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Oliveira M, Azevedo L, Ballard D, Branicki W, Amorim A. Using plants in forensics: State-of-the-art and prospects. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111860. [PMID: 37683985 DOI: 10.1016/j.plantsci.2023.111860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
The increasing use of plant evidence in forensic investigations gave rise to a powerful new discipline - Forensic Botany - that analyses micro- or macroscopic plant materials, such as the totality or fragments of an organ (i.e., leaves, stems, seeds, fruits, roots) and tissue (i.e., pollen grains, spores, fibers, cork) or its chemical composition (i. e., secondary metabolites, isotopes, DNA, starch grains). Forensic botanists frequently use microscopy, chemical analysis, and botanical expertise to identify and interpret evidence crucial to solving civil and criminal issues, collaborating in enforcing laws or regulations, and ensuring public health safeguards. The present work comprehensively examines the current state and future potential of Forensic Botany. The first section conveys the critical steps of plant evidence collection, documentation, and preservation, emphasizing the importance of these initial steps in maintaining the integrity of the items. It explores the different molecular analyses, covering the identification of plant species and varieties or cultivars, and discusses the limitations and challenges of these techniques in forensics. The subsequent section covers the diversity of Forensic Botany approaches, examining how plant evidence exposes food and pharmaceutical frauds, uncovers insufficient or erroneous labeling, traces illegal drug trafficking routes, and combats the illegal collection or trade of protected species and derivatives. National and global security issues, including the implications of biological warfare, bioterrorism, and biocrime are addressed, and a review of the contributions of plant evidence in crime scene investigations is provided, synthesizing a comprehensive overview of the diverse facets of Forensic Botany.
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Affiliation(s)
- Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
| | - Luísa Azevedo
- UMIB - Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - David Ballard
- King's Forensics, King's College London, London, United Kingdom
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland; Institute of Forensic Research, Kraków, Poland
| | - Antonio Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FCUP - Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Monterisi S, Zuluaga MYA, Porceddu A, Cesco S, Pii Y. The Application of High-Resolution Melting Analysis to trnL (UAA) Intron Allowed a Qualitative Identification of Apple Juice Adulterations. Foods 2023; 12:foods12071437. [PMID: 37048258 PMCID: PMC10093500 DOI: 10.3390/foods12071437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Food authenticity plays a pivotal role in the modern age since an increased consumers awareness has led them to pay more attention to food commodities. For this reason, it is important to have reliable and fast techniques able to detect possible adulterations in food, which affect qualitative and economic value. Therefore, the aim of this study was to detect possible adulterations in apple juice from others fruit species (i.e., pear, peach, and kiwi) combining DNA barcoding approach, using trnL (UAA) intron, with high resolution melting analysis (HRMA). A preliminary phylogenetic analysis, using sequences retrieved by the GenBank, confirmed the discriminatory power of trnL (UAA) intron among the four fruit species examined. Moreover, the sequencing of the trnL (UAA) fragments obtained from apple, pear, peach, and kiwi, demonstrated the suitability of an inner shorter sequence, P6 loop, to differentiate the considered species. The HRMA coupled with trnL (UAA) intron allowed discrimination among the four fruits but provided incomplete results for juices. Whereas the HRMA targeting the P6 loop amplicons confirmed the suitability of the technique to qualitatively distinguish fruit juices composed by the combination of apple/pear and apple/peach. However, the impossibility of discriminating apple/kiwi juices from the pure kiwi sample highlighted limitations, most likely related to the DNA extraction process. This hypothesis was further confirmed by analyzing DNA blends obtained by combining nucleic acids extracted from pure matrixes (i.e., apple and kiwi fruits). In this specific case, the application of HRMA allowed both qualitative and quantitative assessment of the samples.
