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Gorini T, Mezzasalma V, Deligia M, De Mattia F, Campone L, Labra M, Frigerio J. Check Your Shopping Cart: DNA Barcoding and Mini-Barcoding for Food Authentication. Foods 2023; 12:2392. [PMID: 37372604 DOI: 10.3390/foods12122392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The molecular approach of DNA barcoding for the characterization and traceability of food products has come into common use in many European countries. However, it is important to address and solve technical and scientific issues such as the efficiency of the barcode sequences and DNA extraction methods to be able to analyze all the products that the food sector offers. The goal of this study is to collect the most defrauded and common food products and identify better workflows for species identification. A total of 212 specimens were collected in collaboration with 38 companies belonging to 5 different fields: seafood, botanicals, agrifood, spices, and probiotics. For all the typologies of specimens, the most suitable workflow was defined, and three species-specific primer pairs for fish were also designed. Results showed that 21.2% of the analyzed products were defrauded. A total of 88.2% of specimens were correctly identified by DNA barcoding analysis. Botanicals (28.8%) have the highest number of non-conformances, followed by spices (28.5%), agrifood (23.5%), seafood (11.4%), and probiotics (7.7%). DNA barcoding and mini-barcoding are confirmed as fast and reliable methods for ensuring quality and safety in the food field.
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Affiliation(s)
- Tommaso Gorini
- FEM2-Ambiente, Piazza della Scienza 2, 20126 Milano, Italy
| | | | - Marta Deligia
- Department of Scienze Agrarie, Forestali e Alimentari, University of Turin, Via Verdi 8, 10124 Torino, Italy
| | | | - Luca Campone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Massimo Labra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Jessica Frigerio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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2
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Sokołowska J, Fuchs H, Celiński K. Assessment of ITS2 Region Relevance for Taxa Discrimination and Phylogenetic Inference among Pinaceae. PLANTS 2022; 11:plants11081078. [PMID: 35448806 PMCID: PMC9029031 DOI: 10.3390/plants11081078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
The internal transcribed spacer 2 (ITS2) is one of the best-known universal DNA barcode regions. This short nuclear region is commonly used not only to discriminate taxa, but also to reconstruct phylogenetic relationships. However, the efficiency of using ITS2 in these applications depends on many factors, including the family under study. Pinaceae represents the largest family of extant gymnosperms, with many species of great ecological, economic, and medical importance. Moreover, many members of this family are representatives of rare, protected, or endangered species. A simple method for the identification of Pinaceae species based on DNA is necessary for their effective protection, authentication of products containing Pinaceae representatives, or phylogenetic inference. In this study, for the first time, we conducted a comprehensive study summarizing the legitimacy of using the ITS2 region for these purposes. A total of 368 sequences representing 71 closely and distantly related taxa of the seven genera and three subfamilies of Pinaceae were characterized for genetic variability and divergence. Intra- and interspecies distances of ITS2 sequences as well as rates of sequence identification and taxa discrimination among Pinaceae at various taxonomic levels, i.e., the species complex, genus, subfamily, and family, were also determined. Our study provides a critical assessment of the suitability of the ITS2 nuclear DNA region for taxa discrimination among Pinaceae. The obtained results clearly show that its usefulness for this purpose is limited.
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Affiliation(s)
- Joanna Sokołowska
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, School of Natural Sciences, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
| | - Hanna Fuchs
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland;
| | - Konrad Celiński
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, School of Natural Sciences, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
- Correspondence:
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3
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Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese Curcuma (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera. FORESTS 2022. [DOI: 10.3390/f13020280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Curcuma is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of Curcuma (Chinese Curcuma, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese Curcuma species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese Curcuma with varying degrees of support using different methods and datasets.
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Mustafa AA, Derise MR, Yong WTL, Rodrigues KF. A Concise Review of Dendrocalamus asper and Related Bamboos: Germplasm Conservation, Propagation and Molecular Biology. PLANTS 2021; 10:plants10091897. [PMID: 34579429 PMCID: PMC8468032 DOI: 10.3390/plants10091897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Bamboos represent an emerging forest resource of economic significance and provide an avenue for sustainable development of forest resources. The development of the commercial bamboo industry is founded upon efficient molecular and technical approaches for the selection and rapid multiplication of elite germplasm for its subsequent propagation via commercial agro-forestry business enterprises. This review will delve into the micropropagation of Dendrocalamus asper, one of the most widely cultivated commercial varieties of bamboo, and will encompass the selection of germplasm, establishment of explants in vitro and micropropagation techniques. The currently available information pertaining to molecular biology, DNA barcoding and breeding, has been included, and potential areas for future research in the area of genetic engineering and gene regulation have been highlighted. This information will be of relevance to both commercial breeders and molecular biologists who have an interest in establishing bamboo as a crop of the future.
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5
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Wróbel A, Klichowska E, Baiakhmetov E, Nowak A, Nobis M. Invasion of Eragrostis albensis in Central Europe: distribution patterns, taxonomy and phylogenetic insight into the Eragrostis pilosa complex. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02507-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractThe Eragrostis pilosa complex (Poaceae) comprises five widely distributed and regionally invasive species—E. albensis, E. amurensis, E. imberbis, E. multicaulis, and E. pilosa, distinguished by tiny and variable morphological characters and with so far unknown phylogenetic relationships. Recently, some doubts have been raised about the status of an invasive glandular morphotype occurring in Central Europe assigned either to E. amurensis or to E. albensis. Here, we addressed this issue by analysing morphology, internal transcribed spacers of nuclear ribosomal DNA, and five inter-simple sequence repeat markers. The genetic evidence supported closer relationship of this glandular morphotype to eglandular E. albensis, widely established in Central Europe, than to glandular E. amurensis described from Asia. We propose to adopt a new taxonomic treatment that E. albensis includes both eglandular and glandular individuals, and to classify the glandular ones as E. albensis var. scholziana M. Nobis & A. Wróbel var. nova. Currently this new taxon is known from a dozen of localities in Central Europe and is invasive in the lower section of the Oder River valley, whereas Eragrostis albensis var. albensis has already spread widely across Europe in riparian phytocenoses and anthropogenic habitats. Since probably the first registered records in 1940s, it has been observed in European part of Russia, Belarus, Ukraine, Poland, Slovakia, Czech Republic, Germany, Austria, the Netherlands, and its further invasion is likely to proceed. We provided distribution maps concerning spread dynamics of E. albensis in Europe from 1947 to 2020. In total, the species has been observed on over 1300 localities so far, most of which were found after 2000.
