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Guo LC, Zhao MM, Sun W, Teng HL, Huang BS, Zhao XP. Differentiation of the Chinese minority medicinal plant genus Berchemia spp. by evaluating three candidate barcodes. SPRINGERPLUS 2016; 5:658. [PMID: 27347459 PMCID: PMC4899350 DOI: 10.1186/s40064-016-2207-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/21/2016] [Indexed: 11/17/2022]
Abstract
The genus Berchemia comprises important Chinese plants with considerable medicinal value; however, these plants are often misidentified in the herbal medicinal market. To differentiate the various morphotypes of Berchemia species, a proficient method employing the screening of universal DNA barcodes was used in this work. Three candidate barcoding loci, namely, psbA-trnH, rbcL, and the second internal transcribed spacer (ITS2), were used to identify an effective DNA barcode that can differentiate the various Berchemia species. Additionally, PCR amplification, efficient sequencing, intra- and inter-specific divergences, and DNA barcoding gaps were employed to assess the ability of each barcode to identify these diverse Berchemia plants authentically; the species were differentiated using the Kimura two-parameter and maximum composite likelihood methods. Sequence data analysis showed that the ITS2 region was the most suitable candidate barcode and exhibited the highest interspecific divergence among the three DNA-barcoding sequences. A clear differentiation was observed at the species level, in which a maximum distance of 0.264 was exhibited between dissimilar species. Clustal analysis also demonstrated that ITS2 clearly differentiated the test species in a more effective manner than that with the two other barcodes at both the hybrid and variety levels. Results indicate that DNA barcoding is ideal for species-level identification of Berchemia and provides a foundation for further identification at the molecular level of other Rhamnaceae medicinal plants.
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Affiliation(s)
- Li-Cheng Guo
- Hubei University of Chinese Medicine, Wuhan, 430065 China ; Guangxi Institute of Minority Medicine, Nanning, 530001 China
| | - Ming-Ming Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China ; Medical Laboratory College, Beihua University, Jilin, 132013 China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Hong-Li Teng
- Guangxi Institute of Minority Medicine, Nanning, 530001 China
| | - Bi-Sheng Huang
- Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Xiang-Pei Zhao
- Guangxi Institute of Minority Medicine, Nanning, 530001 China
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Caetano Wyler S, Naciri Y. Evolutionary histories determine DNA barcoding success in vascular plants: seven case studies using intraspecific broad sampling of closely related species. BMC Evol Biol 2016; 16:103. [PMID: 27178437 PMCID: PMC4866073 DOI: 10.1186/s12862-016-0678-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/05/2016] [Indexed: 12/17/2022] Open
Abstract
Background Four plastid regions, rpoB, rpoC1, matK, and trnH-psbA, have been recommended as DNA barcodes for plants. Their success in delimiting species boundaries depends on the existence of a clear-cut difference between inter- and intraspecific variability. We tested the ability of these regions to discriminate among closely related species in seven genera of flowering plants with different generation times (trees, perennials, and annuals). To ensure a maximum coverage of intraspecific diversity, and therefore to better evaluate the resolution power of each barcode, we applied a population genetics approach by sampling three to 45 individuals per species over a wide geographical range. Results All possible combinations between loci were analysed, which showed that using more than one locus does not always improve the resolution power. The trnH-psbA locus was most effective at discriminating among closely related species (Acer, Lonicera, Geranium, and Veronica), singly or in combination. For Salix, Adenostyles, and Gentiana, the best results were obtained with the combination of matK, rpoB, and trnH-psbA. No barcoding gap was found within six genera analysed, excepting Lonicera. This is due to shared polymorphisms among species, combined with very divergent sequences within species. These genetic patterns reflect incomplete lineage sorting and hybridization events followed by chloroplast capture. Conclusions Our results strongly suggest that adding trnH-psbA to the two obligate DNA barcodes proposed by the CBOL plant-working group (matK and rbcL) should be mandatory for closely related species. In our sampling, generation time had no influence on DNA barcoding success, as the best and worst identification successes were found for the two tree genera (Acer, 64 % success and Salix, 86 % failure). Evolutionary histories are the main factor influencing DNA barcoding success in the studied genera. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0678-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofia Caetano Wyler
- Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques & University of Geneva, Chemin de l'Impératrice, 1, 1292, Chambésy, Geneva, Switzerland.,SwissBOL, University of Geneva, Department of Genetics and Evolution, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
| | - Yamama Naciri
- Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques & University of Geneva, Chemin de l'Impératrice, 1, 1292, Chambésy, Geneva, Switzerland.
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Lee SY, Ng WL, Mahat MN, Nazre M, Mohamed R. DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market. PLoS One 2016; 11:e0154631. [PMID: 27128309 PMCID: PMC4851384 DOI: 10.1371/journal.pone.0154631] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/15/2016] [Indexed: 01/31/2023] Open
Abstract
The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.
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Affiliation(s)
- Shiou Yih Lee
- Forest Biotech Laboratory, Department of Forest Management, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Wei Lun Ng
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Noor Mahat
- Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia
| | - Mohd Nazre
- Department of Forest Management, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Rozi Mohamed
- Forest Biotech Laboratory, Department of Forest Management, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Sun W, Li JJ, Xiong C, Zhao B, Chen SL. The Potential Power of Bar-HRM Technology in Herbal Medicine Identification. FRONTIERS IN PLANT SCIENCE 2016; 7:367. [PMID: 27066026 PMCID: PMC4811891 DOI: 10.3389/fpls.2016.00367] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/09/2016] [Indexed: 05/06/2023]
Abstract
The substitution of low-cost or adulterated herbal products for high-priced herbs makes it important to be able to identify and trace herbal plant species and their processed products in the drug supply chain. PCR-based methods play an increasing role in monitoring the safety of herbal medicines by detecting adulteration. Recent studies have shown the potential of DNA barcoding combined with high resolution melting (Bar-HRM) analysis in herbal medicine identification. This method involves precisely monitoring the change in fluorescence caused by the release of an intercalating DNA dye from a DNA duplex as it is denatured by a gradual increase in temperature. Since the melting profile depends on the GC content, length, and strand complementarity of the amplification product, Bar-HRM analysis opens up the possibility of detecting single-base variants or species-specific differences in a short region of DNA. This review summarizes key factors affecting Bar-HRM analysis and describes how Bar-HRM is performed. We then discuss advances in Bar-HRM analysis of medicinal plant ingredients (herbal materia medica) as a contribution toward safe and effective herbal medicines.
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Affiliation(s)
- Wei Sun
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
| | - Jing-jian Li
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
- College of Forestry and Landscape Architecture South China Agricultural UniversityGuangzhou, China
| | - Chao Xiong
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
| | - Bo Zhao
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
- Zhuhai College of Jilin UniversityZhuhai, China
| | - Shi-lin Chen
- Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing, China
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Osathanunkul M, Suwannapoom C, Osathanunkul K, Madesis P, de Boer H. Evaluation of DNA barcoding coupled high resolution melting for discrimination of closely related species in phytopharmaceuticals. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2016; 23:156-65. [PMID: 26926177 DOI: 10.1016/j.phymed.2015.11.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/11/2015] [Accepted: 11/12/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Phytopharmaceuticals are increasingly popular as alternative medicines, but poorly regulated in many countries. The manufacturers of these products should be subject to strict controls regarding each product's quality and constituents. Routine testing and identification of raw materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. HYPOTHESIS/PURPOSE We have applied DNA Barcoding - High Resolution Melting (Bar-HRM), an emerging method for identifying of medicinal plant species based on DNA dissociation kinetics and DNA barcoding, for the authentication of medicinal plant species. STUDY DESIGN Commonly commercialized Thai medicinal plants that are widely used for medicinal purposes were used in this study. Publicly available sequences of four plastid markers were used for universal primer design. Species discrimination efficiency of the designed primers was evaluated as single and multi-locus analyses by using the primers sets. METHODS HRM analysis was performed in triplicate on each of the 26 taxa to establish the Tm for each primer set (matK, rbcLA, rbcLB, rbcLC, rpoC1, and trnL). The shapes of the melting curves were analyzed to distinguish the different plant species. Bar-HRM species identification success rates were assessed for each single-locus as well as for multi-locus combinations to establish the optimal combination of primer sets. RESULTS In single locus analysis the rpoC1 primer set gave the highest discrimination (58%), and in multi locus analysis this could be increased from 87% to 99% depending on the total number of regions included. Different combinations proved to be more or less effective at discrimination, depending on the genus or family examined. CONCLUSIONS Bar-HRM has proven to be a cost-effective and reliable method for the identification of species in this study of Thai medicinal plants, and results show an identification success rate of 99% among species in the test set.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, 239 Huay Kaew Rd., Suthep, Muang, Chiang Mai 50200, Thailand.