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Decoding herbal materials of TCM preparations with the multi-barcode sequencing approach. Sci Rep 2022; 12:5988. [PMID: 35397643 PMCID: PMC8994760 DOI: 10.1038/s41598-022-09979-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/29/2022] [Indexed: 12/22/2022] Open
Abstract
With the rapid development of high-throughput sequencing technology, approaches for assessing biological ingredients in Traditional Chinese Medicine (TCM) preparations have also advanced. Using a multi-barcode sequencing approach, all biological ingredients could be identified from TCM preparations in theory, as long as their DNA is present. The biological ingredients of several classical TCM preparations were analyzed successfully based on this approach in previous studies. However, the universality, sensitivity and reliability of this approach on a diverse set of TCM preparations remain unclear. In this study, we selected four representative TCM preparations, namely Bazhen Yimu Wan, Da Huoluo Wan, Niuhuang Jiangya Wan, and You Gui Wan, for concrete assessment of the multi-barcode sequencing approach. Based on ITS2 and trnL biomarkers, we have successfully detected the prescribed herbal materials (PHMs) in these representative TCM preparations (minimum sensitivity: 77.8%, maximum sensitivity: 100%). The results based on ITS2 have also shown higher reliability than trnL at species level, while their combination could provide higher sensitivity and reliability. The multi-barcode sequencing approach has shown good universality, sensitivity and reliability in decoding these four representative TCM preparations. In the omics big-data era, this work has undoubtedly made one step forward for applying multi-barcode sequencing approach in PHMs analysis of TCM preparation, towards better digitization and modernization of drug quality control.
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Bosmali I, Lagiotis G, Haider N, Osathanunkul M, Biliaderis C, Madesis P. DNA-Based Identification of Eurasian Vicia Species Using Chloroplast and Nuclear DNA Barcodes. PLANTS 2022; 11:plants11070947. [PMID: 35406927 PMCID: PMC9003045 DOI: 10.3390/plants11070947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/19/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022]
Abstract
Many legume species of the Vicia L. genus (Fabaceae Lindl.) are key components of the Mediterranean diet and have an integral role in sustainable agriculture. Given the importance of the Vicia species for Eurasian culture, it is necessary to implement methodologies, such as DNA barcoding, that can enable the effective authentication and identification of species in the genus. In this study, we analysed the chloroplast trnL and rpoC1, as well as the nuclear ITS2 DNA barcoding regions, to identify 71 Vicia specimens of Eurasian descent. Both the trnL and ITS2 regions were highly effective in discriminating the analysed taxa, while the more conserved rpoC1 region could not identify all of the selected species due to high sequence conservation or non-annotated or absent rpoC1 species sequences in GenBank. A dendrographic representation of the generated trnL data showed sufficient clustering for most of the analysed taxa, although some topological discrepancies were observed. ITS2 and rpoC1 reconstructions were also used for resolving the topological discrepancies observed in the trnL tree. Our analysis suggests that a combination of DNA barcoding regions is essential for accurate species discrimination within the Vicia genus, while single-locus analyses do not provide the necessary resolution.
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Affiliation(s)
- Irene Bosmali
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, 57001 Thessaloniki, Greece; (I.B.); (G.L.)
- Laboratory of Food Chemistry and Biochemistry, Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Georgios Lagiotis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, 57001 Thessaloniki, Greece; (I.B.); (G.L.)
| | - Nadia Haider
- The Department of Molecular Biology and Biotechnology, Atomic Energy Commission (AEC), Damascus 6091, Syria;
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Costas Biliaderis
- Laboratory of Food Chemistry and Biochemistry, Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Panagiotis Madesis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, 57001 Thessaloniki, Greece; (I.B.); (G.L.)
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
- Correspondence:
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5
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Lee CL, Huang YH, Hsu IC, Lee HC. Evaluation of plant seed DNA and botanical evidence for potential forensic applications. Forensic Sci Res 2019; 5:55-63. [PMID: 32490311 PMCID: PMC7241509 DOI: 10.1080/20961790.2019.1594599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 11/27/2022] Open
Abstract
Seeds, the reproductive organs of plants, are common as trace evidence from crime scenes. Seed evidence could be grouped into several categories based on the types of crimes they are associated with, including child abuse, homicides and drugs. Most commonly, seeds are examined microscopically and identified to the plant species level to show a linkage between persons and places. More recently, forensic researchers have evaluated the potential for extracting and typing DNA from seeds to further individualize the samples. As a model system, tomato seeds were examined microscopically after different cooking treatments and assessed for the potential to DNA type seeds for variety identification. A sufficient quantity and quality of DNA were recovered from uncooked, digested and undigested tomato seeds for amplified fragment length polymorphism (AFLP) analysis; however, any form of cooking destroyed the seed DNA. A simple microscopic analysis was able to distinguish between a cooked tomato seed versus an uncooked seed. This article is intended to provide an overview of case examples and current techniques for the forensic examination of seeds as plant-derived evidence.