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Abdel-Hamid AME, Elenazy HH, Abdel-Hameed UK. DNA barcoding of some taxa of genus Acacia and their phylogenetic relationship. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1938702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Amal M. E. Abdel-Hamid
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt
- Department of Biology, College of Sciences and Arts, Taibah University, Al Ula, Kingdom of Saudi Arabia
| | - Hanaa H. Elenazy
- Department of Biology, College of Science, Taibah University, Al Madinah, Kingdom of Saudi Arabia
| | - Usama K. Abdel-Hameed
- Department of Biology, College of Science, Taibah University, Al Madinah, Kingdom of Saudi Arabia
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
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7
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Isola D, Bartoli F, Langone S, Ceschin S, Zucconi L, Caneva G. Plant DNA Barcode as a Tool for Root Identification in Hypogea: The Case of the Etruscan Tombs of Tarquinia (Central Italy). PLANTS (BASEL, SWITZERLAND) 2021; 10:1138. [PMID: 34205139 PMCID: PMC8228792 DOI: 10.3390/plants10061138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022]
Abstract
Roots can produce mechanical and chemical alterations to building structures, especially in the case of underground historical artifacts. In archaeological sites, where vegetation plays the dual role of naturalistic relevance and potential threat, trees and bushes are under supervision. No customized measures can be taken against herbaceous plants lacking fast and reliable root identification methods that are useful to assess their dangerousness. In this study, we aimed to test the efficacy of DNA barcoding in identifying plant rootlets threatening the Etruscan tombs of the Necropolis of Tarquinia. As DNA barcode markers, we selected two sections of the genes rbcL and matK, the nuclear ribosomal internal transcribed spacer (nrITS), and the intergenic spacer psbA-trnH. All fourteen root samples were successfully sequenced and identified at species (92.9%) and genus level (7.01%) by GenBank matching and reference dataset implementation. Some eudicotyledons with taproots, such as Echium italicum L., Foeniculum vulgare Mill., and Reseda lutea L. subsp. lutea, showed a certain recurrence. Further investigations are needed to confirm this promising result, increasing the number of roots and enlarging the reference dataset with attention to meso-Mediterranean perennial herbaceous species. The finding of herbaceous plants roots at more than 3 m deep confirms their potential risk and underlines the importance of vegetation planning, monitoring, and management on archaeological sites.
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Affiliation(s)
- Daniela Isola
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy;
| | - Flavia Bartoli
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Simone Langone
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Simona Ceschin
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy;
| | - Giulia Caneva
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
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Thakur VV, Tripathi N, Tiwari S. DNA barcoding of some medicinally important plant species of Lamiaceae family in India. Mol Biol Rep 2021; 48:3097-3106. [PMID: 33913093 DOI: 10.1007/s11033-021-06356-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/16/2021] [Indexed: 11/24/2022]
Abstract
Several species of the Lamiaceae family are the primary source of bioactive aromatic oils and secondary metabolites, having broader applications in the cosmetics, pharmaceuticals, food, confectionery and liquor industries. Due to the scarcity of raw materials and high costs of this family's economically vital species, its products often adulterated to cater to the market's high demand. The present study provides a DNA based approach for identifying different species of this family. Henceforth, the performance of three already proposed barcode loci (matK, trnH-psbA and trnL) was examined for their PCR amplification and species recognition efficacy on various Lamiaceae species and cultivars using three different approaches such as pairwise genetic distance method, BLASTn and phylogenetic tree based on maximum likelihood (ML) analysis. Results illustrate that among all the DNA barcoding loci, matK locus can accurately and efficiently distinguish all the studied species followed by trnH-psbA and trnL. Present investigation may help diminish the illegal trade and events of adulteration of medicinally important plants species in genus Mentha, Ocimum and Plectranthus. This investigation will also help fulfil the scarcity of sequences of barcode loci of these species in the NCBI database. Apart from providing a molecular level reference for identifying processed herbal products, this technique also offers a convenient method for species identification and germplasm conservation of the Lamiaceae family.
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Affiliation(s)
- Vishwa V Thakur
- Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, 482004, India.,Lac Production Division, ICAR-Indian Institute of Natural Resins and Gums, Namkum, Ranchi, Jharkhand, 834010, India
| | - Niraj Tripathi
- Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, 482004, India
| | - Sharad Tiwari
- Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, 482004, India.
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9
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Jiang KW, Zhang R, Zhang ZF, Pan B, Tian B. DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage. PLANT DIVERSITY 2020; 42:376-385. [PMID: 33134622 PMCID: PMC7584798 DOI: 10.1016/j.pld.2020.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Dumasia taxonomy and classification have long been problematic. Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify. In this study, we evaluated the ability of six DNA barcoding sequences, one nuclear (ITS) and five chloroplast regions (trnH-psbA, matK, rbcL, trnL-trnF, psbB-psbF), to efficiently identify Dumasia species. Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation. Most combined analyses including ITS showed good species resolution and identification efficiency. We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia. The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches, which may result from cryptic differentiation. Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.
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Affiliation(s)
- Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Fu Zhang
- Department of Wetland, Southwest Forestry University, Kunming, 650224, China
| | - Bo Pan
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China
| | - Bin Tian
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
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10
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Ismail M, Ahmad A, Nadeem M, Javed MA, Khan SH, Khawaish I, Sthanadar AA, Qari SH, Alghanem SM, Khan KA, Khan MF, Qamer S. Development of DNA barcodes for selected Acacia species by using rbcL and matK DNA markers. Saudi J Biol Sci 2020; 27:3735-3742. [PMID: 33304185 PMCID: PMC7715041 DOI: 10.1016/j.sjbs.2020.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/28/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Acacia species are very important tree species in tropical and subtropical countries of the World for their economic and medicinal benefits. Precise identification of Acacia is very important to distinguish the invasive species from rare species however, it is difficult to differentiate Acacia species based on morphological charcters. In addition, precise identification is also important for wood charcterization in the forest industry as these species are declining due to illegal logging and deforestation. To overcome thsese limitations of morphological identification, DNA barcoding is being used as an efficient and quick approach for precise identification of tree species. In this study, we selected two chloroplast and plastid base DNA markers (rbcL and matK) for the identification of five selected tree species of Acacia (A. albida, A. ampliceps, A. catechu, A. coriacea and A. tortilis). The genomic DNA of the selected Acacia species was extracted, amplified through PCR using specific primers and subsequently sequenced through Sanger sequencing. In matK DNA marker the average AT nucleotide contents were higher (59.46%) and GC contents were lower (40.44%) as compared to the AT (55.40%) and GC content (44.54%) in rbcL marker. The means genetic distance K2P between the Acacia species was higher in matK (0.704%) as compared to rbcL (0.230%). All Acacia species could be identified based on unique SNPs profile. Based on SNP data profiles, DNA sequence based scannable QR codes were developed for accurate identification of Acacia species. The phylogenetic analysis based on both markers (rbcL and matK) showed that both A. coriacea and A. tortilis were closely related with each other and clustered in the same group while other two species A. albida and A. catechu were grouped together. The specie A. ampliceps remained ungrouped distantly, compared with other four species. These finding highlights the potential of DNA barcoding for efficient and reproducible identification of Acacia species.
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Affiliation(s)
- Muhammad Ismail
- Department of Forestry and Range Management, Faculty of Agriculture, University of Agriculture Faisalabad, Pakistan
| | - Aftab Ahmad
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.,Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Nadeem
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.,Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Asif Javed
- Department of Forestry and Range Management, Faculty of Agriculture, University of Agriculture Faisalabad, Pakistan.,Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Sultan Habibullah Khan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.,Center for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Iqra Khawaish
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.,Department of Biochemistry, Faculty of Sciences, University of Agriculture, Faisalabad, Pakistan
| | | | - Sameer H Qari
- Biology Department, Aljumum, University College, Umm Al-Qura University, Saudi Arabia
| | - Suliman M Alghanem
- Biology Department, Faculty of Science, Tabuk University, Tabuk 71491, Saudi Arabia
| | - Khalid Ali Khan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.,Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.,Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | | | - Samina Qamer
- Department of Zoology, Government College University, Faisalabad, Pakistan
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11
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DNA barcodes for delineating Clerodendrum species of North East India. Sci Rep 2020; 10:13490. [PMID: 32778674 PMCID: PMC7417596 DOI: 10.1038/s41598-020-70405-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
The diversified genus of Clerodendrum with its complex evolutionary history leads to taxonomic mystification. Unlike traditional taxonomic methods, DNA barcoding could be a promising tool for the identification and conservation of Clerodendrum species. This study was attempted to develop an efficient barcode locus in Clerodendrum species of North East India. We evaluated four barcode candidates (ITS2, matK, rbcL, ycf1) and its combinations in different Clerodendrum species. The reliability of barcodes to distinguish the species were calculated using genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods. The results exemplify that matK posse’s maximum number of variables and parsimony-informative sites (103/100), intra- (0.021 ± 0.001) and inter- (0.086 ± 0.005) specific divergences and species resolution rate (89.1%) followed by ITS2, ycf1, and rbcL. Among the combinatorial locus, ITS2 + matK showed the best species discrimination with distinctive barcode gaps. Therefore, we tentatively suggest that the combination of ITS2 + matK as core barcode for Clerodendrum and converted into quick response (QR) code. Hence, this finding indicates that DNA barcoding could provide consistent resources for species discrimination and resolve taxonomic controversies of the genus as well as set a preliminary assessment toward its biodiversity.
