
| | - John Auga
- New Guinea Binatang Research Center, Madang, Papua New Guinea
| | - Kristina Anderson-Teixeira
- Conservation Ecology Center, Smithsonian Conservation Biology Institute; Front Royal, VA, United States of America
- ForestGEO, Smithsonian Tropical Research Institute, Panama City, Panama
| | - Yves Basset
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- ForestGEO, Smithsonian Tropical Research Institute, Panama City, Panama
- Maestria de Entomologia, Universidad de Panama, Panama City, Panama
| | - Saul Beckett
- ForestGEO, Smithsonian Tropical Research Institute, Panama City, Panama
| | - Philip T. Butterill
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Pavel Drozd
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Erika Gonzalez-Akre
- Conservation Ecology Center, Smithsonian Conservation Biology Institute; Front Royal, VA, United States of America
| | - Ondřej Kaman
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Naoto Kamata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Furano, Japan
| | - Benita Laird-Hopkins
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Martin Libra
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Markus Manumbor
- New Guinea Binatang Research Center, Madang, Papua New Guinea
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Kenneth Molem
- New Guinea Binatang Research Center, Madang, Papua New Guinea
| | - Ondřej Mottl
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | | | - Tatsuro Nakaji
- Tomakomai Experimental Forest, Hokkaido University, Tomakomai, Japan
| | - Nichola S. Plowman
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Petr Pyszko
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Šigut
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Šipoš
- Institute of Botany, Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Brno, Czech Republic
| | - Robert Tropek
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - George D. Weiblen
- Bell Museum and Department of Plant & Microbial Biology, University of Minnesota, Saint Paul, MN, United States of America
| | - Vojtech Novotny
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
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11
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Alfeche NKG, Binag SDA, Medecilo MMP, Alejandro GJD. Standard reference material (SRM) DNA barcode library approach for authenticating Antidesma bunius (L.) Spreng. (bignay) derived herbal medicinal products. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:1777-1786. [PMID: 31596175 DOI: 10.1080/19440049.2019.1670868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the Philippines, the herbal medicinal product (HMP) market is flourishing due to the abundance of pharmacologically important species, and the high level of ethnomedicinal knowledge still widely accepted by the public. As such, herbal products from Antidesma bunius (L.) Spreng., locally known as bignay, are popular as medicine for various ailments of the circulatory and digestive systems. Though efficacy is guaranteed, the authenticity of the marketed products is still in question as several other herbal plants can provide the said benefits. Similar morphology between wild species also hinders species identification and contributes confusion especially to the general consumer. The authenticity of the marketed HMPs was established by means of DNA barcoding techniques which offers quick and reliable species identification by means of (1) the Basic Local Alignment Search Tool (BLASTn) and (2) the establishment of the first Standard Reference Material (SRM) Herbal barcode library for Antidesma spp. A total of 56 gene accessions from matK-psbA-trnH-rbcL sequences of 9 wild Antidesma spp. comprised the SRM which was then used to confirm the identity of 11 randomly sampled bignay-derived HMPs. Following the BLASTn and the SRM (maximum likelihood tree reconstruction) criterion, the subjected sequences revealed that only three of the 11 HMPs were authentic A. bunius-derived products. The other eight HMPs contained substitutes that were either fillers or different herbal medicinal plant not indicated in the product labels. These results indicate that product safety should be reinforced with complete HMP authentication using traditional methods supported by molecular data.
