Besse Pascale, Da Silva Denis, Grisoni Michel
UMR PVBMT, Universite de la Reunion, St Pierre, Réunion, France.
Université de La Réunion, UMR PVBMT, St Pierre, La Réunion, France.
Methods Mol Biol. 2021;2222:131-148. doi: 10.1007/978-1-0716-0997-2_8.
Powerful DNA barcodes have been much more difficult to define in plants than in animals. In 2009, the international Consortium for the Barcoding Of Life (CBOL) chose the combination of the chloroplast genes (rbcL + matK) as the proposed official barcode for plants. However, this system has got important limits. First, any barcode system will only be useful if there is a clear barcode gap and if species are monophyletic. Second, chloroplast and mitochondrial (COI gene used for animals) barcodes will not be usable for discriminating hybrid species. Moreover, it was also shown that, using chloroplast regions, maximum species discrimination would be around 70% and very variable among plant groups. This is why many authors have more recently advocated for the addition of the nuclear ITS region to this barcode because it reveals more variations and allows the resolution of hybrid or closely related species. We tested different chloroplast genes (rbcL, matK, psaB, psbC) and the nuclear ITS region in the genus Vanilla, a taxonomically complex group and therefore a good model to test for the efficiency of different barcode systems. We found that the CBOL official barcode system performed relatively poorly in Vanilla (76% species discrimination), and we demonstrate that adding ITS to this barcode system allows to increase resolution (for closely related species and to the subspecies level) and to identify hybrid species. The best species discrimination attained was 96.2% because of one paraphyletic species that could not be resolved.
在植物中定义强大的DNA条形码比在动物中要困难得多。2009年，国际生命条形码联盟（CBOL）选择叶绿体基因组合（rbcL + matK）作为植物的官方条形码提议。然而，该系统存在重要局限性。首先，任何条形码系统只有在存在明显的条形码间隙且物种是单系的情况下才有用。其次，叶绿体和线粒体（用于动物的COI基因）条形码无法用于区分杂交物种。此外，研究还表明，使用叶绿体区域，最大物种区分率约为70%，且在不同植物类群中差异很大。这就是为什么最近许多作者主张在该条形码中添加核ITS区域，因为它能揭示更多变异，并有助于区分杂交或近缘物种。我们在香草属中测试了不同的叶绿体基因（rbcL、matK、psaB、psbC）和核ITS区域，香草属在分类学上较为复杂，因此是测试不同条形码系统效率的良好模型。我们发现CBOL官方条形码系统在香草属中的表现相对较差（物种区分率为76%），并且我们证明在该条形码系统中添加ITS可以提高分辨率（区分近缘物种和亚种水平）并识别杂交物种。由于一个并系物种无法区分，获得的最佳物种区分率为96.2%。