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12
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DNA Fingerprinting and Species Identification Uncovers the Genetic Diversity of Katsouni Pea in the Greek Islands Amorgos and Schinoussa. PLANTS 2020; 9:plants9040479. [PMID: 32283704 PMCID: PMC7238155 DOI: 10.3390/plants9040479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 11/17/2022]
Abstract
Pea (P. sativum L.), one of the most important legume crops worldwide, has been traditionally cultivated in Lesser Cyclades since ancient times. The commonly known traditional pea cultivar, ‘Katsouni’, is endemic to the islands of Amorgos and Schinoussa and is of great local economic importance. Despite the widespread cultivation of ‘Katsouni’ in both islands, it is still unknown whether the current Schinoussa and Amorgos pea populations are distinct landraces, and if they have common evolutionary origin. To assist conservation and breeding of the pea crop, the genetic diversity and phylogenetic relationships of 39 pea samples from Amorgos and 86 from Schinoussa were studied using DNA barcoding and ISSR marker analyses. The results indicate that both populations are different landraces with distinct geographical distribution and are more closely related to P. sativum subsp. elatius than the P. abyssinicum and P. fulvum species. Further characterization of the ‘Katsouni’ landraces for functional polymorphisms regarding pathogen resistance, revealed susceptibility to the powdery mildew (Erysiphe pisi DC.). This work represents the first investigation on the genetic diversity and population structure of the ‘Katsouni’ cultivar. Exploiting the local genetic diversity of traditional landraces is fundamental for conservation practices and crop improvement through breeding strategies.
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13
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DNA barcoding as a valuable molecular tool for the certification of planting materials in bamboo. 3 Biotech 2020; 10:59. [PMID: 32015955 DOI: 10.1007/s13205-019-2018-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
DNA barcodes developed for selected commercially important bamboo species can be utilized for the certification of planting stock in bamboo nurseries in absence of discriminatory features at the juvenile stage. Planting materials such as micropropagated plantlets, rhizome transplants and culm cuttings, generated at nursery level are directly procured for establishment of commercial plantations without any further verification. Very often misidentification and mixing up occur at nursery level and the error is not discovered until several years have passed. The present study evaluated the potentiality of seven Consortium for Barcode of Life (CBOL) recommended standard DNA barcode regions in commercially important bamboo species of India. Among the analyzed barcode regions, multiple sequence alignment (MSA) of psbA-trnH barcode region showed species-specific nucleotide differences in the studied bamboo taxa. The major nucleotide changes observed were transitions/transversions as well as insertions/deletions of nucleotides. Even though species-specific mononucleotide differences could be identified for most of the studied bamboo taxa, a small amount of sequence similarities were found in some of the Dendrocalamus and Bambusa species, which were grouped together in tree-based analysis. In subtribe Melocanninae, Ochlandra travancorica, Melocanna baccifera and M. clarkei showed unique species-specific psbA-trnH barcodes. Similarly, in the genus Oxytenanthera, unique species-specific psbA-trnH barcodes were obtained for O. monadelpha and O. parvifolia. Thus psbA-trnH barcode region generated distinct species-specific barcodes for commercial bamboo species in genera Bambusa, Dendrocalamus, Melocanna, Oxytenanthera as well as Ochlandra. Any national certification agency set up for the purpose can utilize psbA-trnH DNA barcode region to tag species identity and to establish the authenticity of multiplied planting materials in bamboos.
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14
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Garcia-Davila C, Aldana Gomero D, Renno JF, Diaz Soria R, Hidalgo Pizango G, Flores Llampazo G, Castro-Ruiz D, Mejia de Loayza E, Angulo Chavez C, Mader M, Tysklind N, Paredes-Villanueva K, Del Castillo Torres D, Degen B, Honorio Coronado EN. Molecular evidence for three genetic species of Dipteryx in the Peruvian Amazon. Genetica 2019; 148:1-11. [PMID: 31858318 DOI: 10.1007/s10709-019-00082-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/14/2019] [Indexed: 11/30/2022]
Abstract
There is a high international demand for timber from the genus Dipteryx, or "shihuahuaco" as it is known in Peru. Developing tools that allow the identification and discrimination of Dipteryx species is therefore important for supporting management of natural populations and to underpin legal trade of its timber. The objective of this study was the molecular characterization of Dipteryx species in the Peruvian Amazonia. Two plastid regions (cpDNA: trnH-psbA and matK) were sequenced and 11 microsatellite markers (nDNA) were genotyped for 32 individuals identified as Dipteryx charapilla, D. micrantha morphotype 1 and D. micrantha morphotype 2. Using the concatenated sequences of the plastid genes, we identified ten haplotypes that were not shared between the species or between the D. micrantha morphotypes. Haplotypic diversity was greater in D. micrantha morphotype 2 and D. charapilla than in D. micrantha morphotype 1, which presented only one haplotype with a wide distribution in Peru. The microsatellites allowed the discrimination of the same three clades and identified diagnostic alleles for each clade. These results allowed us to demonstrate that the two morphotypes of D. micrantha are different at both the plastid and nuclear markers, which supports the existence of three genetically distinct species in Peru. This study provides information for the genetic discrimination of Dipteryx species and emphasises the importance of conserving the genetic variability of this genus in the Peruvian Amazonia.
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Affiliation(s)
- Carmen Garcia-Davila
- Instituto de Investigaciones de la Amazonía Peruana, Laboratorio de Biología y Genética Molecular (LBGM), Carretera Iquitos-Nauta km 4.5, Iquitos, Peru.