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution State, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Kitisak Osathanunkul
- Department of Computer Science, Faculty of Science, Maejo University, Chiang Mai 50290, Thailand
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Hugo de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden; The Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
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Okoth P, Muoma J, Emmanuel M, Clabe W, Omayio DO, Angienda PO. The Potential of DNA Barcode-Based Delineation Using Seven Putative Candidate Loci of the Plastid Region in Inferring Molecular Diversity of Cowpea at Sub-Species Level. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/ajmb.2016.64014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bolson M, Smidt EDC, Brotto ML, Silva-Pereira V. ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests. PLoS One 2015; 10:e0143049. [PMID: 26630282 PMCID: PMC4704546 DOI: 10.1371/journal.pone.0143049] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023] Open
Abstract
The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the 'best close match' test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.
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Affiliation(s)
- Mônica Bolson
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Eric de Camargo Smidt
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | - Viviane Silva-Pereira
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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Osathanunkul M, Suwannapoom C, Ounjai S, Rora JA, Madesis P, de Boer H. Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species. PLoS One 2015; 10:e0138888. [PMID: 26406615 PMCID: PMC4583236 DOI: 10.1371/journal.pone.0138888] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/04/2015] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Croton (Euphorbiaceae), one of the largest genera of plants with over 1,200 species. Seven primer pairs were evaluated (matK, rbcL1, rbcL2, rbcL3, rpoC, trnL and ITS1) from four plastid regions, matK, rbcL, rpoC, and trnL, and the nuclear ribosomal marker ITS1. The primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL1 primer pair gave the lowest resolution. It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Our Bar-HRM results here also provide further support for the hypothesis that both sequence and base composition affect DNA duplex stability.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- * E-mail:
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Science and Technology Research Institute, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sarawut Ounjai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jantarika A. Rora
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Hugo de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
- The Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
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Shapoval NA, Lukhtanov VA. Intragenomic variations of multicopy ITS2 marker in Agrodiaetus blue butterflies (Lepidoptera, Lycaenidae). COMPARATIVE CYTOGENETICS 2015; 9:483-97. [PMID: 26753069 PMCID: PMC4698565 DOI: 10.3897/compcytogen.v9i4.5429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/20/2015] [Indexed: 05/31/2023]
Abstract
The eukaryotic ribosomal DNA cluster consists of multiple copies of three genes, 18S, 5. 8S and 28S rRNAs, separated by multiple copies of two internal transcribed spacers, ITS1 and ITS2. It is an important, frequently used marker in both molecular cytogenetic and molecular phylogenetic studies. Despite this, little is known about intragenomic variations within the copies of eukaryotic ribosomal DNA genes and spacers. Here we present data on intraindividual variations of ITS2 spacer in three species of Agrodiaetus Hübner, 1822 blue butterflies revealed by cloning technique. We demonstrate that a distinctly different intragenomic ITS2 pattern exists for every individual analysed. ITS2 sequences of these species show significant intragenomic variation (up to 3.68% divergence), setting them apart from each other on inferred phylogenetic tree. This variation is enough to obscure phylogenetic relationships at the species level.
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Affiliation(s)
- Nazar A. Shapoval
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
- Department of Entomology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg 199034, Russia
| | - Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
- Department of Entomology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg 199034, Russia
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Liu MM, Xing YM, Zhang DW, Guo SX. Novel microsatellite markers suitable for genetic studies in Polyporus umbellatus (Polyporales, Basidiomycota). BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Kshirsagar P, Umdale S, Chavan J, Gaikwad N. Molecular Authentication of Medicinal Plant, Swertia chirayita and its Adulterant Species. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40011-015-0556-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Madisha MT, Ponsonby D, Schwaibold U, Kotzé A, Jansen R, Brettschneider H, Dalton DL. Differentiation of two South African otter species ( Aonyx capensis and Lutra maculicollis ) from spraint based on partial CytB primer sets. Glob Ecol Conserv 2015. [DOI: 10.1016/j.gecco.2015.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Huang XC, Ci XQ, Conran JG, Li J. Application of DNA Barcodes in Asian Tropical Trees--A Case Study from Xishuangbanna Nature Reserve, Southwest China. PLoS One 2015; 10:e0129295. [PMID: 26121045 PMCID: PMC4509572 DOI: 10.1371/journal.pone.0129295] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/27/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world. METHODOLOGY AND PRINCIPAL FINDINGS A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH-psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH-psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6-58.1%) and genus (72.8-76.2%) identification. With trnH-psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7-28.5% and 31.6-35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas. CONCLUSIONS/SIGNIFICANCE Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH-psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.
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Affiliation(s)
- Xiao-cui Huang
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiu-qin Ci
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - John G. Conran
- Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, Benham Bldg DX, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Jie Li
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
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Wu CS, Chaw SM. Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion. Genome Biol Evol 2015; 7:2000-9. [PMID: 26116919 PMCID: PMC4524490 DOI: 10.1093/gbe/evv125] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2015] [Indexed: 01/09/2023] Open
Abstract
In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent gene conversions in inverted repeat (IR) than in single copy (SC) regions result in contrasting substitution rates between these two regions. However, little has been known about the effect of gene conversion in the evolution of gymnosperm plastomes. Cycads (Cycadophyta) are the second largest gymnosperm group. Evolutionary study of their plastomes is limited to the basal cycad genus, Cycas. In this study, we addressed three questions. 1) Do the plastomes of other cycad genera evolve slowly as previously observed in the plastome of Cycas taitungensis? 2) Do substitution rates differ between their SC and IR regions? And 3) Does gene conversion occur in the cycad plastomes? If yes, is it AT-biased or GC-biased? Plastomes of eight species from other eight genera of cycads were sequenced. These plastomes are highly conserved in genome organization. Excluding ginkgo, cycad plastomes have significantly lower synonymous and nonsynonymous substitution rates than other gymnosperms, reflecting their evolutionary stasis in nucleotide mutations. In the IRs of cycad plastomes, the reduced substitution rates and GC-biased mutations are associated with a GC-biased gene conversion (gBGC) mechanism. Further investigations suggest that in cycads, gBGC is able to rectify plastome-wide mutations. Therefore, this study is the first to uncover the plastomic gBGC in seed plants. We also propose a gBGC model to interpret the dissimilar evolutionary patterns as well as the compositionally biased mutations in the SC and IR regions of cycad plastomes.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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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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66
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Huang WJ, Li FF, Liu YJ, Long CL. Identification of Crocus sativus and its Adulterants from Chinese Markets by using DNA Barcoding Technique. IRANIAN JOURNAL OF BIOTECHNOLOGY 2015; 13:36-42. [PMID: 28959279 DOI: 10.15171/ijb.1034] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Saffron (Crocus sativus L.) is a common but very expensive herbal medicine. As an important traditional medicine, it has an outstanding effect in treating irregular and painful menstruation. Recently, the over-demand tendency of saffron results in an unusual phenomenon in the medicinal markets. Adulterants and saffron-like substitutes are intentionally mixed into medicinal markets and pharmacies or online stores, affecting drug safety and food quality. OBJECTIVES Our study aimed to identify saffron from its adulterants via DNA barcoding. MATERIALS AND METHODS Samples (13 saffron + 4 others containing Carthamus tinctorius or Chrysanthemum x morifolium) obtained from 12 different provinces of China. Through DNA barcoding, samples were compared using three candidate markers, trnH-psbA, rbcL-a and ITS2. RESULTS trnH-psbA and rbcL-a were capable of distinguishing different accessions. ITS2 could identify samples even at intra-specific level. According to these three barcodes, four samples were identified saffron-like substitutes. CONCLUSIONS The adulterant rate in Chinese markets reaches as high as 33.33% that may cause health risks and further may reduce saffron efficacy once is being used as herbal remedy. In order to make a distinction between C. sativus with other genera as adulterants, DNA barcoding is suggested.
