DNA-based identification of plants and the genomic nature of plant species differences

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.

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Journal
Communications Biology
Published
2026-03-26
DOI
https://doi.org/10.1038/s42003-026-09858-7
Primary Topic
Genomics and Phylogenetic Studies
Type
article
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article

DNA-based identification of plants and the genomic nature of plant species differences

Rowan Schley, Yanqian Ding, Han‐Tao Qin, Philipp M. Schlüter et al.
Communications Biology
Genomics and Phylogenetic Studies
article

DNA-based identification of plants and the genomic nature of plant species differences

Rowan Schley, Yanqian Ding, Han‐Tao Qin, Philipp M. Schlüter, Alex D. Twyford, Lian‐Ming Gao, Catherine Kidner, Jessica D. Stephens, Elliot M. Gardner, Nicolas Salamin, Camille Christe, Matthew A. Streisfeld, Xiu‐Qun Liu, Kyle Graham Dexter, Morgan R. Gostel, Johanna R. Jantzen, Andre A. Naranjo, Margarita Hernandez, James A. Nicholls, De-Zhu Li, Jeffrey P. Rose, Qiu-Yun Jenny Xiang, Wu Huang, Andrew L. Hipp, R. Toby Pennington, Christine D. Bacon, Peter M. Hollingsworth, Jeannine Cavender-Bares, Jacob B. Landis, Alexandre Antonelli, Douglas E. Soltis, Natascha D. Wagner, Pamela Soltis, Mario Fernández-Mazuecos, Xiao-Quan Wang, Mario Durán-Castillo
article en

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.

Communications Biology
University of Hohenheim (DE), Pennsylvania State University (US), Botanical Research Institute of Texas (US), Florida Museum of Natural History (US), University of Wisconsin–Madison (US), Harvard University (US), North Carolina State University (US), Kunming Institute of Botany (CN), Royal Botanic Garden Edinburgh (GB), University of Oregon (US), Florida International University (US), Chinese Academy of Sciences (CN), Huazhong Agricultural University (CN), Cornell University (US), University of Exeter (GB), Royal Botanic Gardens, Kew (GB), Morton Arboretum (US), Jardin Botanique de Genève (CH), University of Florida (US), University of Oxford (GB), Australian National Insect Collection (AU), Wuhan Botanical Garden (CN), Torino e-district (IT), Real Jardín Botánico (ES), Institute of Botany (CN), Westfield State University (US), University of Turin (IT), Case Western Reserve University (US), Shandong Agricultural University (CN), University of Göttingen (DE), University of Gothenburg (SE), University of Lausanne (CH), University of Edinburgh (GB)
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