| | - David Aldana Gomero
- Universidad Nacional Agraria La Molina, Facultad de Ciencias Forestales, Av. La Molina s.n, Lima, Peru
| | | | - Rossana Diaz Soria
- Instituto de Investigaciones de la Amazonía Peruana, Laboratorio de Biología y Genética Molecular (LBGM), Carretera Iquitos-Nauta km 4.5, Iquitos, Peru
| | - Gabriel Hidalgo Pizango
- Instituto de Investigaciones de la Amazonía Peruana, Programa de Investigación en Manejo de Bosques y Servicios Ambientales (PROBOSQUES), Av. Abelardo Quiñones km 2.5, Iquitos, Peru
| | - Gerardo Flores Llampazo
- Instituto de Investigaciones de la Amazonía Peruana, Programa de Investigación en Manejo de Bosques y Servicios Ambientales (PROBOSQUES), Av. Abelardo Quiñones km 2.5, Iquitos, Peru
| | - Diana Castro-Ruiz
- Instituto de Investigaciones de la Amazonía Peruana, Laboratorio de Biología y Genética Molecular (LBGM), Carretera Iquitos-Nauta km 4.5, Iquitos, Peru
| | - Eduardo Mejia de Loayza
- Instituto de Investigaciones de la Amazonía Peruana, Laboratorio de Biología y Genética Molecular (LBGM), Carretera Iquitos-Nauta km 4.5, Iquitos, Peru
| | - Carlos Angulo Chavez
- Instituto de Investigaciones de la Amazonía Peruana, Laboratorio de Biología y Genética Molecular (LBGM), Carretera Iquitos-Nauta km 4.5, Iquitos, Peru
| | - Malte Mader
- Johann Heinrich von Thünen-Institut, Institut für Forstgenetik, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Niklas Tysklind
- INRA, UMR0745 EcoFoG, AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, Campus Agronomique, Avenue de France, 97387, Kourou Cedex, France
| | - Kathelyn Paredes-Villanueva
- Carrera de Ingeniería Foresta, Laboratorio de Dendrocronología, Facultad de Ciencias Agrícolas, Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito, Santa Cruz, Bolivia
| | - Dennis Del Castillo Torres
- Instituto de Investigaciones de la Amazonía Peruana, Programa de Investigación en Manejo de Bosques y Servicios Ambientales (PROBOSQUES), Av. Abelardo Quiñones km 2.5, Iquitos, Peru
| | - Bernd Degen
- Johann Heinrich von Thünen-Institut, Institut für Forstgenetik, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Eurídice N Honorio Coronado
- Instituto de Investigaciones de la Amazonía Peruana, Programa de Investigación en Manejo de Bosques y Servicios Ambientales (PROBOSQUES), Av. Abelardo Quiñones km 2.5, Iquitos, Peru
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Genetic discrimination of the poisonous Urobotrya siamensis from the green-leaf vegetable ‘Pak-wan’. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Hind KR, Adal AM, Upson TM, Mahmoud SS. An assessment of plant DNA barcodes for the identification of cultivated Lavandula (Lamiaceae) taxa. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Wu W, Ng WL, Yang JX, Li WM, Ge XJ. High cryptic species diversity is revealed by genome-wide polymorphisms in a wild relative of banana, Musa itinerans, and implications for its conservation in subtropical China. BMC PLANT BIOLOGY 2018; 18:194. [PMID: 30217175 PMCID: PMC6137913 DOI: 10.1186/s12870-018-1410-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown. RESULTS Using genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event. CONCLUSION Our results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&P.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Wei-Lun Ng
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Jun-Xin Yang
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wei-Ming Li
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650 China
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Yan M, Xiong Y, Liu R, Deng M, Song J. The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks. FRONTIERS IN PLANT SCIENCE 2018; 9:569. [PMID: 29868047 PMCID: PMC5952231 DOI: 10.3389/fpls.2018.00569] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 05/10/2023]
Abstract
The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia - Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiaojiao Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shangrao Normal University, Shangrao, China
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Gale SW, Duangjai S, Li J, Ito Y, Watthana S, Termwutthipreecha P, Cheuk ML, Suddee S. Integrative analyses of Nervilia (Orchidaceae) section Linervia reveal further undescribed cryptic diversity in Thailand. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2017.1415233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Stephan W. Gale
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Sutee Duangjai
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jihong Li
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Yu Ito
- Plant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Santi Watthana
- School of Biology, Institute of Science, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima 30000, Thailand
| | - Phatsara Termwutthipreecha
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Mang Lung Cheuk
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Somran Suddee
- Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok 10900, Thailand
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Assessment of three plastid DNA barcode markers for identification of Clinacanthus nutans (Acanthaceae). 3 Biotech 2018; 8:62. [PMID: 29354373 DOI: 10.1007/s13205-018-1092-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/04/2018] [Indexed: 01/26/2023] Open
Abstract
This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C. nutans was carried out using NCBI's Basic Local Alignment Search Tool (BLAST). The rbcL and trnH-psbA regions successfully identified C. nutans with sequencing rates of 100% through BLAST identification. Molecular Evolutionary Genetics Analysis (MEGA) 6.0 was used to analyze interspecific and intraspecific divergence of plastid DNA sequences. rbcL and matK exhibited the lowest average interspecific distance (0.0487 and 0.0963, respectively), whereas trnH-psbA exhibited the highest average interspecific distance (0.2029). The R package Spider revealed that trnH-psbA correctly identified Barcode of Life Data System (BOLD) 96%, best close match 79%, and near neighbor 100% of the species, compared to matK (BOLD 72%; best close match 64%; near neighbor 78%) and rbcL (BOLD 77%; best close match 62%; near neighbor 88%). These results indicate that trnH-psbA is very effective at identifying C. nutans, as it performed well in discriminating species in Acanthaceae.
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Wu F, Ma J, Meng Y, Zhang D, Pascal Muvunyi B, Luo K, Di H, Guo W, Wang Y, Feng B, Zhang J. Potential DNA barcodes for Melilotus species based on five single loci and their combinations. PLoS One 2017; 12:e0182693. [PMID: 28910286 PMCID: PMC5598934 DOI: 10.1371/journal.pone.0182693] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 07/21/2017] [Indexed: 01/13/2023] Open
Abstract
Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae) and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS) and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI) had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production.
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Affiliation(s)
- Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jinxing Ma
- National Quality Control & Inspection Centre for Grassland Industry Products, National Animal Husbandry Service, Ministry of Agriculture, Beijing, China
| | - Yuqin Meng
- China Agricultural Veterinarian Biology Science and Technology Co. Ltd, Lanzhou, China
| | - Daiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Blaise Pascal Muvunyi
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Kai Luo
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Hongyan Di
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Wenli Guo
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Baochang Feng
- National Quality Control & Inspection Centre for Grassland Industry Products, National Animal Husbandry Service, Ministry of Agriculture, Beijing, China
- * E-mail: (BCF); (JYZ)
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- * E-mail: (BCF); (JYZ)
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Mishra P, Kumar A, Nagireddy A, Shukla AK, Sundaresan V. Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia. PLoS One 2017; 12:e0182836. [PMID: 28829803 PMCID: PMC5567895 DOI: 10.1371/journal.pone.0182836] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is used as a universal tool for delimiting species boundaries in taxonomically challenging groups, with different plastid and nuclear regions (rbcL, matK, ITS and psbA-trnH) being recommended as primary DNA barcodes for plants. We evaluated the feasibility of using these regions in the species-rich genus Terminalia, which exhibits various overlapping morphotypes with pantropical distribution, owing to its complex taxonomy. Terminalia bellerica and T. chebula are ingredients of the famous Ayurvedic Rasayana formulation Triphala, used for detoxification and rejuvenation. High demand for extracted phytochemicals as well as the high trade value of several species renders mandatory the need for the correct identification of traded plant material. Three different analytical methods with single and multilocus barcoding regions were tested to develop a DNA barcode reference library from 222 individuals representing 41 Terminalia species. All the single barcodes tested had a lower discriminatory power than the multilocus regions, and the combination of matK+ITS had the highest resolution rate (94.44%). The average intra-specific variations (0.0188±0.0019) were less than the distance to the nearest neighbour (0.106±0.009) with matK and ITS. Distance-based Neighbour Joining analysis outperformed the character-based Maximum Parsimony method in the identification of traded species such as T. arjuna, T. chebula and T. tomentosa, which are prone to adulteration. rbcL was shown to be a highly conservative region with only 3.45% variability between all of the sequences. The recommended barcode combination, rbcL+matK, failed to perform in the genus Terminalia. Considering the complexity of resolution observed with single regions, the present study proposes the combination of matK+ITS as the most successful barcode in Terminalia.
