Abstract
DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world’s biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world’s herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hebert PDN, Cywinska A, Ball SL et al (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270:313–321
Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859
Chase MW, Fay MF (2009) Barcoding of plants and fungi. Science 325:682–683
de Vere N, Rich TCG, Ford CR et al (2012) DNA barcoding the native flowering plants and conifers of Wales. PLoS One 7:e37945
Asahina H, Shinozaki J, Masuda K et al (2010) Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences. J Nat Med 64:133–138
Chen S, Yao H, Han J et al (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5:e8613
De Mattia F, Bruni I, Galimberti A et al (2011) A comparative study of different DNA barcoding markers for the identification of some members of Lamiacaea. Food Res Int 44:693–702
Jaakola L, Suokas M, Haggman H (2010) Novel approaches based on DNA barcoding and high-resolution melting of amplicons for authenticity analyses of berry species. Food Chem 123:494–500
Kumar S, Kahlon T, Chaudhary S (2011) A rapid screening for adulterants in olive oil using DNA barcodes. Food Chem 127:1335–1341
Stoeckle MY, Gamble CC, Kirpekar R et al (2011) Commercial teas highlight plant DNA barcode identification successes and obstacles. Sci Rep 1:42
Bleeker W, Klausmeyer S, Peintinger M et al (2008) DNA sequences identify invasive alien Cardamine at Lake Constance. Biol Conserv 141:692–698
Saunders GW (2009) Routine DNA barcoding of Canadian Gracilariales (Rhodophyta) reveals the invasive species Gracilaria vermiculophylla in British Columbia. Mol Ecol Resour 9:140–150
Van De Wiel CCM, Van Der Schoot J, Van Valkenburg JLCH et al (2009) DNA barcoding discriminates the noxious invasive plant species, floating pennywort (Hydrocotyle ranunculoides L.f.), from non-invasive relatives. Mol Ecol Resour 9:1086–1091
Kesanakurti PR, Fazekas AJ, Burgess KS et al (2011) Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. Mol Ecol 20:1289–1302
Sonstebo JH, Gielly L, Brysting AK et al (2010) Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Mol Ecol Resour 10:1009–1018
Kress WJ, Erickson DL, Jones FA et al (2009) Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc Natl Acad Sci U S A 106:18621–18626
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
CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci U S A 106:12794–12797
Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS One 6:e19254
Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life data system (www.barcodinglife.org). Mol Ecol Notes 7:355–364
Fazekas A, Kuzmina ML, Newmaster SG et al (2012) DNA barcoding methods for land plants. In: Kress WJ, Erickson DL (eds) Springer protocols methods in molecular biology 858 DNA barcodes methods and protocols. Springer, New York, pp 223–252
Särkinen T, Staats M, Richardson JE et al (2012) How to open the treasure chest? Optimising DNA extraction from herbarium specimens. PLoS One 7:e43808
Bridson D, Forman L (1998) The herbarium handbook, 3rd edn. Royal Botanic Gardens Kew, London
Parker M, Stones-Havas S, Starger C et al (2012) Laboratory information management systems for DNA barcoding. In: Kress WJ, Erickson DL (eds) Springer protocols methods in molecular biology 858 DNA barcodes methods and protocols. Humana, New York, pp 269–310
Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Bininda-Emonds ORP (2005) Transalign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 6:156
Deck J, Gross J, Stones-Havas S et al (2012) Field information management systems for DNA barcoding. In: Kress WJ, Erickson DL (eds) Springer protocols methods in molecular biology 858 DNA barcodes methods and protocols. Humana, New York, pp 255–267
Kreader CA (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62:1102–1106
Ivanova NV, Fazekas AJ, Hebert PDN (2008) Semi-automated, membrane-based protocol for DNA isolation from plants. Plant Mol Biol Rep 26:186–198
Wolfe AD, dePamphilis CW (1998) The effect of relaxed functional constraints on the photosynthetic gene rbcL in photosynthetic and nonphotosynthetic parasitic plants. Mol Biol Evol 15:1243–1258
Dunning LT, Savolainen V (2010) Broad-scale amplification of matK for DNA barcoding plants, a technical note. Bot J Linn Soc 164:1–9
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
Fazekas AJ, Burgess KS, Kesanakurti PR et al (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS One 3:e2802
Fay MF, Swensen SM, Chase MW (1997) Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae). Kew Bull 52:111–120
Ford CS, Ayres KL, Toomey N et al (2009) Selection of candidate coding DNA barcoding regions for use on land plants. Bot J Linn Soc 159:1–11
Cuenoud P, Savolainen V, Chatrou LW et al (2002) Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. Am J Bot 89:132–144
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
de Vere, N., Rich, T.C.G., Trinder, S.A., Long, C. (2015). DNA Barcoding for Plants. In: Batley, J. (eds) Plant Genotyping. Methods in Molecular Biology, vol 1245. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1966-6_8
Download citation
DOI: https://doi.org/10.1007/978-1-4939-1966-6_8
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1965-9
Online ISBN: 978-1-4939-1966-6
eBook Packages: Springer Protocols