DNA-based identification of plants and the genomic nature of plant species differences.
| Title: | DNA-based identification of plants and the genomic nature of plant species differences. |
|---|---|
| Authors: | Huang W; Royal Botanic Garden Edinburgh, Edinburgh, UK. whuang@rbge.org.uk.; Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK. whuang@rbge.org.uk.; Royal Botanic Gardens, Kew, Surrey, UK. whuang@rbge.org.uk.; Li DZ; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.; Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China.; Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Shandong, China.; Antonelli A; Royal Botanic Gardens, Kew, Surrey, UK.; Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.; Department of Biology, University of Oxford, Oxford, UK.; Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.; Bacon CD; Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.; Gao LM; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.; Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China.; Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Shandong, China.; Kidner C; Royal Botanic Garden Edinburgh, Edinburgh, UK.; Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK.; Pennington RT; Royal Botanic Garden Edinburgh, Edinburgh, UK.; Department of Geography, University of Exeter, Exeter, UK.; Soltis DE; Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.; Biodiversity Institute, University of Florida, Gainesville, FL, USA.; Soltis P; Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.; Biodiversity Institute, University of Florida, Gainesville, FL, USA.; Cavender-Bares J; Harvard University Herbaria, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.; Christe C; Conservatoire et Jardin botaniques de Genève, Pregny-Chambésy, Switzerland.; Dexter KG; Royal Botanic Garden Edinburgh, Edinburgh, UK.; School of Geosciences, Grant Institute, University of Edinburgh, Edinburgh, UK.; Department of Life Sciences and Systems Biology, University of Turin, Torino TO, Italy.; Ding Y; Royal Botanic Garden Edinburgh, Edinburgh, UK.; Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.; Durán-Castillo M; Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.; Fernández-Mazuecos M; Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain.; Gardner EM; Department of Biology, Case Western Reserve University, Cleveland, OH, USA.; Gostel MR; Botanical Research Institute of Texas, Fort Worth, TX, USA.; Hernandez M; Department of Anthropology, Penn State University, State College, PA, USA.; Hipp AL; Herbarium and Center for Tree Science, The Morton Arboretum, Lisle, IL, USA.; Jantzen JR; Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.; Biodiversity Institute, University of Florida, Gainesville, FL, USA.; Landis JB; School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA.; Liu XQ; Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.; Naranjo AA; International Center for Tropical Botany, Institute of Environment, Florida International University, Miami, FL, USA.; Nicholls J; Royal Botanic Garden Edinburgh, Edinburgh, UK.; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian National Insect Collection, Acton, ACT, Australia.; Qin HT; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.; Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China.; Rose JP; Department of Botany, University of Wisconsin-Madison, Madison, WI, USA.; Salamin N; Department of Computational Biology, Quartier Centre, University of Lausanne, Lausanne, Switzerland.; Schley R; Department of Geography, University of Exeter, Exeter, UK.; Schlüter PM; Institute of Biology, University of Hohenheim, Stuttgart, Germany.; Stephens JD; Biology Department, Westfield State University, Westfield, MA, USA.; Streisfeld MA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.; Wagner ND; Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany.; Wang XQ; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.; Xiang QJ; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.; Twyford AD; Royal Botanic Garden Edinburgh, Edinburgh, UK. Alex.Twyford@ed.ac.uk.; Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK. Alex.Twyford@ed.ac.uk.; Hollingsworth PM; Royal Botanic Garden Edinburgh, Edinburgh, UK. phollingsworth@rbge.org.uk. |
| Source: | Communications biology [Commun Biol] 2026 Mar 26; Vol. 9 (1). Date of Electronic Publication: 2026 Mar 26. |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Nature Publishing Group UK Country of Publication: England NLM ID: 101719179 Publication Model: Electronic Cited Medium: Internet ISSN: 2399-3642 (Electronic) Linking ISSN: 23993642 NLM ISO Abbreviation: Commun Biol Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: London, United Kingdom : Nature Publishing Group UK, [2018]- |
| MeSH Terms: | DNA, Plant*/genetics ; Plants*/genetics ; Plants*/classification ; Genome, Plant*; Genomics/methods ; Polymorphism, Single Nucleotide ; Species Specificity ; Phylogeny ; Sequence Analysis, DNA |
| Abstract: | Telling species apart using DNA sequence data plays a key role in understanding, monitoring, and managing biodiversity. However, plant species discrimination is often difficult due to the complex nature of plant species boundaries. To inform future strategies for DNA-based identification of plants using the nuclear genome and to gain fundamental insights into the genomic nature of differences between plant species, we conducted a large-scale analysis mining data from 151 studies. Of the 1713 multiple-sampled species evaluated, 1202 resolved as monophyletic (70.2%). We then assessed the density of species-specific SNPs (SSSNPs) in the DNA sequence data - of the 462 species from 27 genera assessed in detail, there was a median density of 193 SSSNPs per Mb and 412 species (89.2%) had at least one SSSNP. Randomly sub-sampling the SNP data showed an asymptote in species discrimination with around 3000 randomly selected SNPs. Finally, we undertook a resampling of 6 target-capture datasets and showed that 1-9 pre-selected loci provided equivalent levels of species discrimination compared to hundreds of nuclear loci. These findings provide an important quantitative assessment of the genomic nature of differences between plant species and provide foundations for the development of enhanced approaches for high-resolution DNA-based plant species discrimination.; (© 2026. The Author(s).) |
| Competing Interests: | Competing interests: The authors declare no competing interests. |
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| Grant Information: | 218328 United Kingdom WT_ Wellcome Trust |
| Substance Nomenclature: | 0 (DNA, Plant) |
| Entry Date(s): | Date Created: 20260326 Date Completed: 20260518 Latest Revision: 20260521 |
| Update Code: | 20260521 |
| PubMed Central ID: | PMC13183946 |
| DOI: | 10.1038/s42003-026-09858-7 |
| PMID: | 41882066 |
| Database: | MEDLINE |
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