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Affiliation(s)
- Priyanka Mishra
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Amit Kumar
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Akshitha Nagireddy
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Ashutosh K. Shukla
- Biotechnology Division, CSIR—Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Velusamy Sundaresan
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
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Daïnou K, Blanc-Jolivet C, Degen B, Kimani P, Ndiade-Bourobou D, Donkpegan ASL, Tosso F, Kaymak E, Bourland N, Doucet JL, Hardy OJ. Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia. BMC Evol Biol 2016; 16:259. [PMID: 27903256 PMCID: PMC5131513 DOI: 10.1186/s12862-016-0831-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 11/17/2016] [Indexed: 12/22/2022] Open
Abstract
Background Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. Results West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. Conclusions Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0831-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kasso Daïnou
- Nature + asbl / TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium. .,Université d'Agriculture de Kétou, BP 43, Kétou, Benin.
| | - Céline Blanc-Jolivet
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Bernd Degen
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Priscilla Kimani
- Kenya Forestry Research Institute, Biotechnology Section, P. O. Box 20412-00200, Nairobi, Kenya
| | | | - Armel S L Donkpegan
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Félicien Tosso
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Esra Kaymak
- Evolutionary Biology and Ecology - CP 160⁄12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. Roosevelt 50, 1050, Brussels, Belgium
| | - Nils Bourland
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology - CP 160⁄12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. Roosevelt 50, 1050, Brussels, Belgium
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Kumar A, Mishra P, Baskaran K, Shukla AK, Shasany AK, Sundaresan V. Higher efficiency of ISSR markers over plastid psbA-trnH region in resolving taxonomical status of genus Ocimum L. Ecol Evol 2016; 6:7671-7682. [PMID: 30128120 PMCID: PMC6093152 DOI: 10.1002/ece3.2483] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 11/23/2022] Open
Abstract
High level of morphological as well as chemical variability exists within the genus Ocimum, and its taxonomy and phylogenetic relationships are still doubtful. For evaluating interspecific genetic relationships among the Ocimum species, genotyping with intersimple sequence repeat (ISSR) markers and sequence analyses of noncoding psbA‐trnH intergenic region belonging to chloroplast DNA were carried out. Although ISSR markers are highly efficient and reproducible, they have not been used extensively in phylogenetic studies. The use of the plastidial barcode candidate was expected to provide more variable and informative insight into evolutionary rates, and was thus employed as a phylogenetic marker to assess interspecific relationships. This study revealed that the ISSR markers were more efficient than psbA‐trnH sequences in resolving the current status of Ocimum L. genus. Distance‐ and character‐based methodological approaches applied on the molecular data with biparental and maternal inheritance were used for deducing the phylogenetic relationships among Ocimum species. Average polymorphic information content (0.344) and resolving power (6.285) depicted through ISSR markers proved to be efficient in discriminating the studied species of Ocimum. The primers used in this study revealed 99.585% polymorphism across the species demonstrating the polymorphic nature of ISSR markers.
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Affiliation(s)
- Amit Kumar
- Department of Plant Biology and Systematics CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre Bengaluru India
| | - Priyanka Mishra
- Department of Plant Biology and Systematics CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre Bengaluru India
| | - Kuppusamy Baskaran
- Department of Plant Biology and Systematics CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre Bengaluru India
| | - Ashutosh K Shukla
- Biotechnology Division CSIR - Central Institute of Medicinal and Aromatic Plants Lucknow India
| | - Ajit K Shasany
- Biotechnology Division CSIR - Central Institute of Medicinal and Aromatic Plants Lucknow India
| | - Velusamy Sundaresan
- Department of Plant Biology and Systematics CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre Bengaluru India
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Shaik RS, Zhu X, Clements DR, Weston LA. Understanding invasion history and predicting invasive niches using genetic sequencing technology in Australia: case studies from Cucurbitaceae and Boraginaceae. CONSERVATION PHYSIOLOGY 2016; 4:cow030. [PMID: 27766152 PMCID: PMC5069847 DOI: 10.1093/conphys/cow030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 05/07/2023]
Abstract
Part of the challenge in dealing with invasive plant species is that they seldom represent a uniform, static entity. Often, an accurate understanding of the history of plant introduction and knowledge of the real levels of genetic diversity present in species and populations of importance is lacking. Currently, the role of genetic diversity in promoting the successful establishment of invasive plants is not well defined. Genetic profiling of invasive plants should enhance our understanding of the dynamics of colonization in the invaded range. Recent advances in DNA sequencing technology have greatly facilitated the rapid and complete assessment of plant population genetics. Here, we apply our current understanding of the genetics and ecophysiology of plant invasions to recent work on Australian plant invaders from the Cucurbitaceae and Boraginaceae. The Cucurbitaceae study showed that both prickly paddy melon (Cucumis myriocarpus) and camel melon (Citrullus lanatus) were represented by only a single genotype in Australia, implying that each was probably introduced as a single introduction event. In contrast, a third invasive melon, Citrullus colocynthis, possessed a moderate level of genetic diversity in Australia and was potentially introduced to the continent at least twice. The Boraginaceae study demonstrated the value of comparing two similar congeneric species; one, Echium plantagineum, is highly invasive and genetically diverse, whereas the other, Echium vulgare, exhibits less genetic diversity and occupies a more limited ecological niche. Sequence analysis provided precise identification of invasive plant species, as well as information on genetic diversity and phylogeographic history. Improved sequencing technologies will continue to allow greater resolution of genetic relationships among invasive plant populations, thereby potentially improving our ability to predict the impact of these relationships upon future spread and better manage invaders possessing potentially diverse biotypes and exhibiting diverse breeding systems, life histories and invasion histories.
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Affiliation(s)
- Razia S. Shaik
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Xiaocheng Zhu
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - David R. Clements
- Department of Biology, Trinity Western University, Langley, BC, CanadaV2Y 1Y1
| | - Leslie A. Weston
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Locked Bag 588, Wagga Wagga, NSW 2678, Australia
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Hassold S, Lowry PP, Bauert MR, Razafintsalama A, Ramamonjisoa L, Widmer A. DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species. PLoS One 2016; 11:e0157881. [PMID: 27362258 PMCID: PMC4928830 DOI: 10.1371/journal.pone.0157881] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/05/2016] [Indexed: 12/01/2022] Open
Abstract
Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world’s most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods.
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Affiliation(s)
- Sonja Hassold
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, Missouri, United States of America
- ISYEB (UMR 7205), Département Systématique et Evolution, Muséum National d’Histoire Naturelle, Paris, France
| | | | | | | | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- * E-mail:
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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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Bhagwat RM, Dholakia BB, Kadoo NY, Balasundaran M, Gupta VS. Two New Potential Barcodes to Discriminate Dalbergia Species. PLoS One 2015; 10:e0142965. [PMID: 26569490 PMCID: PMC4646644 DOI: 10.1371/journal.pone.0142965] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 10/29/2015] [Indexed: 12/13/2022] Open
Abstract
DNA barcoding enables precise identification of species from analysis of unique DNA sequence of a target gene. The present study was undertaken to develop barcodes for different species of the genus Dalbergia, an economically important timber plant and is widely distributed in the tropics. Ten Dalbergia species selected from the Western Ghats of India were evaluated using three regions in the plastid genome (matK, rbcL, trnH-psbA), a nuclear transcribed spacer (nrITS) and their combinations, in order to discriminate them at species level. Five criteria: (i) inter and intraspecific distances, (ii) Neighbor Joining (NJ) trees, (iii) Best Match (BM) and Best Close Match (BCM), (iv) character based rank test and (v) Wilcoxon signed rank test were used for species discrimination. Among the evaluated loci, rbcL had the highest success rate for amplification and sequencing (97.6%), followed by matK (97.0%), trnH-psbA (94.7%) and nrITS (80.5%). The inter and intraspecific distances, along with Wilcoxon signed rank test, indicated a higher divergence for nrITS. The BM and BCM approaches revealed the highest rate of correct species identification (100%) with matK, matK+rbcL and matK+trnH-psb loci. These three loci, along with nrITS, were further supported by character based identification method. Considering the overall performance of these loci and their ranking with different approaches, we suggest matK and matK+rbcL as the most suitable barcodes to unambiguously differentiate Dalbergia species. These findings will potentially be helpful in delineating the various species of Dalbergia genus, as well as other related genera.
