Skip to main content
SpringerLink
Log in

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

  • Protocol
  • First Online:
Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Stoeckle M (2003) Taxonomy, DNA, and the bar code of life. Bioscience 53:796–797. https://doi.org/10.1641/0006-3568(2003)053[0796:TDATBC]2.0.CO;2

    Article  Google Scholar 

  2. Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci 270(Suppl 1):S96–S99. https://doi.org/10.1098/rsbl.2003.0025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Brown WM, George M, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci 76:1967–1971. https://doi.org/10.1073/pnas.76.4.1967

  4. Avise JC (2000) Phylogeography: the history and formation of species. Harvard university press, Cambridge

    Google Scholar 

  5. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci 102:8369–8374. https://doi.org/10.1073/pnas.0503123102

  6. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V (2005) Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc B Biol Sci 360:1889–1895. https://doi.org/10.1098/rstb.2005.1720

  7. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madriñán S, Petersen G, Seberg O, Jørgsensen T, Cameron KM, Carine M (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56:295–299. https://doi.org/10.1002/tax.562004

  8. Cowan RS, Chase MW, Kress WJ, Savolainen V (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 55:611–616. https://doi.org/10.2307/25065638

  9. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SCH (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS One 3:e2802. https://doi.org/10.1371/journal.pone.0002802

  10. Hollingsworth ML, Andra Clark A, Forrest LL, Richardson J, Pennington RT, Long DG, Cowan R, Chase MW, Gaudeul M, Hollingsworth PM (2009) Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol Ecol Resour 9:439–457. https://doi.org/10.1111/j.1755-0998.2008.02439.x

  11. Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One 2:e508. https://doi.org/10.1371/journal.pone.0000508

  12. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci U S A 105:2923–2928. https://doi.org/10.1073/pnas.0709936105

  13. Newmaster S, Fazekas A, Ragupathy S (2006) DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Botany 84:335–341. https://doi.org/10.1139/b06-047

  14. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E (2007) Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35:e14–e14. https://doi.org/10.1093/nar/gkl938

  15. Presting GG (2006) Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function. Botany 84:1434–1443. https://doi.org/10.1139/b06-117

  16. Rubinoff D, Cameron S, Will K (2006) Are plant DNA barcodes a search for the holy grail? Trends Ecol Evol 21:1–2. https://doi.org/10.1016/j.tree.2005.10.019

  17. Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS One 6:e19254. https://doi.org/10.1371/journal.pone.0019254

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. CBOL Plant Working Group, Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL (2009) A DNA barcode for land plants. Proc Natl Acad Sci 106:12794–12797. https://doi.org/10.1073/pnas.0905845106

  19. Ratnasingham S, Hebert PD (2007) BOLD: the barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes 7:355–364. https://doi.org/10.1111/j.1471-8286.2007.01678.x

  20. Liu D, Liu L, Guo G, Wang W, Sun Q, Parani M, Ma J (2013) BOLDMirror: a global mirror system of DNA barcode data. Mol Ecol Resour 13:991–995. https://doi.org/10.1111/1755-0998.12048

    Article  CAS  PubMed  Google Scholar 

  21. Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SCH, Newmaster SG, Hajibabaei M, Husband BC (2009) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Mol Ecol Resour 9(Suppl s1):130–139. https://doi.org/10.1111/j.1755-0998.2009.02652.x

    Article  CAS  PubMed  Google Scholar 

  22. Li D-Z, Gao L-M, Li H-T, Wang H, Ge X-J, Liu J-Q, Chen Z-D, Zhou S-L, Chen S-L, Yang J-B, Fu C-X, Zeng C-X, Yan H-F, Zhu Y-J, Sun Y-S, Chen S-Y, Zhao L, Wang K, Yang T, Duan G-W (2011) Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc Natl Acad Sci U S A 108:19641–19646. https://doi.org/10.1073/pnas.1104551108

    Article  PubMed  PubMed Central  Google Scholar 

  23. Hollingsworth PM (2011) Refining the DNA barcode for land plants. Proc Natl Acad Sci U S A 108:19451–19452. https://doi.org/10.1073/pnas.1116812108

    Article  PubMed  PubMed Central  Google Scholar 

  24. Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, Luo K, Li Y, Li X, Jia X, Lin Y, Leon C (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5:e8613. https://doi.org/10.1371/journal.pone.0008613

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Yao H, Song J, Liu C, Luo K, Han J, Li Y, Pang X, Xu H, Zhu Y, Xiao P, Chen S (2010) Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS One 5:e13102. https://doi.org/10.1371/journal.pone.0013102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Coleman AW (2003) ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet 19:370–375. https://doi.org/10.1016/S0168-9525(03)00118-5

  27. Wang X-C, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang J-H, Cai D, Li J-Q (2015) ITS1: a DNA barcode better than ITS2 in eukaryotes? Mol Ecol Resour 15:573–586. https://doi.org/10.1111/1755-0998.12325

    Article  CAS  PubMed  Google Scholar 

  28. Li H, Bai H, Yu S, Han M, Ning K (2018) Holmes-ITS2: consolidated ITS2 resources and search engines for plant DNA-based marker analyses. bioRxiv 263541. https://doi.org/10.1101/263541

