Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants
Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants
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大数据集的比较分析表明，内部转录间隔区（ITS）应纳入种子植物的核心条形码中
DOI：
10.1073/pnas.1104551108
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发表时间：
2011-12-06
影响因子：
11.1
通讯作者：
Duan, Guang-Wen
中科院分区：
文献类型：
--
作者：
Li, De-Zhu;Gao, Lian-Ming;Duan, Guang-Wen
质体rbcL和matK的双标记组合先前已被推荐为核心植物条形码，并补充有其他标记，如质体trnH-psbA和核核糖体内转录间隔区（ITS）。为了评估这些条形码标记在种子植物中的有效性和普遍性，我们通过使用四种不同的数据分析方法对来自75科（42目）141属1,757种的6,286个个体进行了取样。这些分析表明：（1）这三个质体标记具有高度的通用性（87.1-92.7%），而ITS在被子植物中表现较好（79%），在裸子植物中表现不佳;（ii）在标记的直接测序是可能的分类组中，ITS显示出四个标记中最高的区分能力，ITS与任一质体DNA标记的组合可区分69.9-79.1%的种，而rbcL + matK仅能区分49.7%的种;以及（iii）当测试单个物种的多个个体时，在45.2%的采样属中，基于ITS和质体DNA条形码的归属是不一致的（对于采样超过一个种的属）。这一发现强调了对多个个体进行采样和使用具有不同遗传模式的标记的重要性。在很难扩增和直接测序ITS整体的情况下，仅使用ITS 2是一种有用的备份，因为它更容易扩增和测序标记的这个子集。因此，我们建议将ITS/ITS 2纳入种子植物的核心条形码。
A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.