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Affiliation(s)
- Rasika M. Bhagwat
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Bhushan B. Dholakia
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Narendra Y. Kadoo
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - M. Balasundaran
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India
| | - Vidya S. Gupta
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
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Hartvig I, Czako M, Kjær ED, Nielsen LR, Theilade I. The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.). PLoS One 2015; 10:e0138231. [PMID: 26375850 PMCID: PMC4573973 DOI: 10.1371/journal.pone.0138231] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/26/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions.
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Affiliation(s)
- Ida Hartvig
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Mihaly Czako
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Erik Dahl Kjær
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Lene Rostgaard Nielsen
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Ida Theilade
- Global Development, Department of Food and Resource Economics, University of Copenhagen, Frederiksberg, Denmark
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Sochor M, Vašut RJ, Sharbel TF, Trávníček B. How just a few makes a lot: Speciation via reticulation and apomixis on example of European brambles (Rubus subgen. Rubus, Rosaceae). Mol Phylogenet Evol 2015; 89:13-27. [DOI: 10.1016/j.ympev.2015.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 03/31/2015] [Accepted: 04/06/2015] [Indexed: 10/23/2022]
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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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Williams AV, Boykin LM, Howell KA, Nevill PG, Small I. The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene. PLoS One 2015; 10:e0125768. [PMID: 25955637 PMCID: PMC4425659 DOI: 10.1371/journal.pone.0125768] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 03/26/2015] [Indexed: 11/25/2022] Open
Abstract
Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 158,724 bp in size, comprising inverted repeats of 25,925 bp and single-copy regions of 88,576 bp and 18,298 bp. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease complex.
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Affiliation(s)
- Anna V. Williams
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, Fraser Avenue, Kings Park, Western Australia, Australia
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Laura M. Boykin
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Katharine A. Howell
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Paul G. Nevill
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, Fraser Avenue, Kings Park, Western Australia, Australia
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Crawley, Western Australia, Australia
- * E-mail:
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Utsunomia R, Pansonato-Alves JC, Costa-Silva GJ, Mendonça FF, Scacchetti PC, Oliveira C, Foresti F. Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification. NEOTROPICAL ICHTHYOLOGY 2015. [DOI: 10.1590/1982-0224-20140039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The fish species Synbranchus marmoratushas been reported to exist as a species complex due to high intraspecific karyotypic variability in spite of the difficulty or impossibility to distinguish them using morphological traits alone. The goal of this work was to use cytogenetic and molecular methods to determine the species delimitations and understand the karyoevolution ofS. marmoratususing samples collected from distinct Brazilian localities. Among the analyzed specimens, a large degree of cytogenetic variation related to diploid numbers and karyotype structure was observed, with karyotypes showing 2n=42, 44 and 46 chromosomes. In addition, using sequences of three mitochondrial genes, the phylogenetic relationships between every sample with a known karyotype were determined, which revealed significant nucleotide divergence among the karyomorphs. Also, the analyses indicate that chromosomal rearrangements occurred independently within the distinct lineages of S. marmoratuscomplex, which resulted in the appearance of distinct karyotypic variants in a non-linear fashion related to diploid numbers and in the appearance of similar non-homologous chromosomes. Finally, the integration of both molecular cytogenetic and phylogenetic approaches allowed the determination of specific chromosomes possibly involved in rearrangements and a better understanding about the evolutionary processes involved in the differentiation ofSynbranchusgenus.
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TALLEI TRINAEKAWATI, KOLONDAM BEIVYJONATHAN. DNA Barcoding of Sangihe Nutmeg ( Myristica fragrans ) using mat K Gene. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.4308/hjb.22.1.41] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Yan LJ, Liu J, Möller M, Zhang L, Zhang XM, Li DZ, Gao LM. DNA barcoding ofRhododendron(Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains. Mol Ecol Resour 2014; 15:932-44. [DOI: 10.1111/1755-0998.12353] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/22/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Li-Jun Yan
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Germplasm Bank of Wild Species; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jie Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
| | - Michael Möller
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Royal Botanic Garden Edinburgh; 20A Inverleith Row Edinburgh EH3 5LR UK
| | - Lin Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Xue-Mei Zhang
- Landscape and Horticultural College; Yunnan Agricultural University; Kunming 650201 Yunnan China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Germplasm Bank of Wild Species; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
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Galimberti A, De Mattia F, Bruni I, Scaccabarozzi D, Sandionigi A, Barbuto M, Casiraghi M, Labra M. A DNA barcoding approach to characterize pollen collected by honeybees. PLoS One 2014; 9:e109363. [PMID: 25296114 PMCID: PMC4190116 DOI: 10.1371/journal.pone.0109363] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/02/2014] [Indexed: 11/18/2022] Open
Abstract
In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy). A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study) was assembled. The database was used to identify pollen collected from the hives. Fifty-two plant species were identified at the molecular level. Results suggested rbcL alone could not distinguish among congeneric plants; however, psbA-trnH identified most of the pollen samples at the species level. Substantial variability in pollen composition was observed between the highest elevation locality (Alpe Moconodeno), characterized by arid grasslands and a rocky substrate, and the other two sites (Cornisella and Ortanella) at lower altitudes. Pollen from Ortanella and Cornisella showed the presence of typical deciduous forest species; however in samples collected at Ortanella, pollen of the invasive Lonicera japonica, and the ornamental Pelargonium x hortorum were observed. Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands.
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Affiliation(s)
- Andrea Galimberti
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Fabrizio De Mattia
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Ilaria Bruni
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | | | - Anna Sandionigi
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Michela Barbuto
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Maurizio Casiraghi
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
| | - Massimo Labra
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Milano, Italy
- * E-mail:
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Vivas CV, Moraes RCS, Alves-Araújo A, Alves M, Mariano-Neto E, van den Berg C, Gaiotto FA. DNA barcoding in Atlantic Forest plants: What is the best marker for Sapotaceae species identification? Genet Mol Biol 2014; 37:662-70. [PMID: 25505841 PMCID: PMC4261966 DOI: 10.1590/s1415-47572014005000019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/15/2014] [Indexed: 11/21/2022] Open
Abstract
The Atlantic Forest is a phytogeographic domain with a high rate of endemism and large species diversity. The Sapotaceae is a botanical family for which species identification in the Atlantic Forest is difficult. An approach that facilitates species identification in the Sapotaceae is urgently needed because this family includes threatened species and valuable timber species. In this context, DNA barcoding could provide an important tool for identifying species in the Atlantic Forest. In this work, we evaluated four plant barcode markers (matK, rbcL, trnH-psbA and the nuclear ribosomal internal transcribed spacer region - ITS) in 80 samples from 26 species of Sapotaceae that occur in the Atlantic Forest. ITS yielded the highest average interspecific distance (0.122), followed by trnH-psbA (0.019), matK (0.008) and rbcL (0.002). For species discrimination, ITS provided the best results, followed by matK, trnH-psbA and rbcL. Furthermore, the combined analysis of two, three or four markers did not result in higher rates of discrimination than obtained with ITS alone. These results indicate that the ITS region is the best option for molecular identification of Sapotaceae species from the Atlantic Forest.