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Affiliation(s)
- Cheng-Lung Lee
- Department of Criminal Investigation, Taiwan Police College, Taiwan, China.,Crime Scene Theater, Qatar Police College, Doha, Qatar
| | - Yi-Hsin Huang
- Institute of Business and Management, National Chiao Tung University, Taiwan, China
| | - Ian C Hsu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Taiwan, China
| | - Henry C Lee
- Forensic Science Program, University of New Haven, West Haven, CT, USA
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Elkins KM, Perez ACU, Quinn AA. Simultaneous Identification of Four "Legal High" Plant Species in a Multiplex PCR High-Resolution Melt Assay . J Forensic Sci 2016; 62:593-601. [PMID: 27957736 DOI: 10.1111/1556-4029.13321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/26/2016] [Accepted: 07/31/2016] [Indexed: 11/26/2022]
Abstract
The international prevalence of "legal high" drugs necessitates the development of a method for their detection and identification. Herein, we describe the development and validation of a tetraplex multiplex real-time polymerase chain reaction (PCR) assay used to simultaneously identify morning glory, jimson weed, Hawaiian woodrose, and marijuana detected by high-resolution melt using LCGreen Plus® . The PCR assay was evaluated based on the following: (i) specificity and selectivity-primers were tested on DNA extracted from 30 species and simulated forensic samples, (ii) sensitivity-serial dilutions of the target DNA were prepared, and (iii) reproducibility and reliability-sample replicates were tested and remelted on different days. The assay is ideal for cases in which inexpensive assays are needed to quickly detect and identify trace biological material present on drug paraphernalia that is too compromised for botanical microscopic identification and for which analysts are unfamiliar with the morphology of the emerging "legal high" species.
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Affiliation(s)
- Kelly M Elkins
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
| | - Anjelica C U Perez
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
| | - Alicia A Quinn
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
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Margiotta G, Bacaro G, Carnevali E, Severini S, Bacci M, Gabbrielli M. Forensic botany as a useful tool in the crime scene: Report of a case. J Forensic Leg Med 2015; 34:24-8. [DOI: 10.1016/j.jflm.2015.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 10/23/2022]
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Ferri G, Corradini B, Ferrari F, Santunione AL, Palazzoli F, Alu' M. Forensic botany II, DNA barcode for land plants: Which markers after the international agreement? Forensic Sci Int Genet 2014; 15:131-6. [PMID: 25457632 DOI: 10.1016/j.fsigen.2014.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/23/2014] [Accepted: 10/03/2014] [Indexed: 11/17/2022]
Abstract
The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for forensic botany. Based on obtained results, we recommend the adoption of a two-locus combination with rbcL+trnH-psbA plastid markers, which currently best satisfies forensic needs for botanical species identification.
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Affiliation(s)
- G Ferri
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy.
| | - B Corradini
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Ferrari
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - A L Santunione
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Palazzoli
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - M Alu'
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
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Cheng X, Su X, Chen X, Zhao H, Bo C, Xu J, Bai H, Ning K. Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan. Sci Rep 2014; 4:5147. [PMID: 24888649 PMCID: PMC4042125 DOI: 10.1038/srep05147] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/06/2014] [Indexed: 01/03/2023] Open
Abstract
Although Traditional Chinese Medicine (TCM) preparations have long history with successful applications, the scientific and systematic quality assessment of TCM preparations mainly focuses on chemical constituents and is far from comprehensive. There are currently only few primitive studies on assessment of biological ingredients in TCM preparations. Here, we have proposed a method, M-TCM, for biological assessment of the quality of TCM preparations based on high-throughput sequencing and metagenomic analysis. We have tested this method on Liuwei Dihuang Wan (LDW), a TCM whose ingredients have been well-defined. Our results have shown that firstly, this method could determine the biological ingredients of LDW preparations. Secondly, the quality and stability of LDW varies significantly among different manufacturers. Thirdly, the overall quality of LDW samples is significantly affected by their biological contaminations. This novel strategy has the potential to achieve comprehensive ingredient profiling of TCM preparations.