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Affiliation(s)
- Niña Kathryn G Alfeche
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines.,Plant Sciences Laboratory, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Center, University of Santo Tomas, Manila, Philippines
| | - Sam Dominic A Binag
- Plant Sciences Laboratory, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Center, University of Santo Tomas, Manila, Philippines
| | - Maria Melanie P Medecilo
- Biological Sciences Department and University Research Office, De La Salle University - Dasmarinas, Cavite, Philippines
| | - Grecebio Jonathan D Alejandro
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines.,Plant Sciences Laboratory, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Center, University of Santo Tomas, Manila, Philippines
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12
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Zhang Z, Wang X, Zhang Z, Yao H, Zhang X, Zhang Y, Zhang B. The impact of genetic diversity on the accuracy of DNA barcoding to identify species: A study on the genus Phellodendron. Ecol Evol 2019; 9:10723-10733. [PMID: 31624576 PMCID: PMC6787823 DOI: 10.1002/ece3.5590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 11/30/2022] Open
Abstract
DNA barcoding is widely used in species identification, but there is considerable controversy regarding the extent of sampling in research methods. Some scholars have proposed that this small sample size underestimates the intraspecific genetic diversity, which would impact on the accuracy of DNA barcoding to identify species. In study, we selected all Phellodendron species (including P. amurense Rupr., P. chinense Schneid., and P. chinense var. glabriusculum Schneid.) as the materials, collected 59 P. amurense samples from 35 populations greatly to represent the genetic diversity, and analyzed the haplotype, genetic distance, barcoding gap, and Neighbor-Joining (NJ) trees based on psbA-trnH and internal transcribed spacer gene sequences. Additionally, a sampling simulation was conducted to assess the correlation between genetic diversity and the number of populations. Finally, analysis of critical geographical populations was performed. Based on analysis of haplotype, genetic distance, barcoding gap, and NJ trees, we found that eight P. amurense samples impacted on the effectiveness of DNA barcoding, which genetic information were very important to identify Phellodendron species. Moreover, the result of the NJ tree analysis performed the small-scale P. amurense sample size did not completely match the objective phylogenetic relationship in Phellodendron. In simulation sampling analysis, the data showed the genetic diversity indexes at the same population level gradually decreased and stabilized as the number of simulation sampling populations increased. We found that 1-2 samples from over 24 populations based on uniform geographical distribution could represent 80% of the genetic diversity of P. amurense and ensure authenticity and reliability of DNA barcoding. Thus, we proposed it is particularly important adequately samples to cover infraspecific genetic diversity in order to ensure identification accuracy of DNA barcoding.
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Affiliation(s)
- Zhi‐peng Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Xiao‐yue Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Zhao Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Hui Yao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Xiao‐mei Zhang
- China‐ASEAN Traditional Medicine Cooperation and Exchange CenterGuangxi Botanical Garden of Medicinal PlantsNanningChina
| | - Yang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Ben‐gang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal MedicineMinistry of Education/Institute of Medicinal Plant DevelopmentChinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
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Afzan A, Kasim N, Ismail NH, Azmi N, Ali AM, Mat N, Wolfender JL. Differentiation of Ficus deltoidea varieties and chemical marker determination by UHPLC-TOFMS metabolomics for establishing quality control criteria of this popular Malaysian medicinal herb. Metabolomics 2019; 15:35. [PMID: 30830457 DOI: 10.1007/s11306-019-1489-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Ficus deltoidea Jack (Moraceae) is a plant used in Malaysia for various diseases including as a supplement in diabetes management. Morphology distinction of the 7 main varieties (var. angustifolia, var. bilobata, var. deltoidea, var. intermedia, var. kunstleri, var. motleyana and var. trengganuensis) is challenging due to the extreme leaf heterophylly and unclear varietal boundaries, making it difficult for quality control of F. deltoidea products. OBJECTIVE We aimed to compare the phytochemical composition of 7 varieties growing in different conditions at various geographical locations. We also aimed to establish the quality control markers for the authentication of these varieties. METHODS We applied untargeted UHPLC-TOFMS metabolomics to discriminate 100 leaf samples of F. deltoidea collected from 6 locations in Malaysia. A genetic analysis on 21 leaf samples was also performed to validate the chemotaxonomy differentiation. RESULTS The PCA and HCA analysis revealed the existence of 3 chemotypes based on the differentiation in the flavonoid content. The PLS-DA analysis identified 15 glycosylated flavone markers together with 1 furanocoumarin. These markers were always consistent for the respective varieties, regardless of the geographical locations and growing conditions. The chemotaxonomy differentiation was in agreement with the DNA sequencing. In particular, var. bilobata accession which showed divergent morphology was also differentiated by the chemical fingerprints and genotype. CONCLUSION Chemotype differentiation based on the flavonoid fingerprints along with the proposed markers provide a powerful identification tool to complement morphology and genetic analyses for the quality control of raw materials and products from F. deltoidea.