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Affiliation(s)
- Wei-Juan Huang
- Department of Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China
| | - Fei-Fei Li
- Department of Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China
| | - Yu-Jing Liu
- Department of Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China
| | - Chun-Lin Long
- Department of Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China.,Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, PR China
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67
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Liu MM, Xing YM, Guo SX. Diversity Analysis of Polyporus umbellatus in China Using Inter-simple Sequence Repeat (ISSR) Markers. Biol Pharm Bull 2015. [DOI: 10.1248/bpb.b15-00274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Meng-Meng Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Yong-Mei Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Shun-Xing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College
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68
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A new nuclear DNA marker from ubiquitin ligase gene region for genetic diversity detection of walnut germplasm resources. ACTA ACUST UNITED AC 2014. [PMID: 28626681 PMCID: PMC5466192 DOI: 10.1016/j.btre.2014.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Development of more sensitive nuclear DNA markers for identification of species, particularly closely allied taxa has been a challenging task that has attracted interest from scientists in fields of biotechnological development and genetic diversity detection. In this study, the sequence of the ubiquitin ligase gene (UBE3) region of nuclear DNA was tested for applicability and efficacy in revealing genetic diversity of walnut resources, with an emphasis on inter- and intra-specific levels. Analysis on genetic relationship among the taxa was conducted with the neighbor-joining (NJ) method. The number of variable bases in the UBE3 region was 20 sites. All nine taxa (species/variety/cultivars) were distinguished using the UBE3 sequence. In addition, each taxon was characterized molecularly with a unique nucleotide molecular formula using ten variable base sites derived from the nuclear DNA UBE3 gene sequence. This study presents a good complementary methodology for developing new DNA markers for identification of genus Juglans.
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69
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Retief K, West AG, Pfab MF. Can Stable Isotopes and Radiocarbon Dating Provide a Forensic Solution for Curbing Illegal Harvesting of Threatened Cycads? J Forensic Sci 2014; 59:1541-51. [DOI: 10.1111/1556-4029.12644] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/20/2014] [Accepted: 07/14/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Kirsten Retief
- Department of Biological Sciences University of Cape Town Private Bag X1 Rondebosch Cape Town South Africa
| | - Adam G. West
- Department of Biological Sciences University of Cape Town Private Bag X1 Rondebosch Cape Town South Africa
| | - Michèle F. Pfab
- South African National Biodiversity Institute Private Bag X101 Pretoria South Africa
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70
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Ferri G, Corradini B, Ferrari F, Santunione AL, Palazzoli F, Alu' M. Forensic botany II, DNA barcode for land plants: Which markers after the international agreement? Forensic Sci Int Genet 2014; 15:131-6. [PMID: 25457632 DOI: 10.1016/j.fsigen.2014.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/23/2014] [Accepted: 10/03/2014] [Indexed: 11/17/2022]
Abstract
The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for forensic botany. Based on obtained results, we recommend the adoption of a two-locus combination with rbcL+trnH-psbA plastid markers, which currently best satisfies forensic needs for botanical species identification.
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Affiliation(s)
- G Ferri
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy.
| | - B Corradini
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Ferrari
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - A L Santunione
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Palazzoli
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - M Alu'
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
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71
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Wang XC, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang JH, Cai D, Li JQ. ITS1: a DNA barcode better than ITS2 in eukaryotes? Mol Ecol Resour 2014; 15:573-86. [PMID: 25187125 DOI: 10.1111/1755-0998.12325] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 11/30/2022]
Abstract
A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large-scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.
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Affiliation(s)
- Xin-Cun Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, 151 MaLianWa North Road, Beijing, 100193, China
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72
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Chen J, Zhao J, Erickson DL, Xia N, Kress WJ. Testing DNA barcodes in closely related species ofCurcuma(Zingiberaceae) from Myanmar and China. Mol Ecol Resour 2014; 15:337-48. [DOI: 10.1111/1755-0998.12319] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; the Chinese Academy of Sciences; No 723 Xingke Road Tianhe District Guangzhou 510650 China
| | - Jietang Zhao
- College of Horticulture; South China Agricultural University; Guangzhou 510642 China
| | - David L. Erickson
- Department of Botany; MRC-166; National Museum of Natural History; Smithsonian Institution; P.O. Box 37012 Washington DC 20013-7012 USA
| | - Nianhe Xia
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; the Chinese Academy of Sciences; No 723 Xingke Road Tianhe District Guangzhou 510650 China
| | - W. John Kress
- Department of Botany; MRC-166; National Museum of Natural History; Smithsonian Institution; P.O. Box 37012 Washington DC 20013-7012 USA
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73
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Ojeda DI, Santos-Guerra A, Oliva-Tejera F, Jaen-Molina R, Caujapé-Castells J, Marrero-Rodríguez A, Cronk Q. DNA barcodes successfully identified Macaronesian Lotus (Leguminosae) species within early diverged lineages of Cape Verde and mainland Africa. AOB PLANTS 2014; 6:plu050. [PMID: 25147310 PMCID: PMC4168286 DOI: 10.1093/aobpla/plu050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Plant DNA barcoding currently relies on the application of a two-locus combination, matK + rbcL. Despite the universality of these two gene regions across plants, it is suspected that this combination might not have sufficient variation to discriminate closely related species. In this study, we tested the performance of this two-locus plant barcode along with the additional plastid regions trnH-psbA, rpoC1 and rpoB and the nuclear region internal transcribed spacer (nrITS) in a group of 38 species of Lotus from the Macaronesian region. The group has radiated into the five archipelagos within this region from mid-Miocene to early Pleistocene, and thus provides both early divergent and recent radiations that pose a particularly difficult challenge for barcoding. The group also has 10 species considered under different levels of conservation concern. We found different levels of species discrimination depending on the age of the lineages. We obtained 100 % of the species identification from mainland Africa and Cape Verde when all six regions were combined. These lineages radiated >4.5 Mya; however, in the most recent radiations from the end of the Pliocene to the mid-Pleistocene (3.5-1.5 Mya), only 30 % of the species were identified. Of the regions examined, the intergenic region trnH-psbA was the most variable and had the greatest discriminatory power (18 %) of the plastid regions when analysed alone. The nrITS region was the best region when analysed alone with a discriminatory power of 26 % of the species. Overall, we identified 52 % of the species and 30 % of the endangered or threatened species within this group when all six regions were combined. Our results are consistent with those of other studies that indicate that additional approaches to barcoding will be needed in recently evolved groups, such as the inclusion of faster evolving regions from the nuclear genome.