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Affiliation(s)
- Xinwei Cheng
- Institute of Materia Medica, Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China
- School of Medicine and Life Sciences, , University of Jinan-Shandong Academy of Medical Sciences, Jinan 250062, China
- These authors contributed equally to this work
| | - Xiaoquan Su
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
- These authors contributed equally to this work
| | - Xiaohua Chen
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
| | - Huanxin Zhao
- Institute of Materia Medica, Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China
| | - Cunpei Bo
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
| | - Jian Xu
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
| | - Hong Bai
- Institute of Materia Medica, Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China
| | - Kang Ning
- Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and Bioinformatics Group of SingleCell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao266101, China
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Ganopoulos I, Aravanopoulos F, Madesis P, Pasentsis K, Bosmali I, Ouzounis C, Tsaftaris A. Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing. PLoS One 2013; 8:e60945. [PMID: 23577179 PMCID: PMC3618329 DOI: 10.1371/journal.pone.0060945] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 03/06/2013] [Indexed: 11/19/2022] Open
Abstract
Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples.
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Affiliation(s)
- Ioannis Ganopoulos
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Greece
| | - Filippos Aravanopoulos
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Laboratory of Forest Genetics and Tree Breeding, Faculty of Forestry and Natural Environment, Aristotle University of Thessaloniki, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Konstantinos Pasentsis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Irene Bosmali
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Christos Ouzounis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Athanasios Tsaftaris
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Greece
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Selection and authentication of botanical materials for the development of analytical methods. Anal Bioanal Chem 2012; 405:4419-28. [PMID: 23224664 DOI: 10.1007/s00216-012-6595-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
Herbal products, for example botanical dietary supplements, are widely used. Analytical methods are needed to ensure that botanical ingredients used in commercial products are correctly identified and that research materials are of adequate quality and are sufficiently characterized to enable research to be interpreted and replicated. Adulteration of botanical material in commerce is common for some species. The development of analytical methods for specific botanicals, and accurate reporting of research results, depend critically on correct identification of test materials. Conscious efforts must therefore be made to ensure that the botanical identity of test materials is rigorously confirmed and documented through preservation of vouchers, and that their geographic origin and handling are appropriate. Use of material with an associated herbarium voucher that can be botanically identified is always ideal. Indirect methods of authenticating bulk material in commerce, for example use of organoleptic, anatomical, chemical, or molecular characteristics, are not always acceptable for the chemist's purposes. Familiarity with botanical and pharmacognostic literature is necessary to determine what potential adulterants exist and how they may be distinguished.
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Madesis P, Ganopoulos I, Ralli P, Tsaftaris A. Barcoding the major Mediterranean leguminous crops by combining universal chloroplast and nuclear DNA sequence targets. GENETICS AND MOLECULAR RESEARCH 2012; 11:2548-58. [PMID: 22869075 DOI: 10.4238/2012.july.10.10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The ability to discriminate all species is the ultimate target in barcoding. The Mediterranean basin is a center of origin for legumes and thus they have played a key role in feeding the Mediterranean population. It is also a region with important protected designation of origin and protected geographical indication legumes that provide income in rural areas. We evaluated the use of two chloroplast regions, trnL and rpoC1, and a nuclear internal transcriber region, ITS2, for their efficiency to barcode the main Mediterranean leguminous crops. Twenty-five legume species were studied. Plant material of pasture and legumes was obtained from the Greek GenBank and the Fodder Crops and Pastures Institute (National Agricultural Research Foundation). DNA was extracted with the Qiagen DNeasy plant mini-kit and PCR amplification was performed using the Kapa Taq DNA polymerase using primers amplifying the chloroplast trnL and rpoC1 regions or the nuclear region ITS2. PCR products were sequenced and the sequences were aligned using CLUSTAL W. Species identification based on the sequence similarity approach was performed using the GenBank database. In order to evaluate intraspecific and interspecific divergence in legumes we used Molecular Evolutionary Genetics Analysis 5 and for pairwise Kimura 2-parameter distance calculations for all 3 DNA regions (2 chloroplast regions, trnL and rpoC1, and the nuclear region ITS2). Four tree-based methods (neighbor joining and maximum parsimony, maximum likelihood, and Bayesian inference analyses) were used to exhibit the molecular identification results to represent differences as an uprooted dendrogram. Additionally, the sequence character-based method was used with DnaSP and the information from each site was treated as a character to distinguish the species from one another. The DNA regions trnL and ITS2 successfully (100%) discriminated the Mediterranean crop legume species used, while rpoC1 identified only 72% of them. Furthermore, the use of the trnL region enabled the discrimination of even very closely related species, like Phaseolus lunatus and P. coccineus or Vicia faba subsp major with V. faba subsp minor, which are so closely related that even in NCBI they were both referred as Phaseolus vulgaris and V. faba, respectively. We conclude that trnL and ITS2 are efficient DNA barcoding target regions in order to discriminate Mediterranean leguminous crops and provide a reliable and efficient tool for the scientific, agricultural and industrial community.
