Data for: Plant species identification by genome skimming across the vascular plant tree of life

作者：Chun‐Xia Zeng, Meng‐Yuan Zhou, Alex D. Twyford, Lian‐Ming Gao, Zhiyong Zhang, Yun-heng Ji, Hongtao Li, Peng-Fei Ma, Wen-Bin Yu, Zhi‐Qiong Mo, Zheng‐Yu Zuo, Wu Huang, Ting‐Shuang Yi, Jun-Bo Yang, Peter M. Hollingsworth, Li D · 发表于：Figshare · 年份：2026 · DOI：10.6084/m9.figshare.32346357.v1 · 研究领域：Biology、Evolutionary biology、Computational biology、Ecology

Accurate species identification is essential for biodiversity conservation and sustainable use, yet standard plant DNA barcoding often fails to achieve species-level resolution.We present a large-scale empirical evaluation of genome skimming as a tool to improve plant species discrimination. Using standardized data from 1,969 individuals representing 475 species from 32 genera across major lineages of the vascular plant tree of life, we compare conventional plastid + ITS barcodes with genome skimming approaches.Standard barcoding resolved about half of species (49.3%), with six genera showing <25% species discrimination. In contrast, genome skimming enabled the recovery of complete plastid genomes, yielding 57.6% species discrimination. It also generated sufficient nuclear genomic data for k-mer analysis, achieving 66.8% species discrimination—an average gain of 17.5% over standard barcodes—while eliminating cases of extreme failure (<25% resolution). The recovery of complete plastomes and ribosomal DNAs from genome skims also ensures backward compatibility with existing barcode datasets.Our results demonstrate that genome skimming substantially improves species-level resolution across diverse plant lineages and offers a scalable, high-throughput approach for building comprehensive reference resources to support global biodiversity initiatives.