Plant DNA barcoding principles and limits: A case study in the genus Vanilla

Besse Pascale, Da Silva Denis, Grisoni Michel. 2021. Plant DNA barcoding principles and limits: A case study in the genus Vanilla. In : Molecular plant taxonomy: method and protocols. Besse Pascale (ed.). New York : Humana Press, pp. 131-148. (Methods in Molecular Biology, 2222) ISBN 978-1-0716-0996-5

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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.

Mots-clés Agrovoc : phytogénétique, Vanilla, Marqueur génétique, Génotype, ADN chloroplastique, ADN mitochondrial

Mots-clés complémentaires : barcoding moléculaire

Mots-clés libres : Genotyping by sequencing, Next-generation sequencing, SNP, Plant diversity markers

Classification Agris : F30 - Plant genetics and breeding

Auteurs et affiliations

  • Besse Pascale, Université de la Réunion (REU)
  • Da Silva Denis, Université de la Réunion (REU)
  • Grisoni Michel, CIRAD-BIOS-UMR PVBMT (MDG)

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