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Affiliation(s)
- P Madesis
- Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki, Greece
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13
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Madesis P, Ganopoulos I, Anagnostis A, Tsaftaris A. The application of Bar-HRM (Barcode DNA-High Resolution Melting) analysis for authenticity testing and quantitative detection of bean crops (Leguminosae) without prior DNA purification. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.11.034] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Botanical DNA evidence in criminal cases: Knotgrass (Polygonum aviculare L.) as a model species. Forensic Sci Int Genet 2012; 6:366-74. [DOI: 10.1016/j.fsigen.2011.07.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 07/25/2011] [Accepted: 07/26/2011] [Indexed: 11/19/2022]
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Barcode High Resolution Melting (Bar-HRM) analysis for detection and quantification of PDO "Fava Santorinis" (Lathyrus clymenum) adulterants. Food Chem 2012; 133:505-12. [PMID: 25683426 DOI: 10.1016/j.foodchem.2012.01.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 08/10/2011] [Accepted: 01/11/2012] [Indexed: 11/23/2022]
Abstract
Legumes considered as one of the most important crops worldwide. Due to high price as a PDO product, commercial products of "Fava Santorinis" are often subjected to adulterations from other legume products coming from other Lathyrus or Vicia and Pisum species. Using plant DNA barcoding regions (trnL and rpoC) coupled with High Resolution Melting (Bar-HRM) we have developed a method allowing us to detect and authenticate PDO "Fava Santorinis". Bar-HRM proved to be a very sensitive tool able to genotype Lathyrus and its closed relative species and to detect admixtures, being sensitive enough to as low as 1:100 of non-"Fava Santorinis" in "Fava Santorinis" commercial products. In conclusion, Bar-HRM analysis can be a faster, with higher resolution and cost effectiveness alternative method to authenticate PDO "Fava Santorinis" and to quantitatively detect adulterations in "Fava Santorinis" with other relative commercial "Fava" food products.
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16
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Tobe S, Thatcher R, Gracie K, Watson N. Molecular analysis of botanical evidence by DNA thermal dissociation temperature. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.08.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Lee EJ, Hwang IK, Kim NY, Lee KL, Han MS, Lee YH, Kim MY, Yang MS. An assessment of the utility of universal and specific genetic markers for opium poppy identification. J Forensic Sci 2011; 55:1202-8. [PMID: 20487152 DOI: 10.1111/j.1556-4029.2010.01423.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proper identification of illicit plants such as Papaver somniferum L (opium poppy) is important for law enforcement agencies. The identification of opium poppy was presently tested using 10 genetic markers that are universal for all plants or specific to a few poppy plants. The genetic distances of universal markers such as nuclear internal transcribed spacer (ITS), 18S rRNA, plastid rbcL, and trnL-trnF intergenic spacer (IGS) of 14 species included in the Papaveraceae and Fumariaceae family were acquired by sequence comparisons. Both the ITS region and trnL-trnF IGS showed high levels of interspecific divergence. Six Papaver genera-specific markers were developed from coding regions involved in morphine biosynthesis. Three markers (TYDC, NCS, and BBE) produced amplicons only in opium poppy, providing a presence/absence test for opium poppy, while three additional markers (CYP80B1, SAT, and COR) were genus specific. These 10 markers might be useful for the forensic DNA analysis of opium poppy.
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Affiliation(s)
- Eun J Lee
- DNA Analysis Sector, Western District Office of National Institute of Scientific Investigation, Jangsung-Gun, Chonnam, South Korea.
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18
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Kikkawa HS, Sugita R, Matsuki R, Suzuki S. Potential utility of DNA sequence analysis of long-term-stored plant leaf fragments for forensic discrimination and identification. ANAL SCI 2010; 26:913-6. [PMID: 20702948 DOI: 10.2116/analsci.26.913] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study examined the potential utility of DNA sequence analysis to discriminate and identify plant material in forensic investigations. DNA was extracted from plant leaf fragments of 11 species stored for 5 to 22 years after collection. The trnH-psbA intergenic spacer and 316 bp of the rbcL gene were successfully amplified and sequenced for all fragments except for the trnH-psbA spacer of one sample. All of the plant samples were discriminated in pairwise comparisons of the sequences. Using a combination of local and global genetic databases is likely to provide greater reliability in search results to identify forensic samples from sequence data.