  29. Merget B, Koetschan C, Hackl T, Förster F, Dandekar T, Müller T, Schultz J, Wolf M (2012) The ITS2 database. J Vis Exp (61):e3806. https://doi.org/10.3791/3806

  30. Ankenbrand MJ, Keller A, Wolf M, Schultz J, Förster F (2015) ITS2 database V: twice as much. Mol Biol Evol 32:3030–3032. https://doi.org/10.1093/molbev/msv174

  31. Arenas MS, Cameron K (2003) Vanilla. In: Genera Orchidacearum: Orchidoideae. Oxford University Press, New York, pp 321–334

    Google Scholar 

  32. Arenas MAS, Cribb P (2009) A new infrageneric classification and synopsis of the genus Vanilla Plum. ex Mill.(Orchidaceae: Vanillinae). Lankesteriana 9:355–398. https://doi.org/10.15517/lank.v0i0.12071

  33. Bory S, Brown S, Duval M-F, Besse P (2010) Evolutionary processes and diversification in the genus Vanilla. In: Vanilla. Crc Press, Florida, pp 15–29

    Google Scholar 

  34. Ennos RA, French GC, Hollingsworth PM (2005) Conserving taxonomic complexity. Trends Ecol Evol 20:164–168. https://doi.org/10.1016/j.tree.2005.01.012

  35. Rodolphe G, Séverine B, Michel G, Pascale B (2011) Biodiversity and evolution in the Vanilla genus. In: The dynamical processes of biodiversity –case studies of evolution and spatial distribution, pp 1–27

    Google Scholar 

  36. Nielsen LR, Siegismund HR (1999) Interspecific differentiation and hybridization in Vanilla species (Orchidaceae). Heredity 83:560–567. https://doi.org/10.1046/j.1365-2540.1999.00588.x

  37. Nielsen LR (2000) Natural hybridization between Vanilla claviculata (W. Wright) Sw. and V. barbellata Rchb. f.(Orchidaceae): genetic, morphological, and pollination experimental data. Bot J Linn Soc 133:285–302. https://doi.org/10.1111/j.1095-8339.2000.tb01547.x

  38. Lubinsky P, Cameron KM, Molina MC, Wong M, Lepers-Andrzejewski S, Gómez-Pompa A, Kim S (2008) Neotropical roots of a Polynesian spice: the hybrid origin of Tahitian vanilla, Vanilla tahitensis (Orchidaceae). Am J Bot 95:1040–1047. https://doi.org/10.3732/ajb.0800067

  39. Bory S, Catrice O, Brown S, Leitch IJ, Gigant R, Chiroleu F, Grisoni M, Duval M-F, Besse P (2008) Natural polyploidy in Vanilla planifolia (Orchidaceae). Genome 51:816–826. https://doi.org/10.1139/G08-068

  40. Bouetard A, Lefeuvre P, Gigant R, Bory S, Pignal M, Besse P, Grisoni M (2010) Evidence of transoceanic dispersion of the genus Vanilla based on plastid DNA phylogenetic analysis. Mol Phylogenet Evol 55:621–630. https://doi.org/10.1016/j.ympev.2010.01.021

  41. Duvignau M (2012) Utilisation de marqueurs moléculaires pour une avancée dans la résolution de la phylogénie du genre# Vanilla. Master 2 thesis, Montpellier 2

    Google Scholar 

  42. Gigant R (2008) L’aphyllie dans le genre Vanilla: étude phylogénétique des espèces de l’Océan Indien. Master 2 thesis Biodiversité et écosystèmes tropicaux, Université de la Réunion

    Google Scholar 

  43. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. https://doi.org/10.1093/molbev/msr121

  44. Collins RA, Cruickshank RH (2013) The seven deadly sins of DNA barcoding. Mol Ecol Resour 13:969–975. https://doi.org/10.1111/1755-0998.12046

    Article  CAS  PubMed  Google Scholar 

  45. Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. Plos Biol 3:e422. https://doi.org/10.1371/journal.pbio.0030422

  46. Blagoev G, Hebert P, Adamowicz S, Robinson E (2009) Prospects for using DNA barcoding to identify spiders in species-rich genera. ZooKeys 16:27. https://doi.org/10.3897/zookeys.16.239

  47. Azofeifa-Bolaños JB, Gigant LR, Nicolás-García M, Pignal M, Tavares-González FB, Hágsater E, Salazar-Chávez GA, Reyes-López D, Archila-Morales FL, García-García JA (2017) A new vanilla species from Costa Rica closely related to V. planifolia (Orchidaceae). Eur J Taxon 284:1–26. https://doi.org/10.5852/ejt.2017.284

  48. Soto-Arenas MA, Dressler RL (2010) A revision of the Mexican and Central American species of Vanilla Plumier ex Miller with a characterization of their ITS region of the nuclear ribosomal DNA. Lankesteriana 9:285–354. https://doi.org/10.15517/lank.v0i0.12065

Download references

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).

Author information

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

Authors
  1. Pascale Besse
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Denis Da Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michel Grisoni
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pascale Besse .

Editor information

Editors and Affiliations

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

    Pascale Besse

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

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

Download citation

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

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0996-5

  • Online ISBN: 978-1-0716-0997-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation