Standard plant DNA barcodes based on 2–3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3–4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.

中文翻译：

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测试基因组撇脂以区分大而分类学上困难的杜鹃花属

基于 2-3 个质体区域的标准植物 DNA 条形码和 nrDNA ITS 显示出不同的分辨率水平，并且无法区分许多植物群中的物种。已提出基因组撇取以恢复完整的质体基因组序列和 nrDNA 阵列作为解决这些分辨率限制的解决方案。然而，很少有研究对实践中取得的收益进行了实证检验。特别令人感兴趣的是，添加更多的质体和 nrDNA 特征是否会导致辨别力的增加，或者标准植物条形码的分辨率限制是否从根本上是由于质体基因组和 nrDNA 没有跟踪物种边界。为了解决这个问题，我们使用基因组撇取从杜鹃花中恢复近乎完整的质体基因组和核糖体 DNA物种并将区分成功与标准植物条形码进行比较。我们采样了代表这一物种丰富且分类困难的属的 145 个物种的 218 个个体，重点关注喜马拉雅-横断山脉的全球生物多样性热点。使用 ITS+ matK + rbcL + trnH - psbA只有 33% 的物种被区分. 相比之下，使用质体基因组和 nrDNA 序列区分了 55% 的物种。这种增加的绝大部分是由于额外的质体特征。因此，尽管之前的研究显示在超过 3-4 个质体区域的区分成功方面渐近线，但这些结果表明，使用广泛的质体基因组数据可能会显着增加区分能力。然而，尽管取得了这些成果，许多物种仍未得到解决，而且这些结果也强化了访问多个不相关的核位点以获得植物物种歧视方面的变革性成果的必要性。