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Affiliation(s)
- Adlin Afzan
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, Rue Michel-Servet 1, 1206, Geneva, Switzerland
- Phytochemistry Unit, Herbal Medicine Research Center, Institute for Medical Research, Jalan Pahang, 50588, Kuala Lumpur, Malaysia
| | - Noraini Kasim
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA, Kampus Puncak Alam, 42300, Selangor, Malaysia
| | - Nor Hadiani Ismail
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA, Kampus Puncak Alam, 42300, Selangor, Malaysia
| | - Norfaizura Azmi
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200, Besut, Terengganu, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200, Besut, Terengganu, Malaysia
- Institute of Agropolis, Universiti Sultan Zainal Abidin, Campus Besut, 22200, Besut, Terengganu, Malaysia
- Natural Medicine Center, Universiti Islam, Cyberjaya, 63000, Cyberjaya, Selangor, Malaysia
| | - Nashriyah Mat
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, 22200, Besut, Terengganu, Malaysia
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, Rue Michel-Servet 1, 1206, Geneva, Switzerland.
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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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DNA Barcoding Analysis and Phylogenetic Relation of Mangroves in Guangdong Province, China. FORESTS 2019. [DOI: 10.3390/f10010056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mangroves are distributed in the transition zone between sea and land, mostly in tropical and subtropical areas. They provide important ecosystem services and are therefore economically valuable. DNA barcoding is a useful tool for species identification and phylogenetic reconstruction. To evaluate the effectiveness of DNA barcoding in identifying mangrove species, we sampled 135 individuals representing 23 species, 22 genera, and 17 families from Zhanjiang, Shenzhen, Huizhou, and Shantou in the Guangdong province, China. We tested the universality of four DNA barcodes, namely rbcL, matK, trnH-psbA, and the internal transcribed spacer of nuclear ribosomal DNA (ITS), and examined their efficacy for species identification and the phylogenetic reconstruction of mangroves. The success rates for PCR amplification of rbcL, matK, trnH-psbA, and ITS were 100%, 80.29% ± 8.48%, 99.38% ± 1.25%, and 97.18% ± 3.25%, respectively, and the rates of DNA sequencing were 100%, 75.04% ± 6.26%, 94.57% ± 5.06%, and 83.35% ± 4.05%, respectively. These results suggest that both rbcL and trnH–psbA are universal in mangrove species from the Guangdong province. The highest success rate for species identification was 84.48% ± 12.09% with trnH-psbA, followed by rbcL (82.16% ± 9.68%), ITS (66.48% ± 5.97%), and matK (65.09% ± 6.00%), which increased to 91.25% ± 9.78% with the addition of rbcL. Additionally, the identification rate of mangroves was not significantly different between rbcL + trnH-psbA and other random fragment combinations. In conclusion, rbcL and trnH-psbA were the most suitable DNA barcode fragments for species identification in mangrove plants. When the phylogenetic relationships were constructed with random fragment combinations, the optimal evolutionary tree with high supporting values (86.33% ± 4.16%) was established using the combination of matK + rbcL + trnH-psbA + ITS in mangroves. In total, the 476 newly acquired sequences in this study lay the foundation for a DNA barcode database of mangroves.
