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Molecular Plant Taxonomy pp 131–148Cite as

Plant DNA Barcoding Principles and Limits: A Case Study in the Genus Vanilla

Part of the Methods in Molecular Biology book series (MIMB,volume 2222)

Abstract

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.

Key words

  • DNA barcoding
  • ITS
  • rbcL
  • matK
  • Barcode gap
  • Species discrimination

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Acknowledgments

We thank M. Duvigneau for generating many of the sequences used and A. Vancassel for preliminary analyses of barcode data during their MSc thesis. This work was partly funded by the Vanitax (ANR Bibliothèque du Vivant) and ANR (ANR11-EBIM-005-01) and Reunion Regional Council (DGADD/PE/20120590 and 20120589) through the VaBiome project (ERA-NET-Net-Biome funded project).

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Authors and Affiliations

  1. UMR PVBMT, Universite de la Reunion, St Pierre, Réunion, France

    Pascale Besse

  2. Université de La Réunion, UMR PVBMT, St Pierre, La Réunion, France

    Denis Da Silva

  3. CIRAD, UMR PVBMT, St Pierre, La Réunion, France

    Michel Grisoni

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  1. Pascale Besse
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  2. Denis Da Silva
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Correspondence to Pascale Besse .

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  1. UMR PVBMT, Universite de la Reunion, St Pierre, Réunion, France

    Pascale Besse

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Besse, P., Da Silva, D., Grisoni, M. (2021). Plant DNA Barcoding Principles and Limits: A Case Study in the Genus Vanilla. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 2222. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0997-2_8

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  • DOI: https://doi.org/10.1007/978-1-0716-0997-2_8

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