DNA Barcodes for Insects

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 858)

Abstract

DNA barcoding refers to the technique of sequencing a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene, the “DNA barcode,” from a taxonomically unknown specimen and performing comparisons with a reference library of barcodes of known species origin to establish a species-level identification. The library barcodes gain their value due to an intimate association—through the vouchered specimens from where they came—with other data; particularly Linnaean names, collection localities, and morphology in the form of digital images. Consequently, this chapter details means of efficiently obtaining barcodes along two general streams: rapid barcode assembly to populate the library and retrieval of barcodes from highly prized specimens, but also emphasizes organization and collection of the barcode collaterals.

Key words

BOLD Databasing Tissue subsampling DNA extraction High-throughput DNA amplification Sequencing Sequence editing Sequence aligning Cytochrome oxidase DNA barcoding 

References

  1. 1.
    Floyd R, Wilson JJ, Hebert PDN (2009) DNA barcodes and insect biodiversity. In: Footit RG, Adler PH (eds) Insect biodiversity: science and society. Blackwell Publishing, Oxford, pp 417–431CrossRefGoogle Scholar
  2. 2.
    Ratnasingham S, Hebert PDN (2007) BOLD: The barcode of life data system (www.barcodinglife.org). Mol Ecol Notes 7:355–364
  3. 3.
    Janzen DH, Hajibabaei M, Burns JM et al (2005) Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Phil Trans R Soc Lond B 360:1835–1845CrossRefGoogle Scholar
  4. 4.
    Janzen DH, Hallwachs W, Blandin P, Burns JM, Cadiou J-M, Chacon I et al (2009) Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Mol Ecol Res 9:1–25CrossRefGoogle Scholar
  5. 5.
    Xhou X, Robinson JL, Geraci CJ, Parker CR et al (2011) Accelerated construction of a regional DNA-barcode reference library: caddisflies (Trichoptera) in the Great Smoky Mountains National Park. J Nor Amer Benth Soc 30:131–162CrossRefGoogle Scholar
  6. 6.
    iBOL (2010) Barcoding blitz targets Australian Lepidoptera. Barcode Bulletin 1(4):5Google Scholar
  7. 7.
    Vaglia T, Haxaire J, Kitching IJ et al (2008) Morphology and DNA barcoding reveal three cryptic species within the Xylophanes neoptolemus and loelia species-group (Lepidoptera: Sphingidae). Zootaxa 1923:18–36Google Scholar
  8. 8.
    Hausmann A, Hebert PDN, Mitchell A et al (2009) Revision of the Australian Oenochroma vinaria Guenée, 1858 species-complex (Lepidoptera, Geometridae, Oenochrominae): DNA barcoding reveals cryptic diversity and assesses status of type specimen without dissection. Zootaxa 2239:1–21Google Scholar
  9. 9.
    Wilson JJ, Landry JF, Janzen DH et al (2010) Identity of the ailanthus webworm moth, a complex of two species: evidence from DNA barcoding, morphology and ecology. Zookeys 46: 41–60Google Scholar
  10. 10.
    Dinca˘ V, Zakharov EV, Hebert PDN, Vila R (2011) Complete DNA barcode reference library for a country’s butterfly fauna reveals high performance for temperate Europe. Proc R Soc Lond B 278:347–355CrossRefGoogle Scholar
  11. 11.
    Virgilio M, Backeljau T, Nevado B, de Meyer M (2010) Comparative performances of DNA barcoding across insect orders. BMC Bioinformatics 11:4567–4573CrossRefGoogle Scholar
  12. 12.
    Vogler AP (2006) Will DNA barcoding advance efforts to conserve biodiversity more efficiently than traditional taxonomic methods? Front Ecol Environ 4:270–272Google Scholar
  13. 13.
    Pons J, Barraclough TG, Gomez-Zurita J et al (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Sys Biol 55:595–609CrossRefGoogle Scholar
  14. 14.
    Winter WD Jr (2000) Basic techniques for observing and studying moths & butterflies (Memoir No 5). The Lepidopterist’s Society, CambridgeGoogle Scholar
  15. 15.
    Hanner R. (2005) Proposed standards for BARCODE records in INSDC (BRIs). http://barcoding.si.edu/PDF/DWG_data_standards-Final.pdf
  16. 16.
    Regier JC (2008) Protocols, concepts, and reagents for preparing DNA sequencing templates. Version 12/4/08. http://www.umbi.umd.edu/users/jcrlab/PCR_primers.pdf
  17. 17.
    Porco D, Rougerie R, Deharveng L, Hebert PDN (2010) Coupling non-destructive DNA extraction and voucher retrieval for small soft-bodied Arthropods in a high-throughput context: the example of Collembola. Mol Ecol Res 10: 942–945CrossRefGoogle Scholar
  18. 18.
    Knölke S, Erlacher S, Hausmann A et al (2005) A procedure for combined genitalia extraction and DNA extraction in Lepidoptera. Insect Syst Evol 35:401–409CrossRefGoogle Scholar
  19. 19.
    Ivanova NV, deWaard J, Hebert PDN (2006) An inexpensive, automation-friendly protocol for recovering high-quality DNA. Mol Ecol Notes 6:998–1002CrossRefGoogle Scholar
  20. 20.
    Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotech 3: 294–299Google Scholar
  21. 21.
    Wilson JJ (2010) Assessing the value of DNA barcodes and other priority gene regions for molecular phylogenetics of Lepidoptera. PLoS ONE 5:e10525PubMedCrossRefGoogle Scholar
  22. 22.
    Ivanova N, and Grainger C (2006) Protocols: Sequencing. Canadian Centre for DNA Barcoding CCDB Protocols. http://www.dnabarcoding.ca
  23. 23.
    Shokralla S, Singer GAC, Hajibabaei M (2010) Direct PCR amplification and sequencing of specimens’ DNA from preservative ethanol. BioTechniques 48:232–234CrossRefGoogle Scholar
  24. 24.
    Hebert PDN, Penton EH, Burns J, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly, Astraptes fulgerator. Proc Nat Acad Sci USA 101: 14812–14817PubMedCrossRefGoogle Scholar
  25. 25.
    Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Nat Acad Sci USA 103:968–971PubMedCrossRefGoogle Scholar
  26. 26.
    Messing J (1983) New M13 vectors for cloning. Meth Enzymol 101:20–78PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Biodiversity Institute of OntarioUniversity of GuelphGuelphCanada

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