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Arshed MJC, Valdez MB, Alejandro GJD. Evaluating the Feasibility of Five Candidate DNA Barcoding Loci for Philippine Lasianthus Jack ( Lasiantheae: Rubiaceae). Pharmacogn Mag 2017; 13:553-558. [PMID: 29200712 PMCID: PMC5701390 DOI: 10.4103/pm.pm_1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/01/2017] [Indexed: 11/04/2022] Open
Abstract
Introduction The pantropical genus Lasianthus Jack is identified for high phenotypic plasticity making traditional taxonomic identification difficult. Having some members with important medicinal properties, a precise complimentary identification through DNA barcoding is needed for species delineation. Materials and Methods In this study, 12 samples representing six Philippine Lasianthus species were used to determine the most efficient barcoding loci among the cpDNA markers (matK, rbcL, rps16, and trnT-F) and nrDNA (ITS) based on the criteria of universality, discriminatory power, and resolution of species. Results The results revealed that ITS has the recommended primer universality, greatest interspecific divergences, and average resolution of species. Among the cpDNA markers, matK and rbcL are recommended but with minimal resolution of species. While trnT-F showed moderate interspecific variations and resolution of Lasianthus species, rps16 has the lowest interspecific divergence and resolution of species. Conclusion Consequently, ITS is the potential ideal DNA barcode for Lasianthus species. SUMMARY ITS, matK, and rps16 markers have the excellent amplification and sequence qualityITS marker has the highest interspecific divergence with the maximum values, followed by matK, rbcL, trnT-F, and rps16, respectivelyAll markers except rps16 yielded average resolution to Lasianthus speciesITS marker is the most ideal locus in terms of excellent universality, high interspecific discriminatory ability, and average species resolution. Abbreviations used: ITS: Internal Transcribe Spacer, matK: maturase K, rbcL: ribulose-1,5-biphospahte-carboxylase, rps16: ribosomal protein 16 small subunit gene.
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Affiliation(s)
| | - Marcos B Valdez
- Department of Biological Sciences, Institute of Arts and Sciences, Far Eastern University, Nicanor Reyes Street, Sampaloc, 1008 Manila, Philippines
| | - Grecebio Jonathan D Alejandro
- The Graduate School and Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd, 1015 Manila, Philippines
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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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18
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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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Saddhe AA, Jamdade RA, Kumar K. Evaluation of multilocus marker efficacy for delineating mangrove species of West Coast India. PLoS One 2017; 12:e0183245. [PMID: 28817640 PMCID: PMC5560660 DOI: 10.1371/journal.pone.0183245] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 08/01/2017] [Indexed: 01/31/2023] Open
Abstract
The plant DNA barcoding is a complex and requires more than one marker(s) as compared to animal barcoding. Mangroves are diverse estuarine ecosystem prevalent in the tropical and subtropical zone, but anthropogenic activity turned them into the vulnerable ecosystem. There is a need to build a molecular reference library of mangrove plant species based on molecular barcode marker along with morphological characteristics. In this study, we tested the core plant barcode (rbcL and matK) and four promising complementary barcodes (ITS2, psbK-psbI, rpoC1 and atpF-atpH) in 14 mangroves species belonging to 5 families from West Coast India. Data analysis was performed based on barcode gap analysis, intra- and inter-specific genetic distance, Automated Barcode Gap Discovery (ABGD), TaxonDNA (BM, BCM), Poisson Tree Processes (PTP) and General Mixed Yule-coalescent (GMYC). matK+ITS2 marker based on GMYC method resolved 57.14% of mangroves species and TaxonDNA, ABGD, and PTP discriminated 42.85% of mangrove species. With a single locus analysis, ITS2 exhibited the higher discriminatory power (87.82%) and combinations of matK + ITS2 provided the highest discrimination success (89.74%) rate except for Avicennia genus. Further, we explored 3 additional markers (psbK-psbI, rpoC1, and atpF-atpH) for Avicennia genera (A. alba, A. officinalis and A. marina) and atpF-atpH locus was able to discriminate three species of Avicennia genera. Our analysis underscored the efficacy of matK + ITS2 markers along with atpF-atpH as the best combination for mangrove identification in West Coast India regions.