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Affiliation(s)
- Caio Vinicius Vivas
- Departamento de Ciências Biológicas,
Universidade Estadual de Santa Cruz,
Ilhéus,
BA,
Brazil
| | | | - Anderson Alves-Araújo
- Departamento de Ciências Agrárias e Biológicas,
Universidade Federal do Espírito Santo,
São Mateus,
ES,
Brazil
| | - Marccus Alves
- Departamento de Botânica,
Universidade Federal de Pernambuco,
Recife,
PE,
Brazil
| | | | - Cássio van den Berg
- Departamento de Ciências Biológicas,
Universidade Estadual de Feira de Santana,
Feira de Santana,
BA,
Brazil
| | - Fernanda Amato Gaiotto
- Departamento de Ciências Biológicas,
Universidade Estadual de Santa Cruz,
Ilhéus,
BA,
Brazil
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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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Bruni I, Galimberti A, Caridi L, Scaccabarozzi D, De Mattia F, Casiraghi M, Labra M. A DNA barcoding approach to identify plant species in multiflower honey. Food Chem 2014; 170:308-15. [PMID: 25306350 DOI: 10.1016/j.foodchem.2014.08.060] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 05/25/2014] [Accepted: 08/13/2014] [Indexed: 01/09/2023]
Abstract
The purpose of this study was to test the ability of DNA barcoding to identify the plant origins of processed honey. Four multifloral honeys produced at different sites in a floristically rich area in the northern Italian Alps were examined by using the rbcL and trnH-psbA plastid regions as barcode markers. An extensive reference database of barcode sequences was generated for the local flora to determine the taxonomic composition of honey. Thirty-nine plant species were identified in the four honey samples, each of which originated from a mix of common plants belonging to Castanea, Quercus, Fagus and several herbaceous taxa. Interestingly, at least one endemic plant was found in all four honey samples, providing a clear signature for the geographic identity of these products. DNA of the toxic plant Atropa belladonna was detected in one sample, illustrating the usefulness of DNA barcoding for evaluating the safety of honey.
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Affiliation(s)
- I Bruni
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, 20126 Milano, Italy
| | - A Galimberti
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, 20126 Milano, Italy
| | - L Caridi
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, 20126 Milano, Italy
| | - D Scaccabarozzi
- Parco Regionale della Grigna Settentrionale, Via Fornace Merlo 2, 23816 Barzio, Italy
| | - F De Mattia
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, 20126 Milano, Italy
| | - M Casiraghi
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, 20126 Milano, Italy
| | - M Labra
- Università degli Studi di Milano-Bicocca, ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Piazza della Scienza 2, 20126 Milano, Italy.
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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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Vinitha MR, Kumar US, Aishwarya K, Sabu M, Thomas G. Prospects for discriminating Zingiberaceae species in India using DNA barcodes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:760-773. [PMID: 24612741 DOI: 10.1111/jipb.12189] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/20/2014] [Indexed: 06/03/2023]
Abstract
We evaluated nine plastid (matK, rbcL, rpoC1, rpoB, rpl36-rps8, ndhJ, trnL-F, trnH-psbA, accD) and two nuclear (ITS and ITS2) barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction (PCR) amplicons in all the accessions tested. However, only 35 (58%) and 40 accessions (66%) yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species (75%) into monophyletic groups and five species into two paraphyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species (60%), and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence of natural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of ITS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.
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Gao T, Ma X, Zhu X. Use of the psbA-trnH region to authenticate medicinal species of Fabaceae. Biol Pharm Bull 2014; 36:1975-9. [PMID: 24432382 DOI: 10.1248/bpb.b13-00611] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fabaceae is a huge family that contains a large number of medicinal plants, many of which are commonly used in Chinese traditional medicine. However, traditional taxonomy has not been able to meet the complicated demands of species discrimination within Fabaceae. Thus, we employed a famous DNA barcode, the psbA-trnH region, to discriminate commonly used medicinal species of the family Fabaceae. Here, the psbA-trnH regions derived from 152 samples were amplified. These samples represented 104 Fabaceae medicinal species from 60 genera, including 25 authentic Fabaceae species listed in the Chinese pharmacopoeia and common adulterant species. The results indicate that the psbA-trnH region performed well in terms of its universality and high variability in length and composition. Species discriminative power analysis of the psbA-trnH region showed that 91.3% of species could be identified successfully by the BLAST1 method in conjunction with the nearest distance method. And, the species resolution rate of the TaxonGap method exceeded 93%. The results provide support for the use of the psbA-trnH plastid region as a sensitive marker to the authentication of Fabaceae medicinal plants.
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Studying genetic variability of pomegranate (Punica granatum L.) based on chloroplast DNA and barcode genes. Mol Biotechnol 2014; 55:249-59. [PMID: 23797804 DOI: 10.1007/s12033-013-9676-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Chloroplast DNA has been used extensively to analyze plant phylogenies at different taxonomic levels because of its size, organization and sequence conservation. In the present research, two chloroplastic regions, petA–psaJ, trnC–trnD and four DNA barcodes (trnH–psbA, ITS, rbcL, matK), were used to introduce suitable regions for the assessment of genetic diversity among P. granatum L. genotypes. Analysis of psbE–petL in petA–psaJ region revealed 1,300 nucleotides with 4.29 % genetic diversity among genotypes, while trnC–petN in trnC–trnD region showed 1.8 % genetic diversity. Therefore, despite the results obtained from the study of other plants, the trnC–trnD region had a low potential for the evaluation of diversity among pomegranate genotypes. Analysis of DNA barcodes in pomegranate showed that trnH–psbA (genetic diversity 2.91 %) provides the highest intra-species variation, followed by ITS (genetic diversity 0.44 %). Eighteen genotypes from different geographical origins of Iran were used to investigate psbE–petL and trnH–psbA potential as novel barcodes to determine genetic polymorphism and characterize pomegranate genotypes. The results suggested that two regions, psbE–petL and trnH–psbA, were more suitable for determining intra-species relationships of pomegranate.
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44
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Ajmal Ali M, Gyulai G, Hidvégi N, Kerti B, Al Hemaid FM, Pandey AK, Lee J. The changing epitome of species identification - DNA barcoding. Saudi J Biol Sci 2014; 21:204-31. [PMID: 24955007 PMCID: PMC4061418 DOI: 10.1016/j.sjbs.2014.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/22/2014] [Accepted: 03/23/2014] [Indexed: 01/11/2023] Open
Abstract
The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.
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Affiliation(s)
- M. Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Gábor Gyulai
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Norbert Hidvégi
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Balázs Kerti
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Fahad M.A. Al Hemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Arun K. Pandey
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Joongku Lee
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305 806, South Korea
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45
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Souza IM, Funch LS, de Queiroz LP. Morphological analyses suggest a new taxonomic circumscription for Hymenaea courbaril L. (Leguminosae, Caesalpinioideae). PHYTOKEYS 2014; 38:101-118. [PMID: 25009440 PMCID: PMC4086212 DOI: 10.3897/phytokeys.38.7408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/02/2014] [Indexed: 06/03/2023]
Abstract
Hymenaea is a genus of the Resin-producing Clade of the tribe Detarieae (Leguminosae: Caesalpinioideae) with 14 species. Hymenaea courbaril is the most widespread species of the genus, ranging from southern Mexico to southeastern Brazil. As currently circumscribed, Hymenaea courbaril is a polytypic species with six varieties: var. altissima, var. courbaril, var. longifolia, var. stilbocarpa, var. subsessilis, and var. villosa. These varieties are distinguishable mostly by traits related to leaflet shape and indumentation, and calyx indumentation. We carried out morphometric analyses of 14 quantitative (continuous) leaf characters in order to assess the taxonomy of Hymenaea courbaril under the Unified Species Concept framework. Cluster analysis used the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Bray-Curtis dissimilarity matrices. Principal Component Analyses (PCA) were carried out based on the same morphometric matrix. Two sets of Analyses of Similarity and Non Parametric Multivariate Analysis of Variance were carried out to evaluate statistical support (1) for the major groups recovered using UPGMA and PCA, and (2) for the varieties. All analyses recovered three major groups coincident with (1) var. altissima, (2) var. longifolia, and (3) all other varieties. These results, together with geographical and habitat information, were taken as evidence of three separate metapopulation lineages recognized here as three distinct species. Nomenclatural adjustments, including reclassifying formerly misapplied types, are proposed.