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Affiliation(s)
- Dario I Ojeda
- The Biodiversity Research Centre, Department of Botany, University of British Columbia, 6804 SW Marine Drive, Vancouver V6T 1Z4, Canada
| | | | - Felicia Oliva-Tejera
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Ruth Jaen-Molina
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Juli Caujapé-Castells
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Aguedo Marrero-Rodríguez
- Jardín Botánico Canario 'Viera y Clavijo'-Unidad Asociada CSIC, Cabildo de Gran Canaria Las Palmas, Gran Canaria, Spain
| | - Quentin Cronk
- The Biodiversity Research Centre, Department of Botany, University of British Columbia, 6804 SW Marine Drive, Vancouver V6T 1Z4, Canada
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Yuan QJ, Zhang B, Jiang D, Zhang WJ, Lin TY, Wang NH, Chiou SJ, Huang LQ. Identification of species and materia medica within Angelica L. (Umbelliferae) based on phylogeny inferred from DNA barcodes. Mol Ecol Resour 2014; 15:358-71. [PMID: 24961287 PMCID: PMC4344822 DOI: 10.1111/1755-0998.12296] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 06/05/2014] [Accepted: 06/20/2014] [Indexed: 11/29/2022]
Abstract
DNA barcodes have been increasingly used in authentication of medicinal plants, while their wide application in materia medica is limited in their accuracy due to incomplete sampling of species and absence of identification for materia medica. In this study, 95 leaf accessions of 23 species (including one variety) and materia medica of three Pharmacopoeia-recorded species of Angelica in China were collected to evaluate the effectiveness of four DNA barcodes (rbcL, matK, trnH-psbA and ITS). Our results showed that ITS provided the best discriminatory power by resolving 17 species as monophyletic lineages without shared alleles and exhibited the largest barcoding gap among the four single barcodes. The phylogenetic analysis of ITS showed that Levisticum officinale and Angelica sinensis were sister taxa, which indicates that L. officinale should be considered as a species of Angelica. The combination of ITS + rbcL + matK + trnH-psbA performed slight better discriminatory power than ITS, recovering 23 species without shared alleles and 19 species as monophyletic clades in ML tree. Authentication of materia medica using ITS revealed that the decoction pieces of A. sinensis and A. biserrata were partially adulterated with those of L. officinale, and the temperature around 80 °C processing A. dahurica decoction pieces obviously reduced the efficiency of PCR and sequencing. The examination of two cultivated varieties of A. dahurica from different localities indicated that the four DNA barcodes are inefficient for discriminating geographical authenticity of conspecific materia medica. This study provides an empirical paradigm in identification of medicinal plants and their materia medica using DNA barcodes.
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Affiliation(s)
- Qing-Jun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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75
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Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S. Plant DNA barcoding: from gene to genome. Biol Rev Camb Philos Soc 2014; 90:157-66. [DOI: 10.1111/brv.12104] [Citation(s) in RCA: 438] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 02/05/2014] [Accepted: 02/27/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Xiwen Li
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Yang Yang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland; Brisbane Queensland 4072 Australia
| | - Maurizio Rossetto
- National Herbarium of NSW, The Royal Botanic Gardens and Domain Trust; Mrs Macquaries Road Sydney New South Wales 2000 Australia
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences, University of Macau; Macau 999078 China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences; Beijing 100700 China
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76
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Chakraborty M, Ghosh SK. Unraveling the sequence information in COI barcode to achieve higher taxon assignment based on Indian freshwater fishes. ACTA ACUST UNITED AC 2014; 26:175-7. [PMID: 24409929 DOI: 10.3109/19401736.2013.855923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Efficacy of cytochrome c oxidase subunit I (COI) DNA barcode in higher taxon assignment is still under debate in spite of several attempts, using the conventional DNA barcoding methods, to assign higher taxa. Here we try to understand whether nucleotide and amino acid sequence in COI gene carry sufficient information to assign species to their higher taxonomic rank, using 160 species of Indian freshwater fishes. Our results reveal that with increase in the taxonomic rank, sequence conservation decreases for both nucleotides and amino acids. Order level exhibits lowest conservation with 50% of the nucleotides and amino acids being conserved. Among the variable sites, 30-50% were found to carry high information content within an order, while it was 70-80% within a family and 80-99% within a genus. High information content shows sites with almost conserved sequence but varying at one or two locations, which can be due to variations at species or population level. Thus, the potential of COI gene in higher taxon assignment is revealed with validation of ample inherent signals latent in the gene.
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Affiliation(s)
- Mohua Chakraborty
- Department of Biotechnology, Assam University , Silchar, Assam , India
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77
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de Boer HJ, Ouarghidi A, Martin G, Abbad A, Kool A. DNA barcoding reveals limited accuracy of identifications based on folk taxonomy. PLoS One 2014; 9:e84291. [PMID: 24416210 PMCID: PMC3885563 DOI: 10.1371/journal.pone.0084291] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 11/13/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The trade of plant roots as traditional medicine is an important source of income for many people around the world. Destructive harvesting practices threaten the existence of some plant species. Harvesters of medicinal roots identify the collected species according to their own folk taxonomies, but once the dried or powdered roots enter the chain of commercialization, accurate identification becomes more challenging. METHODOLOGY A survey of morphological diversity among four root products traded in the medina of Marrakech was conducted. Fifty-one root samples were selected for molecular identification using DNA barcoding using three markers, trnH-psbA, rpoC1, and ITS. Sequences were searched using BLAST against a tailored reference database of Moroccan medicinal plants and their closest relatives submitted to NCBI GenBank. PRINCIPAL FINDINGS Combining psbA-trnH, rpoC1, and ITS allowed the majority of the market samples to be identified to species level. Few of the species level barcoding identifications matched the scientific names given in the literature, including the most authoritative and widely cited pharmacopeia. CONCLUSIONS/SIGNIFICANCE The four root complexes selected from the medicinal plant products traded in Marrakech all comprise more than one species, but not those previously asserted. The findings have major implications for the monitoring of trade in endangered plant species as morphology-based species identifications alone may not be accurate. As a result, trade in certain species may be overestimated, whereas the commercialization of other species may not be recorded at all.
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Affiliation(s)
- Hugo J. de Boer
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Abderrahim Ouarghidi
- Faculty of Science Semlalia, Cadi Ayyad University, Marrakech, Morocco
- Global Diversity Foundation, Marrakech, Morocco
| | - Gary Martin
- Global Diversity Foundation, Marrakech, Morocco
| | - Abdelaziz Abbad
- Faculty of Science Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Anneleen Kool
- Natural History Museum, University of Oslo, Oslo, Norway
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Salas-Leiva DE, Meerow AW, Calonje M, Griffith MP, Francisco-Ortega J, Nakamura K, Stevenson DW, Lewis CE, Namoff S. Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods. ANNALS OF BOTANY 2013; 112:1263-78. [PMID: 23997230 PMCID: PMC3806525 DOI: 10.1093/aob/mct192] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/15/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene tree-species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera. METHODS DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree-species tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted. KEY RESULTS Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (Macrozamia-Lepidozamia-Encephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia. CONCLUSIONS A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae.
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Affiliation(s)
- Dayana E. Salas-Leiva
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- USDA-ARS-SHRS, National Germplasm Repository, Miami, FL 33158, USA
| | - Alan W. Meerow
- USDA-ARS-SHRS, National Germplasm Repository, Miami, FL 33158, USA
| | - Michael Calonje
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Montgomery Botanical Center, Miami, FL 33156, USA
| | | | - Javier Francisco-Ortega
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Fairchild Tropical Botanic Garden, Coral Gables, FL 33156, USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS, National Germplasm Repository, Miami, FL 33158, USA
| | | | | | - Sandra Namoff
- Rancho Santa Ana Botanic Garden and Claremont Graduate University, Claremont, CA 91711, USA
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Krawczyk K, Szczecińska M, Sawicki J. Evaluation of 11 single-locus and seven multilocus DNA barcodes inLamiumL. (Lamiaceae). Mol Ecol Resour 2013; 14:272-85. [DOI: 10.1111/1755-0998.12175] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 09/06/2013] [Accepted: 09/13/2013] [Indexed: 11/28/2022]
Affiliation(s)
- K. Krawczyk
- Department of Botany and Nature Protection; University of Warmia and Mazury in Olsztyn; Plac Lodzki 1 10-727 Olsztyn Poland
| | - M. Szczecińska
- Department of Botany and Nature Protection; University of Warmia and Mazury in Olsztyn; Plac Lodzki 1 10-727 Olsztyn Poland
| | - J. Sawicki
- Department of Botany and Nature Protection; University of Warmia and Mazury in Olsztyn; Plac Lodzki 1 10-727 Olsztyn Poland
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80
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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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81
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Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences. Gene 2013; 528:206-15. [DOI: 10.1016/j.gene.2013.07.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/17/2013] [Accepted: 07/02/2013] [Indexed: 11/21/2022]
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82
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Feng J, Jiang D, Shang H, Dong M, Wang G, He X, Zhao C, Mao K. Barcoding poplars (Populus L.) from western China. PLoS One 2013; 8:e71710. [PMID: 23977122 PMCID: PMC3747233 DOI: 10.1371/journal.pone.0071710] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/01/2013] [Indexed: 01/23/2023] Open
Abstract
Background Populus is an ecologically and economically important genus of trees, but distinguishing between wild species is relatively difficult due to extensive interspecific hybridization and introgression, and the high level of intraspecific morphological variation. The DNA barcoding approach is a potential solution to this problem. Methodology/Principal Findings Here, we tested the discrimination power of five chloroplast barcodes and one nuclear barcode (ITS) among 95 trees that represent 21 Populus species from western China. Among all single barcode candidates, the discrimination power is highest for the nuclear ITS, progressively lower for chloroplast barcodes matK (M), trnG-psbK (G) and psbK-psbI (P), and trnH-psbA (H) and rbcL (R); the discrimination efficiency of the nuclear ITS (I) is also higher than any two-, three-, or even the five-locus combination of chloroplast barcodes. Among the five combinations of a single chloroplast barcode plus the nuclear ITS, H+I and P+I differentiated the highest and lowest portion of species, respectively. The highest discrimination rate for the barcodes or barcode combinations examined here is 55.0% (H+I), and usually discrimination failures occurred among species from sympatric or parapatric areas. Conclusions/Significance In this case study, we showed that when discriminating Populus species from western China, the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions. Meanwhile, combining the ITS region with chloroplast regions may improve the barcoding success rate and assist in detecting recent interspecific hybridizations. Failure to discriminate among several groups of Populus species from sympatric or parapatric areas may have been the result of incomplete lineage sorting, frequent interspecific hybridizations and introgressions. We agree with a previous proposal for constructing a tiered barcoding system in plants, especially for taxonomic groups that have complex evolutionary histories (e.g. Populus).