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Affiliation(s)
- Ankush Ashok Saddhe
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, India
| | | | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K. K. Birla Goa Campus, Goa, India
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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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O. Elansary H, Ashfaq M, Ali HM, Yessoufou K. The first initiative of DNA barcoding of ornamental plants from Egypt and potential applications in horticulture industry. PLoS One 2017; 12:e0172170. [PMID: 28199378 PMCID: PMC5310869 DOI: 10.1371/journal.pone.0172170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/31/2017] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding relies on short and standardized gene regions to identify species. The agricultural and horticultural applications of barcoding such as for marketplace regulation and copyright protection remain poorly explored. This study examines the effectiveness of the standard plant barcode markers (matK and rbcL) for the identification of plant species in private and public nurseries in northern Egypt. These two markers were sequenced from 225 specimens of 161 species and 62 plant families of horticultural importance. The sequence recovery was similar for rbcL (96.4%) and matK (84%), but the number of specimens assigned correctly to the respective genera and species was lower for rbcL (75% and 29%) than matK (85% and 40%). The combination of rbcL and matK brought the number of correct generic and species assignments to 83.4% and 40%, respectively. Individually, the efficiency of both markers varied among different plant families; for example, all palm specimens (Arecaceae) were correctly assigned to species while only one individual of Asteraceae was correctly assigned to species. Further, barcodes reliably assigned ornamental horticultural and medicinal plants correctly to genus while they showed a lower or no success in assigning these plants to species and cultivars. For future, we recommend the combination of a complementary barcode (e.g. ITS or trnH-psbA) with rbcL + matK to increase the performance of taxa identification. By aiding species identification of horticultural crops and ornamental palms, the analysis of the barcode regions will have large impact on horticultural industry.
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Affiliation(s)
- Hosam O. Elansary
- Floriculture, Ornamental Horticulture and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
- * E-mail: ,
| | - Muhammad Ashfaq
- Biodiversity Institute of Ontario, University of Guelph, ON, Guelph, Canada
| | - Hayssam M. Ali
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Timber Trees Research Department, Sabahia Horticulture Research Station, Horticulture Research Institute, Agriculture Research Center, Alexandria, Egypt
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, APK campus, Johannesburg, South Africa
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22
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Wang DY, Wang Q, Wang YL, Xiang XG, Huang LQ, Jin XH. Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera. PLoS One 2017; 12:e0170286. [PMID: 28182623 PMCID: PMC5300163 DOI: 10.1371/journal.pone.0170286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/03/2017] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera.
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Affiliation(s)
- De-Yi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Wang
- Baotou Medical College, Donghe District, Baotou City, Inner Mongolia, China
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lu-Qi Huang
- National Resource Centre for Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Menglun, Mengla, Yunnan, China
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Saddhe AA, Jamdade RA, Kumar K. Assessment of mangroves from Goa, west coast India using DNA barcode. SPRINGERPLUS 2016; 5:1554. [PMID: 27652127 PMCID: PMC5021661 DOI: 10.1186/s40064-016-3191-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 09/01/2016] [Indexed: 11/16/2022]
Abstract
Mangroves are salt-tolerant forest ecosystems of tropical and subtropical intertidal regions. They are among most productive, diverse, biologically important ecosystem and inclined toward threatened system. Identification of mangrove species is of critical importance in conserving and utilizing biodiversity, which apparently hindered by a lack of taxonomic expertise. In recent years, DNA barcoding using plastid markers rbcL and matK has been suggested as an effective method to enrich traditional taxonomic expertise for rapid species identification and biodiversity inventories. In the present study, we performed assessment of available 14 mangrove species of Goa, west coast India based on core DNA barcode markers, rbcL and matK. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in rbcL (97.7 %) and matK (95.5 %) region. The two candidate chloroplast barcoding regions (rbcL, matK) yielded barcode gaps. Our results clearly demonstrated that matK locus assigned highest correct identification rates (72.09 %) based on TaxonDNA Best Match criteria. The concatenated rbcL + matK loci were able to adequately discriminate all mangrove genera and species to some extent except those in Rhizophora, Sonneratia and Avicennia. Our study provides the first endorsement of the species resolution among mangroves using plastid genes with few exceptions. Our future work will be focused on evaluation of other barcode markers to delineate complete resolution of mangrove species and identification of putative hybrids.