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Affiliation(s)
- Isys Mascarenhas Souza
- Universidade Estadual de Feira de Santana, Programa de Pós-graduação em Botânica,Herbário, Km 03-BR 116, Campus. 44031-460, Feira de Santana, Bahia, Brasil
| | - Ligia Silveira Funch
- Universidade Estadual de Feira de Santana, Programa de Pós-graduação em Botânica,Herbário, Km 03-BR 116, Campus. 44031-460, Feira de Santana, Bahia, Brasil
| | - Luciano Paganucci de Queiroz
- Universidade Estadual de Feira de Santana, Programa de Pós-graduação em Botânica,Herbário, Km 03-BR 116, Campus. 44031-460, Feira de Santana, Bahia, Brasil
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Papadopoulou A, Chesters D, Coronado I, De la Cadena G, Cardoso A, Reyes JC, Maes JM, Rueda RM, Gómez-Zurita J. Automated DNA-based plant identification for large-scale biodiversity assessment. Mol Ecol Resour 2014; 15:136-52. [PMID: 24666885 DOI: 10.1111/1755-0998.12256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/17/2014] [Accepted: 02/22/2014] [Indexed: 11/29/2022]
Abstract
Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable, markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic inference. We describe the strategies used to establish these steps and the optimization of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.
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Affiliation(s)
- Anna Papadopoulou
- Animal Biodiversity and Evolution, Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), 08003, Barcelona, Spain
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47
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Gere J, Yessoufou K, Daru BH, Mankga LT, Maurin O, van der Bank M. Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae. Zookeys 2013; 365:129-47. [PMID: 24453555 PMCID: PMC3890675 DOI: 10.3897/zookeys.365.5728] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 09/13/2013] [Indexed: 11/19/2022] Open
Abstract
Recent studies indicate that the discriminatory power of the core DNA barcodes (rbcLa + matK) for land plants may have been overestimated since their performance have been tested only on few closely related species. In this study we focused mainly on how the addition of complementary barcodes (nrITS and trnH-psbA) to the core barcodes will affect the performance of the core barcodes in discriminating closely related species from family to section levels. In general, we found that the core barcodes performed poorly compared to the various combinations tested. Using multiple criteria, we finally advocated for the use of the core + trnH-psbA as potential DNA barcode for the family Combretaceae at least in southern Africa. Our results also indicate that the success of DNA barcoding in discriminating closely related species may be related to evolutionary and possibly the biogeographic histories of the taxonomic group tested.
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Affiliation(s)
- Jephris Gere
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
| | - Kowiyou Yessoufou
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
- C4 EcoSolutions, 9 Mohr Road Tokai, Cape Town, South Africa 7945
| | - Barnabas H. Daru
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
| | - Ledile T. Mankga
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
| | - Olivier Maurin
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
| | - Michelle van der Bank
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, South Africa
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48
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Laiou A, Mandolini LA, Piredda R, Bellarosa R, Simeone MC. DNA barcoding as a complementary tool for conservation and valorisation of forest resources. Zookeys 2013; 365:197-213. [PMID: 24453558 PMCID: PMC3890678 DOI: 10.3897/zookeys.365.5670] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 12/06/2013] [Indexed: 11/17/2022] Open
Abstract
Since the pre-historic era, humans have been using forests as a food, drugs and handcraft reservoir. Today, the use of botanical raw material to produce pharmaceuticals, herbal remedies, teas, spirits, cosmetics, sweets, dietary supplements, special industrial compounds and crude materials constitute an important global resource in terms of healthcare and economy. In recent years, DNA barcoding has been suggested as a useful molecular technique to complement traditional taxonomic expertise for fast species identification and biodiversity inventories. In this study, in situ application of DNA barcodes was tested on a selected group of forest tree species with the aim of contributing to the identification, conservation and trade control of these valuable plant resources. The "core barcode" for land plants (rbcL, matK, and trnH-psbA) was tested on 68 tree specimens (24 taxa). Universality of the method, ease of data retrieval and correct species assignment using sequence character states, presence of DNA barcoding gaps and GenBank discrimination assessment were evaluated. The markers showed different prospects of reliable applicability. RbcL and trnH-psbA displayed 100% amplification and sequencing success, while matK did not amplify in some plant groups. The majority of species had a single haplotype. The trnH-psbA region showed the highest genetic variability, but in most cases the high intraspecific sequence divergence revealed the absence of a clear DNA barcoding gap. We also faced an important limitation because the taxonomic coverage of the public reference database is incomplete. Overall, species identification success was 66.7%. This work illustrates current limitations in the applicability of DNA barcoding to taxonomic forest surveys. These difficulties urge for an improvement of technical protocols and an increase of the number of sequences and taxa in public databases.
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Affiliation(s)
- Angeliki Laiou
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
| | - Luca Aconiti Mandolini
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
| | - Roberta Piredda
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
| | - Rosanna Bellarosa
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
| | - Marco Cosimo Simeone
- Department of Agriculture, Forests, Nature and Energy (DAFNE) - Università degli Studi della Tuscia, via S. Camillo de’ Lellis, 01100 Viterbo, Italy
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Christina VLP, Annamalai A. Nucleotide based validation of Ocimum species by evaluating three candidate barcodes of the chloroplast region. Mol Ecol Resour 2013; 14:60-8. [PMID: 24164957 DOI: 10.1111/1755-0998.12167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 08/29/2013] [Accepted: 08/29/2013] [Indexed: 11/27/2022]
Abstract
The genus Ocimum comprises of several medicinally important species which frequently fall prey to adulteration due to misidentification. A proficient method is hence required to solve the problems that exist in differentiating its various morphotypes. In plants, candidate DNA barcodes of the chloroplast and nuclear regions have proved to be a great success in the validation of several plant families. Hence, this study involves the use of the molecular-based DNA barcoding method to identify some of the most common and useful species of the genus Ocimum (Tulsi). Here, DNA amplification of three candidate barcodes of the chloroplast genome viz. matK, rbcL and psbA-trnH was performed, to access their ability to produce high sequence variability. The discrimination among species was performed using the Kimura 2-parameter and maximum composite likelihood methods. On analysing the sequence data, the psbA-trnH region proved to be the most suitable candidate barcode and gave an overall variation of 7.3% at the interspecies level. A clear differentiation was found at the species level, showing a maximum distance of 0.264 between dissimilar species. Also, phylogenetic analysis led to the successful identification of hybrids, while it failed to do so at the variety level. Hence, it can be inferred that DNA barcoding is ideal for species-level identification of the genus Ocimum.
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Affiliation(s)
- V L P Christina
- Department of Biotechnology, School of Biotechnology and Health Sciences, Karunya Institute of Technology and Sciences, Karunya University, Coimbatore, 641114, Tamil Nadu, India
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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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