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Affiliation(s)
- Hitomi S Kikkawa
- Third Department of Forensic Science, National Research Institute of Police Science, Kashiwa, Chiba 277-0882, Japan.
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19
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Spaniolas S, Bazakos C, Spano T, Zoghby C, Kalaitzis P. The potential of plastid trnL (UAA) intron polymorphisms for the identification of the botanical origin of plant oils. Food Chem 2010. [DOI: 10.1016/j.foodchem.2010.02.039] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Ward J, Gilmore SR, Robertson J, Peakall R. A grass molecular identification system for forensic botany: a critical evaluation of the strengths and limitations. J Forensic Sci 2009; 54:1254-60. [PMID: 19818109 DOI: 10.1111/j.1556-4029.2009.01196.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Plant material is frequently encountered in criminal investigations but often overlooked as potential evidence. We designed a DNA-based molecular identification system for 100 Australian grasses that consisted of a series of polymerase chain reaction assays that enabled the progressive identification of grasses to different taxonomic levels. The identification system was based on DNA sequence variation at four chloroplast and two mitochondrial loci. Seventeen informative indels and 68 single-nucleotide polymorphisms were utilized as molecular markers for subfamily to species-level identification. To identify an unknown sample to subfamily level required a minimum of four markers or nine markers for species identification. The accuracy of the system was confirmed by blind tests. We have demonstrated "proof of concept" of a molecular identification system for trace botanical samples. Our evaluation suggests that the adoption of a system that combines this approach with DNA sequencing could assist the morphological identification of grasses found as forensic evidence.
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Affiliation(s)
- Jodie Ward
- School of Botany and Zoology, The Australian National University, Canberra, ACT 0200, Australia.
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21
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Ferri G, Alù M, Corradini B, Beduschi G. Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach. Int J Legal Med 2009; 123:395-401. [PMID: 19504263 DOI: 10.1007/s00414-009-0356-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 05/12/2009] [Indexed: 11/26/2022]
Abstract
Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.
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Affiliation(s)
- Gianmarco Ferri
- Department of Diagnostic and Laboratory Services and Legal Medicine, Section of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy.
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22
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Howard C, Gilmore S, Robertson J, Peakall R. ACannabis sativaSTR Genotype Database for Australian Seizures: Forensic Applications and Limitations. J Forensic Sci 2009; 54:556-63. [DOI: 10.1111/j.1556-4029.2009.01014.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Forensic botany: Usability of bryophyte material in forensic studies. Forensic Sci Int 2007; 172:161-3. [DOI: 10.1016/j.forsciint.2006.11.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 11/16/2006] [Accepted: 11/19/2006] [Indexed: 11/20/2022]
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24
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Identification of the endangered Australian orchid Microtis angusii using an allele-specific PCR assay. CONSERV GENET 2007. [DOI: 10.1007/s10592-006-9198-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Wells JD, Wall R, Stevens JR. Phylogenetic analysis of forensically important Lucilia flies based on cytochrome oxidase I sequence: a cautionary tale for forensic species determination. Int J Legal Med 2007; 121:229-33. [PMID: 17226055 DOI: 10.1007/s00414-006-0147-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Accepted: 12/11/2006] [Indexed: 10/23/2022]
Abstract
Forensic scientists are increasingly using DNA to identify the species of a tissue sample. However, little attention has been paid to basic experimental design issues such as replication and the selection of taxa when designing a species diagnostic test. We present an example using the forensically important fly genus Lucilia in which an increasingly larger sample size revealed that species diagnosis based on the commonly used cytochrome oxidase I gene (COI) was less straightforward than we initially thought. This locus may still be useful for diagnosing Lucilia specimens, but additional knowledge other than the genotype will be required to reduce the list of candidate species to include only forms that can be distinguished by COI. We believe that these results illustrate the importance of study design and biological knowledge of the study species when proposing a DNA-based identification test for any taxonomic group.
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Affiliation(s)
- Jeffrey D Wells
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
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26
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Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 2006; 35:e14. [PMID: 17169982 PMCID: PMC1807943 DOI: 10.1093/nar/gkl938] [Citation(s) in RCA: 553] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254–767 bp) and of a shorter fragment of this intron (the P6 loop, 10–143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.
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Affiliation(s)
- Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France.
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