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Affiliation(s)
- Ankush Ashok Saddhe
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa Campus, Sancoale, Goa 403726 India
| | - Rahul Arvind Jamdade
- Department of Zoology, Yashwantrao Chavan Institute of Science, Satara, Maharashtra 415001 India
| | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa Campus, Sancoale, Goa 403726 India
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Olivar JEC, Alaba JPEP, Atienza JFM, Tan JJS, Umali MT, Alejandro GJD. Establishment of a standard reference material (SRM) herbal DNA barcode library of Vitex negundo L. (lagundi) for quality control measures. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2016; 33:741-8. [PMID: 26982211 DOI: 10.1080/19440049.2016.1166525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The majority of the population in the Philippines relies on herbal products as their primary source for their healthcare needs. After the recognition of Vitex negundo L. (lagundi) as an important and effective alternative medicine for cough, sore throat, asthma and fever by the Philippine Department of Health (DOH), there was an increase in the production of lagundi-based herbal products in the form of teas, capsules and syrups. The efficiency of these products is greatly reliant on the use of authentic plant material, and to this day no standard protocol has been established to authenticate plant materials. DNA barcoding offers a quick and reliable species authentication tool, but its application to plant material has been less successful due to (1) lack of a standard DNA barcoding loci in plants and (2) poor DNA yield from powderised plant products. This study reports the successful application of DNA barcoding in the authentication of five V. negundo herbal products sold in the Philippines. Also, the first standard reference material (SRM) herbal library for the recognition of authentic V. negundo samples was established using 42 gene accessions of ITS, psbA-trnH and matK barcoding loci. Authentication of the herbal products utilised the SRM following the BLASTn and maximum-likelihood (ML) tree construction criterion. Barcode sequences were retrieved for ITS and psbA-trnH of all products tested and the results of the study revealed that only one out of five herbal products satisfied both BLASTn and ML criterion and was considered to contain authentic V. negundo. The results prompt the urgent need to utilise DNA barcoding in authenticating herbal products available in the Philippine market. Authentication of these products will secure consumer health by preventing the negative effects of adulteration, substitution and contamination.
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Affiliation(s)
- Jay Edneil C Olivar
- a The Graduate School , University of Santo Tomas , España , Manila , Philippines.,b Research Center for the Natural and Applied Sciences , University of Santo Tomas , España , Manila , Philippines
| | - Joanner Paulus Erik P Alaba
- c Department of Biological Sciences, College of Science , University of Santo Tomas , España , Manila , Philippines
| | - Jose Francisco M Atienza
- c Department of Biological Sciences, College of Science , University of Santo Tomas , España , Manila , Philippines
| | - Jerick Jeffrey S Tan
- c Department of Biological Sciences, College of Science , University of Santo Tomas , España , Manila , Philippines
| | - Maximo T Umali
- c Department of Biological Sciences, College of Science , University of Santo Tomas , España , Manila , Philippines
| | - Grecebio Jonathan D Alejandro
- a The Graduate School , University of Santo Tomas , España , Manila , Philippines.,b Research Center for the Natural and Applied Sciences , University of Santo Tomas , España , Manila , Philippines.,c Department of Biological Sciences, College of Science , University of Santo Tomas , España , Manila , Philippines
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25
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Liu J, Yan HF, Ge XJ. The Use of DNA Barcoding on Recently Diverged Species in the Genus Gentiana (Gentianaceae) in China. PLoS One 2016; 11:e0153008. [PMID: 27050315 PMCID: PMC4822852 DOI: 10.1371/journal.pone.0153008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/21/2016] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding of plants poses particular challenges, especially in differentiating, recently diverged taxa. The genus Gentiana (Gentianaceae) is a species-rich plant group which rapidly radiated in the Himalaya-Hengduan Mountains in China. In this study, we tested the core plant barcode (rbcL + matK) and three promising complementary barcodes (trnH-psbA, ITS and ITS2) in 30 Gentiana species across 6 sections using three methods (the genetic distance-based method, Best Close Match and tree-based method). rbcL had the highest PCR efficiency