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Corradini B, Gianfreda D, Ferri G, Ferrari F, Borciani I, Santunione AL, Cecchi R. Forensic species identification: practical guide for animal and plant DNA analysis. Int J Legal Med 2024:10.1007/s00414-024-03284-2. [PMID: 38985195 DOI: 10.1007/s00414-024-03284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024]
Abstract
The importance of non-human DNA in the forensic field has increased greatly in recent years, together with the type of applications. The molecular species identification of animal and botanical material may be crucial both for wildlife trafficking and crime scene investigation. However, especially for forensic botany, several challenges slow down the implementation of the discipline in the routine.Although the importance of molecular analysis of animal origin samples is widely recognized and the same value is acknowledged to the botanical counterpart, the latter does not find the same degree of application.The availability of molecular methods, especially useful in cases where the material is fragmented, scarce or spoiled preventing the morphological identification, is not well known. This work is intended to reaffirm the relevance of non-human forensic genetics (NHFG), highlighting differences, benefits and pitfalls of the current most common molecular analysis workflow for animal and botanical samples, giving a practical guide. A flowchart describing the analysis paths, divided in three major working areas (inspection and sampling, molecular analysis, data processing and interpretation), is provided. More real casework examples of the utility of non-human evidence in forensic investigations should be shared by the scientific community, especially for plants. Moreover, concrete efforts to encourage initiatives in order to promote quality and standardization in the NHFG field are also needed.
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Affiliation(s)
- Beatrice Corradini
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy.
| | - Denise Gianfreda
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Gianmarco Ferri
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Ilaria Borciani
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Anna Laura Santunione
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Rossana Cecchi
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
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Quaresma A, Ankenbrand MJ, Garcia CAY, Rufino J, Honrado M, Amaral J, Brodschneider R, Brusbardis V, Gratzer K, Hatjina F, Kilpinen O, Pietropaoli M, Roessink I, van der Steen J, Vejsnæs F, Pinto MA, Keller A. Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding. Sci Data 2024; 11:129. [PMID: 38272945 PMCID: PMC10810873 DOI: 10.1038/s41597-024-02962-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.
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Affiliation(s)
- Andreia Quaresma
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, S/N, Edifício FC4, 4169-007, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Vila do Conde, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Vila do Conde, Portugal
| | - Markus J Ankenbrand
- Center for Computational and Theoretical Biology, Faculty of Biology, Julius-Maximilians-Universität Würzburg, Klara-Oppenheimer-Weg 32, 97074, Würzburg, Germany
| | - Carlos Ariel Yadró Garcia
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - José Rufino
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Research Centre in Digitalization and Intelligent Robotics (CeDRI), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Mónica Honrado
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Joana Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Robert Brodschneider
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Valters Brusbardis
- Latvian Beekeepers' Association (LBA), Rigas iela 22, LV-3004, Jelgava, Latvia
| | - Kristina Gratzer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Fani Hatjina
- Ellinikos Georgikos Organismos DIMITRA (ELGO- DIMITRA), Kourtidou 56-58, GR-11145, Athina, Greece
| | - Ole Kilpinen
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - Marco Pietropaoli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri" (IZSLT), Via Appia Nuova 1411, IT-00178, Roma, Italy
| | - Ivo Roessink
- Wageningen Environmental Research, WageningenUniversity&Research, Droevendaalsesteeg 3, 6700 AA, Wageningen, Netherlands
| | | | - Flemming Vejsnæs
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Alexander Keller
- Cellular and Organismic Interactions, Biocenter, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany.
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Liu Y, Xu C, Dong W, Chen X, Zhang W, Sun Y, Wang G, Wang Y, Zhou S. What determines plant species diversity along the Modern Silk Road in the east? IMETA 2023; 2:e74. [PMID: 38868351 PMCID: PMC10989921 DOI: 10.1002/imt2.74] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 06/14/2024]
Abstract
As primary producers, plants provide food, oxygen, and other resources for global ecosystems, and should therefore be given priority in biodiversity protection. Most biodiversity research focuses on biodiversity hotspots, while biodiversity coldspots, such as deserts, are largely ignored. We propose that the factors shaping plant species diversity differ between biodiversity hot spots and cold spots, especially for desert ecosystems. To test this hypothesis, we investigated plant species diversity along the Modern Silk Road in the Northwest China desert, an area characterized by low precipitation, scarce vegetation, a limited number of species, and variable human activities. Surface soil was sampled from 144 plots, environmental DNA (eDNA) was extracted from soil samples, and seed plant species were identified using DNA metabarcoding technology. A total of 671 seed plant species were detected, which was more diverse than indicated by plot survey data. Plant species diversity gradually decreased from east to west along the Silk Road. In this area, temperature determines plant species diversity more than precipitation. Additionally, human activity has altered plant species diversity by introducing crops and invasive plants and eliminating environmentally adapted indigenous plants. Our results demonstrate the potential of eDNA metabarcoding technology for plant species diversity surveying. Desert plants have adapted to dry environments by relying on underground water or utilizing occasional rainfall as ephemerals, which are often not visible during surface surveys because of their short aboveground life cycle but can be detected with eDNA metabarcoding technology. Groundwater maintenance and human activity control are recommended for plant species diversity conservation and desertification control.
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Affiliation(s)
- Yanlei Liu
- School of Landscape and Ecological EngineeringHebei University of EngineeringHandanChina
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Xun Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- Hulunbuir UniversityHulunbuirChina
| | - Wen Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Yuzhe Sun
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Guohong Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Yufei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
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