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Affiliation(s)
- Jianju Feng
- School of Earth and Environmental Sciences & State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
- College of Plant Sciences, Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarimu University, Alar, Xinjiang, People’s Republic of China
| | - Dechun Jiang
- School of Earth and Environmental Sciences & State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
| | - Huiying Shang
- School of Earth and Environmental Sciences & State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
| | - Miao Dong
- School of Earth and Environmental Sciences & State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
| | - Gaini Wang
- School of Earth and Environmental Sciences & State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
| | - Xinyu He
- School of Earth and Environmental Sciences & State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
| | - Changming Zhao
- School of Earth and Environmental Sciences & State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
| | - Kangshan Mao
- School of Earth and Environmental Sciences & State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People’s Republic of China
- * E-mail:
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Ganopoulos I, Aravanopoulos F, Madesis P, Pasentsis K, Bosmali I, Ouzounis C, Tsaftaris A. Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing. PLoS One 2013; 8:e60945. [PMID: 23577179 PMCID: PMC3618329 DOI: 10.1371/journal.pone.0060945] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 03/06/2013] [Indexed: 11/19/2022] Open
Abstract
Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples.
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Affiliation(s)
- Ioannis Ganopoulos
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Greece
| | - Filippos Aravanopoulos
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Laboratory of Forest Genetics and Tree Breeding, Faculty of Forestry and Natural Environment, Aristotle University of Thessaloniki, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Konstantinos Pasentsis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Irene Bosmali
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Christos Ouzounis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Athanasios Tsaftaris
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Greece
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84
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Tripathi AM, Tyagi A, Kumar A, Singh A, Singh S, Chaudhary LB, Roy S. The internal transcribed spacer (ITS) region and trnH-psbA [corrected] are suitable candidate loci for DNA barcoding of tropical tree species of India. PLoS One 2013; 8:e57934. [PMID: 23460915 PMCID: PMC3584017 DOI: 10.1371/journal.pone.0057934] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 01/29/2013] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND DNA barcoding as a tool for species identification has been successful in animals and other organisms, including certain groups of plants. The exploration of this new tool for species identification, particularly in tree species, is very scanty from biodiversity-rich countries like India. rbcL and matK are standard barcode loci while ITS, and trnH-psbA are considered as supplementary loci for plants. METHODOLOGY AND PRINCIPAL FINDINGS Plant barcode loci, namely, rbcL, matK, ITS, trnH-psbA, and the recently proposed ITS2, were tested for their efficacy as barcode loci using 300 accessions of tropical tree species. We tested these loci for PCR, sequencing success, and species discrimination ability using three methods. rbcL was the best locus as far as PCR and sequencing success rate were concerned, but not for the species discrimination ability of tropical tree species. ITS and trnH-psbA were the second best loci in PCR and sequencing success, respectively. The species discrimination ability of ITS ranged from 24.4 percent to 74.3 percent and that of trnH-psbA was 25.6 percent to 67.7 percent, depending upon the data set and the method used. matK provided the least PCR success, followed by ITS2 (59. 0%). Species resolution by ITS2 and rbcL ranged from 9.0 percent to 48.7 percent and 13.2 percent to 43.6 percent, respectively. Further, we observed that the NCBI nucleotide database is poorly represented by the sequences of barcode loci studied here for tree species. CONCLUSION Although a conservative approach of a success rate of 60-70 percent by both ITS and trnH-psbA may not be considered as highly successful but would certainly help in large-scale biodiversity inventorization, particularly for tropical tree species, considering the standard success rate of plant DNA barcode program reported so far. The recommended matK and rbcL primers combination may not work in tropical tree species as barcode markers.
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Affiliation(s)
- Abhinandan Mani Tripathi
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Antariksh Tyagi
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Anoop Kumar
- Plant Diversity, Systematic and Herbarium Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Akanksha Singh
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Shivani Singh
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Lal Babu Chaudhary
- Plant Diversity, Systematic and Herbarium Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Sribash Roy
- Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
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Han J, Zhu Y, Chen X, Liao B, Yao H, Song J, Chen S, Meng F. The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS. BIOMED RESEARCH INTERNATIONAL 2013; 2013:741476. [PMID: 23484151 PMCID: PMC3581084 DOI: 10.1155/2013/741476] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/26/2012] [Indexed: 11/22/2022]
Abstract
An ideal DNA barcoding region should be short enough to be amplified from degraded DNA. In this paper, we discuss the possibility of using a short nuclear DNA sequence as a barcode to identify a wide range of medicinal plant species. First, the PCR and sequencing success rates of ITS and ITS2 were evaluated based entirely on materials from dry medicinal product and herbarium voucher specimens, including some samples collected back to 90 years ago. The results showed that ITS2 could recover 91% while ITS could recover only 23% efficiency of PCR and sequencing by using one pair of primer. Second, 12861 ITS and ITS2 plant sequences were used to compare the identification efficiency of the two regions. Four identification criteria (BLAST, inter- and intradivergence Wilcoxon signed rank tests, and TaxonDNA) were evaluated. Our results supported the hypothesis that ITS2 can be used as a minibarcode to effectively identify species in a wide variety of specimens and medicinal materials.
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Affiliation(s)
- Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, China
| | - Yingjie Zhu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, China
| | - Xiaochen Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, China
| | - Baoshen Liao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, China
| | - Shilin Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, China
| | - Fanyun Meng
- College of Resources Science & Technology, Beijing Normal University, Beijing 100875, China
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DNA barcode ITS effectively distinguishes the medicinal plant Boerhavia diffusa from its adulterants. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:364-7. [PMID: 23317705 PMCID: PMC5054712 DOI: 10.1016/j.gpb.2012.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 03/09/2012] [Accepted: 03/21/2012] [Indexed: 10/27/2022]
Abstract
Boerhavia diffusa (B. diffusa), also known as Punarnava, is an indigenous plant in India and an important component in traditional Indian medicine. The accurate identification and collection of this medicinal herb is vital to enhance the drug's efficacy and biosafety. In this study, a DNA barcoding technique has been applied to identify and distinguish B. diffusa from its closely-related species. The phylogenetic analysis was carried out for the four species of Boerhavia using barcode candidates including nuclear ribosomal DNA regions ITS, ITS1, ITS2 and the chloroplast plastid gene psbA-trnH. Sequence alignment revealed 26% polymorphic sites in ITS, 30% in ITS1, 16% in ITS2 and 6% in psbA-trnH, respectively. Additionally, a phylogenetic tree was constructed for 15 species using ITS sequences which clearly distinguished B. diffusa from the other species. The ITS1 demonstrates a higher transition/transversion ratio, percentage of variation and pairwise distance which differentiate B. diffusa from other species of Boerhavia. Our study revealed that ITS and ITS1 could be used as potential candidate regions for identifying B. diffusa and for authenticating its herbal products.
