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DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates. DIVERSITY 2022. [DOI: 10.3390/d14040262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The need for herbal medicinal plants is steadily increasing. Hence, the accurate identification of plant material has become vital for safe usage, avoiding adulteration, and medicinal plant trading. DNA barcoding has shown to be a valuable molecular identification tool for medicinal plants, ensuring the safety and efficacy of plant materials of therapeutic significance. Using morphological characters in genera with closely related species, species delimitation is often difficult. Here, we evaluated the capability of the nuclear barcode ITS2 and plastid DNA barcodes rbcL and matK to identify 20 medicinally important plant species of Caryophyllales. In our analysis, we applied an integrative approach for species discrimination using pairwise distance-based unsupervised operational taxonomic unit “OTU picking” methods, viz., ABGD (Automated Barcode Gap Analysis) and ASAP (Assemble Species by Automatic Partitioning). Along with the unsupervised OTU picking methods, Supervised Machine Learning methods (SML) were also implemented to recognize divergent taxa. Our results indicated that ITS2 was more successful in distinguishing between examined species, implying that it could be used to detect the contamination and adulteration of these medicinally important plants. Moreover, this study suggests that the combination of more than one method could assist in the resolution of morphologically similar or closely related taxa.
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The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants. Sci Rep 2021; 11:1424. [PMID: 33446865 PMCID: PMC7809279 DOI: 10.1038/s41598-021-81087-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/04/2021] [Indexed: 11/08/2022] Open
Abstract
DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.
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Kolter A, Gemeinholzer B. Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases. Genome 2020; 64:265-298. [PMID: 32649839 DOI: 10.1139/gen-2019-0198] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The problem of low species-level identification rates in plants by DNA barcoding is exacerbated by the fact that reference databases are far from being comprehensive. We investigate the impact of increased sampling depth on identification success by analyzing the efficacy of established plant barcode marker sequences (rbcL, matK, trnL-trnF, psbA-trnH, ITS). Adding sequences of the same species to the reference database led to an increase in correct species assignment of +10.9% for rbcL and +19.0% for ITS. Simultaneously, erroneous identification dropped from ∼40% to ∼12.5%. Despite its evolutionary constraints, ITS showed the highest identification rate and identification gain by increased sampling effort, which makes it a very suitable marker in the planning phase of a barcode study. The limited sequence availability of trnL-trnF is problematic for an otherwise very promising plastid plant barcoding marker. Future developments in machine learning algorithms have the potential to give new impetus to plant barcoding, but are dependent on extensive reference databases. We expect that our results will be incorporated into future plans for the development of DNA barcoding reference databases and will lead to these being developed with greater depth and taxonomic coverage.
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Affiliation(s)
- Andreas Kolter
- Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany.,Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany
| | - Birgit Gemeinholzer
- Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany.,Justus Liebig University Giessen, Systematic Botany, Heinrich-Buff-Ring 38, Giessen, Hessen, DE 35390, Germany
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Yang J, Vázquez L, Chen X, Li H, Zhang H, Liu Z, Zhao G. Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks ( Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes. FRONTIERS IN PLANT SCIENCE 2017; 8:816. [PMID: 28579999 PMCID: PMC5437370 DOI: 10.3389/fpls.2017.00816] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/01/2017] [Indexed: 05/04/2023]
Abstract
Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species (Quercus rubra and Castanea mollissima) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in Quercus subgenus Quercus, a diverse species group without sufficient molecular differentiation. With the comparison, nine and 14 plastid markers were selected as barcoding and phylogeographic candidates for the Chinese oaks. Five (psbA-trnH, matK-trnK, ycf3-trnS, matK, and ycf1) of the nine plastid candidate barcodes, with the addition of newly designed ITS and a single-copy nuclear gene (SAP), were then tested on 35 Chinese oak species employing four different barcoding approaches (genetic distance-, BLAST-, character-, and tree-based methods). The four methods showed different species identification powers with character-based method performing the best. Of the seven barcodes tested, a barcoding gap was absent in all of them across the Chinese oaks, while ITS and psbA-trnH provided the highest species resolution (30.30%) with the character- and BLAST-based methods, respectively. The six-marker combination (psbA-trnH + matK-trnK + matK + ycf1 + ITS + SAP) showed the best species resolution (84.85%) using the character-based method for barcoding the Chinese oaks. The barcoding results provided additional implications for taxonomy of the Chinese oaks in subg. Quercus, basically identifying three major infrageneric clades of the Chinese oaks (corresponding to Groups Quercus, Cerris, and Ilex) referenced to previous phylogenetic classification of Quercus. While the morphology-based allocations proposed for the Chinese oaks in subg. Quercus were challenged. A low variation rate of the chloroplast genome, and complex speciation patterns involving incomplete lineage sorting, interspecific hybridization and introgression, possibly have negative impacts on the species assignment and phylogeny of oak species.
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Affiliation(s)
- Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Lucía Vázquez
- Biology Department, University of Illinois at SpringfieldSpringfield, IL, United States
| | - Xiaodan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Huimin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Hao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Zhanlin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest UniversityXi'an, China
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Zou S, Fei C, Wang C, Gao Z, Bao Y, He M, Wang C. How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae). Sci Rep 2016; 6:36822. [PMID: 27827440 PMCID: PMC5101840 DOI: 10.1038/srep36822] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/21/2016] [Indexed: 12/17/2022] Open
Abstract
Microalgae identification is extremely difficult. The efficiency of DNA barcoding in microalgae identification involves ideal gene markers and approaches employed, which however, is still under the way. Although Scenedesmus has obtained much research in producing lipids its identification is difficult. Here we present a comprehensive coalescent, distance and character-based DNA barcoding for 118 Scenedesmus strains based on rbcL, tufA, ITS and 16S. The four genes, and their combined data rbcL + tufA + ITS + 16S, rbcL + tufA and ITS + 16S were analyzed by all of GMYC, P ID, PTP, ABGD, and character-based barcoding respectively. It was apparent that the three combined gene data showed a higher proportion of resolution success than the single gene. In comparison, the GMYC and PTP analysis produced more taxonomic lineages. The ABGD generated various resolution in discrimination among the single and combined data. The character-based barcoding was proved to be the most effective approach for species discrimination in both single and combined data which produced consistent species identification. All the integrated results recovered 11 species, five out of which were revealed as potential cryptic species. We suggest that the character-based DNA barcoding together with other approaches based on multiple genes and their combined data could be more effective in microalgae diversity revelation.
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Affiliation(s)
- Shanmei Zou
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Cong Fei
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chun Wang
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhan Gao
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yachao Bao
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Meilin He
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Changhai Wang
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
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Zou S, Fei C, Song J, Bao Y, He M, Wang C. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta). PLoS One 2016; 11:e0153833. [PMID: 27092945 PMCID: PMC4841637 DOI: 10.1371/journal.pone.0153833] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/13/2016] [Indexed: 01/19/2023] Open
Abstract
Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.
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Affiliation(s)
- Shanmei Zou
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Cong Fei
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiameng Song
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yachao Bao
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Meilin He
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Changhai Wang
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
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Albaina A, Aguirre M, Abad D, Santos M, Estonba A. 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species. Ecol Evol 2016; 6:1809-24. [PMID: 27087935 PMCID: PMC4801955 DOI: 10.1002/ece3.1986] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 12/23/2015] [Accepted: 01/03/2016] [Indexed: 01/26/2023] Open
Abstract
The potential of the 18S rRNA V9 metabarcoding approach for diet assessment was explored using MiSeq paired‐end (PE; 2 × 150 bp) technology. To critically evaluate the method′s performance with degraded/digested DNA, the diets of two zooplanktivorous fish species from the Bay of Biscay, European sardine (Sardina pilchardus) and European sprat (Sprattus sprattus), were analysed. The taxonomic resolution and quantitative potential of the 18S V9 metabarcoding was first assessed both in silico and with mock and field plankton samples. Our method was capable of discriminating species within the reference database in a reliable way providing there was at least one variable position in the 18S V9 region. Furthermore, it successfully discriminated diet between both fish species, including habitat and diel differences among sardines, overcoming some of the limitations of traditional visual‐based diet analysis methods. The high sensitivity and semi‐quantitative nature of the 18S V9 metabarcoding approach was supported by both visual microscopy and qPCR‐based results. This molecular approach provides an alternative cost and time effective tool for food‐web analysis.
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Affiliation(s)
- Aitor Albaina
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - Mikel Aguirre
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - David Abad
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - María Santos
- Marine Research Division AZTI Tecnalia Herrera Kaia Portualdea z/g P.O. Box 20110 Pasaia Gipuzkoa Spain
| | - Andone Estonba
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
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