and sequencing success (100%), while the lowest sequence recoverability was from ITS (68.35%). The presence of indels and inversions in trnH-psbA in Gentiana led to difficulties in sequence alignment. When using a single region for analysis, ITS exhibited the highest discriminatory power (60%-74.42%). Of the combinations, matK + ITS provided the highest discrimination success (71.43%-88.24%) and is recommended as the DNA barcode for the genus Gentiana. DNA barcoding proved effective in assigning most species to sections, though it performed poorly in some closely related species in sect. Cruciata because of hybridization events. Our analysis suggests that the status of G. pseudosquarrosa needs to be studied further. The utility of DNA barcoding was also verified in authenticating 'Qin-Jiao' Gentiana medicinal plants (G. macrophylla, G. crassicaulis, G. straminea, and G. dahurica), which can help ensure safe and correct usage of these well-known Chinese traditional medicinal herbs.
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Affiliation(s)
- Juan Liu
- Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, Jiangxi Agriculture University, Nanchang, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
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Feng S, Jiang Y, Wang S, Jiang M, Chen Z, Ying Q, Wang H. Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study. Int J Mol Sci 2015; 16:21975-88. [PMID: 26378526 PMCID: PMC4613292 DOI: 10.3390/ijms160921975] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/22/2022] Open
Abstract
The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the application of the ITS2 region in barcoding and phylogenetic analyses of Dendrobium species (Orchidaceae). For barcoding, ITS2 regions of 43 samples in Dendrobium were amplified. In combination with sequences from GenBank, the sequences were aligned using Clustal W and genetic distances were computed using MEGA V5.1. The success rate of PCR amplification and sequencing was 100%. There was a significant divergence between the inter- and intra-specific genetic distances of ITS2 regions, while the presence of a barcoding gap was obvious. Based on the BLAST1, nearest distance and TaxonGAP methods, our results showed that the ITS2 regions could successfully identify the species of most Dendrobium samples examined; Second, we used ITS2 as a DNA marker to infer phylogenetic relationships of 64 Dendrobium species. The results showed that cluster analysis using the ITS2 region mainly supported the relationship between the species of Dendrobium established by traditional morphological methods and many previous molecular analyses. To sum up, the ITS2 region can not only be used as an efficient barcode to identify Dendrobium species, but also has the potential to contribute to the phylogenetic analysis of the genus Dendrobium.
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Affiliation(s)
- Shangguo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - Yan Jiang
- Zhejiang Institute of Chinese Meteria Medica, Hangzhou 310023, China.
| | - Shang Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
| | - Mengying Jiang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
| | - Zhe Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
| | - Qicai Ying
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310018, China.
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Yan HF, Liu YJ, Xie XF, Zhang CY, Hu CM, Hao G, Ge XJ. DNA barcoding evaluation and its taxonomic implications in the species-rich genus Primula L. in China. PLoS One 2015; 10:e0122903. [PMID: 25875620 PMCID: PMC4395239 DOI: 10.1371/journal.pone.0122903] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/24/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Primula is extremely diverse in the east Himalaya-Hengduan Mountains (HHM) in China as a result of rapid radiation. In order to overcome the difficulty of morphological classification of this genus, we surveyed three plastid regions (rbcL, matK, and trnH-psbA) and two nuclear markers (ITS and ITS2) from 227 accessions representing 66 Primula species across 18 sections, to assess their discriminatory power as barcodes. We found that ITS alone or combined with plastid regions showed the best discrimination across different infrageneric ranks and at species level. We suggest rbcL + matK + ITS as the first choice at present to barcode Primula plants. Although the present barcoding combination performed poorly in many closely related species of Primula, it still provided many new insights into current Primula taxonomy, such as the underlying presence of cryptic species, and several potential improper taxonomic treatments. DNA barcoding is one useful technique in the integrative taxonomy of the genus Primula, but it still requires further efforts to improve its effectiveness in some taxonomically challenging groups.
