DNA Barcodes: Methods and Protocols

  • W. John KressEmail author
  • David L. Erickson
Part of the Methods in Molecular Biology book series (MIMB, volume 858)


DNA barcoding, a new method for the quick identification of any species based on extracting a DNA sequence from a tiny tissue sample of any organism, is now being applied to taxa across the tree of life. As a research tool for taxonomists, DNA barcoding assists in identification by expanding the ability to diagnose species by including all life history stages of an organism. As a biodiversity discovery tool, DNA barcoding helps to flag species that are potentially new to science. As a biological tool, DNA barcoding is being used to address fundamental ecological and evolutionary questions, such as how species in plant communities are assembled. The process of DNA barcoding entails two basic steps: (1) building the DNA barcode library of known species and (2) matching the barcode sequence of the unknown sample against the barcode library for identification. Although DNA barcoding as a methodology has been in use for less than a decade, it has grown exponentially in terms of the number of sequences generated as barcodes as well as its applications. This volume provides the latest information on generating, applying, and analyzing DNA barcodes across the Tree of Life from animals and fungi to protists, algae, and plants.

Key words

DNA barcode Identification Taxonomy Discovery Ecology Evolution 


  1. 1.
    Janzen DH (2005) Foreword: how to conserve wild plants? Give the world the power to read them. In: Krupnick GA, Kress WJ (eds) Plant conservation: a natural history approach. University of Chicago Press, Chicago, pp ix–xiiiGoogle Scholar
  2. 2.
    Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc B 270:313–321. doi: 10.1098/rspb.2002.2218 PubMedCrossRefGoogle Scholar
  3. 3.
    Savolainen V, Cowan RS, Vogler AP et al (2005) Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philos Trans Ser B 360:1850–1811. doi: 10.1098/rstb.2005.1730 CrossRefGoogle Scholar
  4. 4.
    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 55:611–616CrossRefGoogle Scholar
  5. 5.
    Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312. doi: 10.1371/journal.pbio.0020312 PubMedCrossRefGoogle Scholar
  6. 6.
    Kress WJ, Wurdack KJ, Zimmer EA et al (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102: 8369–8374PubMedCrossRefGoogle Scholar
  7. 7.
    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. doi: 10.1371/journal.pone.0000508 PubMedCrossRefGoogle Scholar
  8. 8.
    Chase MW, Salamin N, Wilkinson M et al (2005) Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci 360:1889–1895. doi: 10.1098/rstb.2005.1720 PubMedCrossRefGoogle Scholar
  9. 9.
    Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J (2008) Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Resour 8:480–490PubMedCrossRefGoogle Scholar
  10. 10.
    Lahaye R, Van der Bank M, Bogarin D, Warner J et al (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA 105:2923–2928PubMedCrossRefGoogle Scholar
  11. 11.
    CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci 106:12794–12797CrossRefGoogle Scholar
  12. 12.
    Kress WJ, Erickson DL, Jones FA, Swenson NG, Perez R, Sanjur O, Bermingham E (2009) Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc Natl Acad Sci USA 106:18621–18626.
  13. 13.
    Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JA, et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109:6241–6246Google Scholar
  14. 14.
    Hebert PDN, Penton EH, Burns JM et al (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical ­skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–14817. doi: 10.1073/pnas.0406166101 PubMedCrossRefGoogle Scholar
  15. 15.
    Kress WJ, Erickson DL, Swenson NG et al (2010) Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot. PLoS One 5:e15409. doi: 10.1371/journal.pone.0015409 PubMedCrossRefGoogle Scholar
  16. 16.
    Jurado-Rivera JA et al (2009) DNA barcoding insect-host plant associations. Proc R Soc Lond B Biol Sci 276:639–648CrossRefGoogle Scholar
  17. 17.
    Kress WJ, Erickson DL (2008) Commentary DNA barcoding: genes, genomics, and bioinformatics. Proc Natl Acad Sci USA 105: 2761–2762PubMedCrossRefGoogle Scholar
  18. 18.
    Ratnasingham S, Hebert PDN (2007) BOLD: The barcode of life data system ( Mol Ecol Notes 7:355–364
  19. 19.
    Erickson DL, Spouge J, Resch A et al (2008) DNA barcoding in land plants: developing standards to quantify and maximize success. Taxon 57:1304–1316PubMedGoogle Scholar
  20. 20.
    Taberlet P, Coissac E, Pompanon F et al (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35:e14. doi: 10.1093/nar/gkl938 PubMedCrossRefGoogle Scholar
  21. 21.
    Chase MW, Cowan RS, Hollingsworth PM et al (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56: 295–299Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of BotanySmithsonian Institution, National Museum of Natural HistoryWashingtonUSA

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