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87
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Kuzmina ML, Johnson KL, Barron HR, Hebert PD. Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library. BMC Ecol 2012; 12:25. [PMID: 23190419 PMCID: PMC3538695 DOI: 10.1186/1472-6785-12-25] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 11/26/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Because arctic plant communities are highly vulnerable to climate change, shifts in their composition require rapid, accurate identifications, often for specimens that lack diagnostic floral characters. The present study examines the role that DNA barcoding can play in aiding floristic evaluations in the arctic by testing the effectiveness of the core plant barcode regions (rbcL, matK) and a supplemental ribosomal DNA (ITS2) marker for a well-studied flora near Churchill, Manitoba. RESULTS This investigation examined 900 specimens representing 312 of the 354 species of vascular plants known from Churchill. Sequencing success was high for rbcL: 95% for fresh specimens and 85% for herbarium samples (mean age 20 years). ITS2 worked equally well for the fresh and herbarium material (89% and 88%). However, sequencing success was lower for matK, despite two rounds of PCR amplification, which reflected less effective primer binding and sensitivity to the DNA degradation (76% of fresh, 45% of herbaria samples). A species was considered as taxonomically resolved if its members showed at least one diagnostic difference from any other taxon in the study and formed a monophyletic clade. The highest species resolution (69%) was obtained by combining information from all three genes. The joint sequence information for rbcL and matK distinguished 54% of 286 species, while rbcL and ITS2 distinguished 63% of 285 species. Discrimination of species within Salix, which constituted 8% of the flora, was particularly problematic. Despite incomplete resolution, the barcode results revealed 22 misidentified herbarium specimens, and enabled the identification of field specimens which were otherwise too immature to identify. Although seven cases of ITS2 paralogy were noted in the families Cyperaceae, Juncaceae and Juncaginaceae, this intergenic spacer played an important role in resolving congeneric plant species at Churchill. CONCLUSIONS Our results provided fast and cost-effective solution to create a comprehensive, effective DNA barcode reference library for a local flora.
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Affiliation(s)
- Maria L Kuzmina
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada.
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88
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Aubriot X, Lowry PP, Cruaud C, Couloux A, Haevermans T. DNA
barcoding in a biodiversity hot spot: potential value for the identification of
M
alagasy
E
uphorbia
L. listed in
CITES A
ppendices I and
II. Mol Ecol Resour 2012; 13:57-65. [DOI: 10.1111/1755-0998.12028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/06/2012] [Accepted: 07/17/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Xavier Aubriot
- Muséum national d'histoire naturelle Département Systématique et Evolution UMR 7205 MNHN/CNRS Origine Structure et Evolution de la Biodiversité (OSEB) Herbier Plantes Vasculaires CP 39, 57 rue Cuvier 75231 Paris CEDEX 05 France
| | - Porter P. Lowry
- Muséum national d'histoire naturelle Département Systématique et Evolution UMR 7205 MNHN/CNRS Origine Structure et Evolution de la Biodiversité (OSEB) Herbier Plantes Vasculaires CP 39, 57 rue Cuvier 75231 Paris CEDEX 05 France
- Missouri Botanical Garden PO Box 299 St. Louis MO 63166–0299 USA
| | - Corinne Cruaud
- Genoscope Centre National de Séquençage CP 5706, 2 rue Gaston Crémieux 91057 Evry CEDEX France
| | - Arnaud Couloux
- Genoscope Centre National de Séquençage CP 5706, 2 rue Gaston Crémieux 91057 Evry CEDEX France
| | - Thomas Haevermans
- Muséum national d'histoire naturelle Département Systématique et Evolution UMR 7205 MNHN/CNRS Origine Structure et Evolution de la Biodiversité (OSEB) Herbier Plantes Vasculaires CP 39, 57 rue Cuvier 75231 Paris CEDEX 05 France
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Pang X, Luo H, Sun C. Assessing the potential of candidate DNA barcodes for identifying non-flowering seed plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:839-844. [PMID: 22309105 DOI: 10.1111/j.1438-8677.2011.00554.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In plants, matK and rbcL have been selected as core barcodes by the Consortium for the Barcode of Life (CBOL) Plant Working Group (PWG), and ITS/ITS2 and psbA-trnH were suggested as supplementary loci. Yet, research on DNA barcoding of non-flowering seed plants has been less extensive, and the evaluation of DNA barcodes in this division has been limited thus far. Here, we evaluated seven markers (psbA-trnH, matK, rbcL, rpoB, rpoC1, ITS and ITS2) from non-flowering seed plants. The usefulness of each region was assessed using four criteria: the success rate of PCR amplification, the differential intra- and inter-specific divergences, the DNA barcoding gap and the ability to discriminate species. Among the seven loci tested, ITS2 produced the best results in the barcoding of non-flowering seed plants. In addition, we compared the abilities of the five most-recommended markers (psbA-trnH, matK, rbcL, ITS and ITS2) to identify additional species using a large database of gymnosperms from GenBank. ITS2 remained effective for species identification in a wide range of non-flowering seed plants: for the 1531 samples from 608 species of 80 diverse genera, ITS2 correctly authenticated 66% of them at the species level. In conclusion, the ITS2 region can serve as a useful barcode to discriminate non-flowering seed plants, and this study will contribute valuable information for the barcoding of plant species.
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Affiliation(s)
- X Pang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - H Luo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - C Sun
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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90
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Zaytseva OO, Bogdanova VS, Kosterin OE. Phylogenetic reconstruction at the species and intraspecies levels in the genus Pisum (L.) (peas) using a histone H1 gene. Gene 2012; 504:192-202. [PMID: 22613846 DOI: 10.1016/j.gene.2012.05.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 04/20/2012] [Accepted: 05/12/2012] [Indexed: 10/28/2022]
Abstract
A phylogenetic analysis of the genus Pisum (peas), embracing diverse wild and cultivated forms, which evoke problems with species delimitation, was carried out based on a gene coding for histone H1, a protein that has a long and variable functional C-terminal domain. Phylogenetic trees were reconstructed on the basis of the coding sequence of the gene His5 of H1 subtype 5 in 65 pea accessions. Early separation of a clear-cut wild species Pisum fulvum is well supported, while cultivated species Pisum abyssinicum appears as a small branch within Pisum sativum. Another robust branch within P. sativum includes some wild and almost all cultivated representatives of P. sativum. Other wild representatives form diverse but rather subtle branches. In a subset of accessions, PsbA-trnH chloroplast intergenic spacer was also analysed and found less informative than His5. A number of accessions of cultivated peas from remote regions have a His5 allele of identical sequence, encoding an electrophoretically slow protein product, which earlier attracted attention as likely positively selected in harsh climate conditions. In PsbA-trnH, a 8bp deletion was found, which marks cultivated representatives of P. sativum.
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Affiliation(s)
- Olga O Zaytseva
- Institute of Cytology and Genetics SB RAS, Acad. Lavrentyev ave. 10, Novosibirsk, Russia
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91
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Li CP, Yu ZG, Han GS, Chu KH. Analyzing multi-locus plant barcoding datasets with a composition vector method based on adjustable weighted distance. PLoS One 2012; 7:e42154. [PMID: 22848736 PMCID: PMC3407124 DOI: 10.1371/journal.pone.0042154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/02/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The composition vector (CV) method has been proved to be a reliable and fast alignment-free method to analyze large COI barcoding data. In this study, we modify this method for analyzing multi-gene datasets for plant DNA barcoding. The modified method includes an adjustable-weighted algorithm for the vector distance according to the ratio in sequence length of the candidate genes for each pair of taxa. METHODOLOGY/PRINCIPAL FINDINGS Three datasets, matK+rbcL dataset with 2,083 sequences, matK+rbcL dataset with 397 sequences and matK+rbcL+trnH-psbA dataset with 397 sequences, were tested. We showed that the success rates of grouping sequences at the genus/species level based on this modified CV approach are always higher than those based on the traditional K2P/NJ method. For the matK+rbcL datasets, the modified CV approach outperformed the K2P-NJ approach by 7.9% in both the 2,083-sequence and 397-sequence datasets, and for the matK+rbcL+trnH-psbA dataset, the CV approach outperformed the traditional approach by 16.7%. CONCLUSIONS We conclude that the modified CV approach is an efficient method for analyzing large multi-gene datasets for plant DNA barcoding. Source code, implemented in C++ and supported on MS Windows, is freely available for download at http://math.xtu.edu.cn/myphp/math/research/source/Barcode_source_codes.zip.
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Affiliation(s)
- Chi Pang Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zu Guo Yu
- School of Mathematics and Computational Science, Xiangtan University, Hunan, China
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Guo Sheng Han
- School of Mathematics and Computational Science, Xiangtan University, Hunan, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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92
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Kool A, de Boer HJ, Krüger A, Rydberg A, Abbad A, Björk L, Martin G. Molecular identification of commercialized medicinal plants in southern Morocco. PLoS One 2012; 7:e39459. [PMID: 22761800 PMCID: PMC3384669 DOI: 10.1371/journal.pone.0039459] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/21/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Medicinal plant trade is important for local livelihoods. However, many medicinal plants are difficult to identify when they are sold as roots, powders or bark. DNA barcoding involves using a short, agreed-upon region of a genome as a unique identifier for species- ideally, as a global standard. RESEARCH QUESTION What is the functionality, efficacy and accuracy of the use of barcoding for identifying root material, using medicinal plant roots sold by herbalists in Marrakech, Morocco, as a test dataset. METHODOLOGY In total, 111 root samples were sequenced for four proposed barcode regions rpoC1, psbA-trnH, matK and ITS. Sequences were searched against a tailored reference database of Moroccan medicinal plants and their closest relatives using BLAST and Blastclust, and through inference of RAxML phylograms of the aligned market and reference samples. PRINCIPAL FINDINGS Sequencing success was high for rpoC1, psbA-trnH, and ITS, but low for matK. Searches using rpoC1 alone resulted in a number of ambiguous identifications, indicating insufficient DNA variation for accurate species-level identification. Combining rpoC1, psbA-trnH and ITS allowed the majority of the market samples to be identified to genus level. For a minority of the market samples, the barcoding identification differed significantly from previous hypotheses based on the vernacular names. CONCLUSIONS/SIGNIFICANCE Endemic plant species are commercialized in Marrakech. Adulteration is common and this may indicate that the products are becoming locally endangered. Nevertheless the majority of the traded roots belong to species that are common and not known to be endangered. A significant conclusion from our results is that unknown samples are more difficult to identify than earlier suggested, especially if the reference sequences were obtained from different populations. A global barcoding database should therefore contain sequences from different populations of the same species to assure the reference sequences characterize the species throughout its distributional range.
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Affiliation(s)
- Anneleen Kool
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
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93
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LI H, CHEN J, WANG S, XIONG S. Evaluation of six candidate DNA barcoding loci in
Ficus
(Moraceae) of China. Mol Ecol Resour 2012; 12:783-90. [DOI: 10.1111/j.1755-0998.2012.03147.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - S. WANG
- School of Life Science, East China Normal University, Shanghai 200241, China
| | - S.‐Z. XIONG
- School of Life Science, East China Normal University, Shanghai 200241, China
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94
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Dong W, Liu J, Yu J, Wang L, Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One 2012; 7:e35071. [PMID: 22511980 PMCID: PMC3325284 DOI: 10.1371/journal.pone.0035071] [Citation(s) in RCA: 353] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Accepted: 03/13/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences. Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species. METHODOLOGY/PRINCIPAL FINDINGS We scanned the entire chloroplast genomes of 12 genera to search for highly variable regions. The sequence data of 9 genera were from GenBank and 3 genera were of our own. We identified nearly 5% of the most variable loci from all variable loci in the chloroplast genomes of each genus, and then selected 23 loci that were present in at least three genera. The 23 loci included 4 coding regions, 2 introns, and 17 intergenic spacers. Of the 23 loci, the most variable (in order from highest variability to lowest) were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnS(UGA)-trnG(UCC), petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnS(UGA)-trnG(UCC), trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity per site (π values) across three genera. Other loci may have strong potential for resolving phylogenetic and species identification problems at the species level. The loci accD-psaI, rbcL-accD, rpl32-trnL, rps16-trnQ, and ycf1 are absent from some genera. To amplify and sequence the highly variable loci identified in this study, we designed primers from their conserved flanking regions. We tested the applicability of the primers to amplify target sequences in eight species representing basal angiosperms, monocots, eudicots, rosids, and asterids, and confirmed that the primers amplified the desired sequences of these species. SIGNIFICANCE/CONCLUSIONS Chloroplast genome sequences contain regions that are highly variable. Such regions are the first consideration when screening the suitable loci to resolve closely related species or genera in phylogenetic analyses, and for DNA barcoding.
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Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Jing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Jing Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ling Wang
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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95
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Arca M, Hinsinger DD, Cruaud C, Tillier A, Bousquet J, Frascaria-Lacoste N. Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus. PLoS One 2012; 7:e34089. [PMID: 22479532 PMCID: PMC3313964 DOI: 10.1371/journal.pone.0034089] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/21/2012] [Indexed: 02/01/2023] Open
Abstract
The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA "universal" barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed.
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Affiliation(s)
- Mariangela Arca
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
| | - Damien Daniel Hinsinger
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt, Université Laval, Québec, Québec, Canada
| | | | - Annie Tillier
- Département systématique et évolution and Service de systématique moléculaire, Muséum national d'histoire naturelle, Paris, France
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt, Université Laval, Québec, Québec, Canada
| | - Nathalie Frascaria-Lacoste
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
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96
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Chen LY, Chen JM, Gituru RW, Wang QF. Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae. BMC Evol Biol 2012; 12:30. [PMID: 22404786 PMCID: PMC3317846 DOI: 10.1186/1471-2148-12-30] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/10/2012] [Indexed: 11/17/2022] Open
Abstract
Background Hydrocharitaceae is a fully aquatic monocot family, consists of 18 genera with approximately 120 species. The family includes both fresh and marine aquatics and exhibits great diversity in form and habit including annual and perennial life histories; submersed, partially submersed and floating leaf habits and linear to orbicular leaf shapes. The family has a cosmopolitan distribution and is well represented in the Tertiary fossil record in Europe. At present, the historical biogeography of the family is not well understood and the generic relationships remain controversial. In this study we investigated the phylogeny and biogeography of Hydrocharitaceae by integrating fossils and DNA sequences from eight genes. We also conducted ancestral state reconstruction for three morphological characters. Results Phylogenetic analyses produced a phylogeny with most branches strongly supported by bootstrap values greater than 95 and Bayesian posterior probability values of 1.0. Stratiotes is the first diverging lineage with the remaining genera in two clades, one clade consists of Lagarosiphon, Ottelia, Blyxa, Apalanthe, Elodea and Egeria; and the other consists of Hydrocharis-Limnobium, Thalassia, Enhalus, Halophila, Najas, Hydrilla, Vallisneria, Nechamandra and Maidenia. Biogeographic analyses (DIVA, Mesquite) and divergence time estimates (BEAST) resolved the most recent common ancestor of Hydrocharitaceae as being in Asia during the Late Cretaceous and Palaeocene (54.7-72.6 Ma). Dispersals (including long-distance dispersal and migrations through Tethys seaway and land bridges) probably played major roles in the intercontinental distribution of this family. Ancestral state reconstruction suggested that in Hydrocharitaceae evolution of dioecy is bidirectional, viz., from dioecy to hermaphroditism, and from hermaphroditism to dioecy, and that the aerial-submerged leaf habit and short-linear leaf shape are the ancestral states. Conclusions Our study has shed light on the previously controversial generic phylogeny of Hydrocharitaceae. The study has resolved the historical biogeography of this family and supported dispersal as the most likely explanation for the intercontinental distribution. We have also provided valuable information for understanding the evolution of breeding system and leaf phenotype in aquatic monocots.