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Affiliation(s)
- Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yun-Jiao Liu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xiu-Feng Xie
- Tropical Agriculture department, Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, China
| | - Cai-Yun Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chi-Ming Hu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- * E-mail: (GH); (XJG)
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (GH); (XJG)
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28
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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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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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Liu J, Yan HF, Newmaster SG, Pei N, Ragupathy S, Ge XJ. The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12276] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Juan Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
| | - Steven G. Newmaster
- Centre for Biodiversity Genomics; Biodiversity Institute of Ontario (BIO); University of Guelph; Guelph ON N1G 2W1 Canada
| | - Nancai Pei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
| | - Subramanyam Ragupathy
- Centre for Biodiversity Genomics; Biodiversity Institute of Ontario (BIO); University of Guelph; Guelph ON N1G 2W1 Canada
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
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31
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Kim HM, Oh SH, Bhandari GS, Kim CS, Park CW. DNA barcoding of Orchidaceae in Korea. Mol Ecol Resour 2013; 14:499-507. [PMID: 24267156 DOI: 10.1111/1755-0998.12207] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/12/2013] [Accepted: 11/18/2013] [Indexed: 11/26/2022]
Abstract
Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK-psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF-atpH IGS (0.0648), trnH-psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH-psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.
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Affiliation(s)
- Hye Min Kim
- School of Biological Sciences, Seoul National University, Seoul, 151-747, Korea
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S Alves TL, Chauveau O, Eggers L, de Souza-Chies TT. Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus. Mol Ecol Resour 2013; 14:324-35. [PMID: 24119215 DOI: 10.1111/1755-0998.12182] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/19/2013] [Accepted: 09/29/2013] [Indexed: 11/28/2022]
Abstract
DNA barcoding aims to develop an efficient tool for species identification based on short and standardized DNA sequences. In this study, the DNA barcode paradigm was tested among the genera of the tribe Sisyrinchieae (Iridoideae). Sisyrinchium, with more than 77% of the species richness in the tribe, is a taxonomically complex genus. A total of 185 samples belonging to 98 species of Sisyrinchium, Olsynium, Orthrosanthus and Solenomelus were tested using matK, trnH-psbA and internal transcribed spacer (ITS). Candidate DNA barcodes were analysed either as single markers or in combination. Detection of a barcoding gap, similarity-based methods and tree-based analyses were used to assess the discrimination efficiency of DNA barcodes. The levels of species identification obtained from plastid barcodes were low and ranged from 17.35% to 20.41% for matK and 5.11% to 7.14% for trnH-psbA. The ITS provided better results with 30.61-38.78% of species identified. The analyses of the combined data sets did not result in a significant improvement in the discrimination rate. Among the tree-based methods, the best taxonomic resolution was obtained with Bayesian inference, particularly when the three data sets were combined. The study illustrates the difficulties for DNA barcoding to identify species in evolutionary complex lineages. Plastid markers are not recommended for barcoding Sisyrinchium due to the low discrimination power observed. ITS gave better results and may be used as a starting point for species identification.
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Affiliation(s)
- Tiago L S Alves
- Programa de Pós-Graduação em Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500 - Prédio 43433, 91501-970, Porto Alegre, Brazil
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33
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Saarela JM, Sokoloff PC, Gillespie LJ, Consaul LL, Bull RD. DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. PLoS One 2013; 8:e77982. [PMID: 24348895 PMCID: PMC3865322 DOI: 10.1371/journal.pone.0077982] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/08/2013] [Indexed: 01/16/2023] Open
Abstract
Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.
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Affiliation(s)
- Jeffery M. Saarela
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Paul C. Sokoloff
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Lynn J. Gillespie
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Laurie L. Consaul
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Roger D. Bull
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
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