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Affiliation(s)
- Ling-Yun Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Chinese Academy of Sciences, Wuhan 430074, Hubei, P R China
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97
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Theodoridis S, Stefanaki A, Tezcan M, Aki C, Kokkini S, Vlachonasios KE. DNA barcoding in native plants of the Labiatae (Lamiaceae) family from Chios Island (Greece) and the adjacent Çeşme-Karaburun Peninsula (Turkey). Mol Ecol Resour 2012; 12:620-33. [PMID: 22394710 DOI: 10.1111/j.1755-0998.2012.03129.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The plant family Labiatae (Lamiaceae) is known for its fine medicinal and aromatic herbs like lavender, mint, oregano, sage and thyme and is a rich source of essential oils for the food, pharmaceutical and cosmetic industry. Besides its great economic importance, the Labiatae family contributes significantly to the endemic flora of Greece and Turkey. Owing to its economic and biological significance and to the difficult identification based on morphological characters of several of its taxa, the Labiatae family is an ideal case for developing DNA barcodes. The purpose of this study is to evaluate the utility of DNA barcoding on a local scale in discriminating Labiatae species in Chios Island (Greece) and the adjacent Çeşme-Karaburun Peninsula (Turkey). We chose three cpDNA regions (matK, rbcL, trnH-psbA) that were proposed by previous studies and tested them either as single region or as multiregion barcodes based on the criteria determined by Consortium for the Barcode of Life (CBOL). Our results show that matK and trnH-psbA taken as useful in discriminating species of the Labiatae, for the species we examined, as any multiregion combination. matK and trnH-psbA could serve as single-region barcodes for Labiatae species contributing to the conservation and the trade control of valuable plant resources.
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Affiliation(s)
- Spyros Theodoridis
- Postgraduate Studies Program, Conservation of Biodiversity and Sustainable Exploitation of Native Plants (BNP), School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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98
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Sun XQ, Zhu YJ, Guo JL, Peng B, Bai MM, Hang YY. DNA barcoding the Dioscorea in China, a vital group in the evolution of monocotyledon: use of matK gene for species discrimination. PLoS One 2012; 7:e32057. [PMID: 22363795 PMCID: PMC3282793 DOI: 10.1371/journal.pone.0032057] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 01/23/2012] [Indexed: 11/18/2022] Open
Abstract
Background Dioscorea is an important plant genus in terms of food supply and pharmaceutical applications. However, its classification and identification are controversial. DNA barcoding is a recent aid to taxonomic identification and uses a short standardized DNA region to discriminate plant species. In this study, the applicability of three candidate DNA barcodes (rbcL, matK, and psbA-trnH) to identify species within Dioscorea was tested. Methodology/Principal Findings One-hundred and forty-eight individual plant samples of Dioscorea, encompassing 38 species, seven varieties and one subspecies, representing majority species distributed in China of this genus, were collected from its main distributing areas. Samples were assessed by PCR amplification, sequence quality, extent of specific genetic divergence, DNA barcoding gap, and the ability to discriminate between species. matK successfully identified 23.26% of all species, compared with 9.30% for rbcL and 11.63% for psbA-trnH. Therefore, matK is recommended as the best DNA barcoding candidate. We found that the combination of two or three loci achieved a higher success rate of species discrimination than one locus alone. However, experimental cost would be much higher if two or three loci, rather than a single locus, were assessed. Conclusions We conclude that matK is a strong, although not perfect, candidate as a DNA barcode for Dioscorea identification. This assessment takes into account both its ability for species discrimination and the cost of experiments.
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Affiliation(s)
- Xiao-Qin Sun
- Jiangsu Province Key Laboratory for Plant Ex Situ Conservation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, People's Republic of China
| | - Ying-Jie Zhu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
| | - Jian-Lin Guo
- Jiangsu Province Key Laboratory for Plant Ex Situ Conservation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, People's Republic of China
| | - Bin Peng
- Jiangsu Province Key Laboratory for Plant Ex Situ Conservation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, People's Republic of China
| | - Ming-Ming Bai
- Jiangsu Province Key Laboratory for Plant Ex Situ Conservation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, People's Republic of China
| | - Yue-Yu Hang
- Jiangsu Province Key Laboratory for Plant Ex Situ Conservation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, People's Republic of China
- * E-mail:
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99
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Singh HK, Parveen I, Raghuvanshi S, Babbar SB. The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species. BMC Res Notes 2012; 5:42. [PMID: 22260646 PMCID: PMC3292824 DOI: 10.1186/1756-0500-5-42] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/19/2012] [Indexed: 11/27/2022] Open
Abstract
Background Based on the testing of several loci, predominantly against floristic backgrounds, individual or different combinations of loci have been suggested as possible universal DNA barcodes for plants. The present investigation was undertaken to check the applicability of the recommended locus/loci for congeneric species with Dendrobium species as an illustrative example. Results Six loci, matK, rbcL, rpoB, rpoC1, trnH-psbA spacer from the chloroplast genome and ITS, from the nuclear genome, were compared for their amplification, sequencing and species discrimination success rates among multiple accessions of 36 Dendrobium species. The trnH-psbA spacer could not be considered for analysis as good quality sequences were not obtained with its forward primer. Among the tested loci, ITS, recommended by some as a possible barcode for plants, provided 100% species identification. Another locus, matK, also recommended as a universal barcode for plants, resolved 80.56% species. ITS remained the best even when sequences of investigated loci of additional Dendrobium species available on the NCBI GenBank (93, 33, 20, 18 and 17 of ITS, matK, rbcL, rpoB and rpoC1, respectively) were also considered for calculating the percent species resolution capabilities. The species discrimination of various combinations of the loci was also compared based on the 36 investigated species and additional 16 for which sequences of all the five loci were available on GenBank. Two-locus combination of matK+rbcL recommended by the Plant Working Group of Consortium for Barcoding of Life (CBOL) could discriminate 86.11% of 36 species. The species discriminating ability of this barcode was reduced to 80.77% when additional sequences available on NCBI were included in the analysis. Among the recommended combinations, the barcode based on three loci - matK, rpoB and rpoC1- resolved maximum number of species. Conclusions Any recommended barcode based on the loci tested so far, is not likely to provide 100% species identification across the plant kingdom and thus is not likely to act as a universal barcode. It appears that barcodes, if based on single or limited locus(i), would be taxa specific as is exemplified by the success of ITS among Dendrobium species, though it may not be suitable for other plants because of the problems that are discussed.
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100
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Evaluation of the internal transcribed spacer 2 (ITS2) as a molecular marker for phylogenetic inference using sequence and secondary structure information in blow flies (Diptera: Calliphoridae). Genetica 2011; 139:1189-207. [PMID: 22198224 DOI: 10.1007/s10709-011-9621-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
Abstract
The internal transcribed spacer 2 (ITS2) is a small non-coding region located inside the nuclear ribosomal DNA cluster. ITS2 sequence variability is thought to be appropriate to differentiate species and for phylogenetic reconstructions analyses, which can be further improved if structural information is considered. We evaluated the potential of ITS2 as a molecular marker for phylogenetic inference in Calliphoridae (Diptera: Brachycera) using a broad range of inference methods and different substitution models, accounting or not for structural information. Sequence analyses revealed a hierarchically organized pattern of sequence variation and a small level of nucleotide substitution saturation. Intragenomic variation due to small sequence repeats was found mainly in the most variable domain (IV), but it has no significant impact on the phylogenetic signal at the species level. Inferred secondary structures revealed that GC pairs are more frequently found flanking bulges and loops regions in more conserved domains, thus ensuring structure stability. In the phylogenetic analyses, the use of substitution models accounting for structural information significantly improves phylogenetic inference in both neighbour-joining and Bayesian analyses, although the former provides limited resolution for dealing with highly divergent sequences. For Bayesian analyses, a significant improvement in likelihood was observed when considering structure information, although with small changes in topology and overall support, probably reflecting better evolutionary rates estimates. Based on these findings, ITS2 is a suitable molecular marker for phylogenetic analyses in Calliphoridae, at both species and generic level.
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