DNA barcoding has been proposed as a mechanism for speeding up the process of cataloguing life on earth. It is based on the premise of using a standard short region of DNA as a universal tool for identifying organisms. The aim is to establish a large-scale reference sequence database against which unknown samples can be queried for identification. Where sequences are found that are divergent from others in the database, the corresponding specimens are flagged up as potential new species warranting further investigation.
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Current research effort on DNA barcoding includes:
Selecting an appropriate region of DNA for barcoding land plants
Pete Hollingsworth is chair of the Plant Working Group of the Consortium for the Barcode of Life (CBOL PWG). This group has been comparing the performance of different candidate barcoding loci with the aim of reaching agreement on a standard DNA barcode for land plants. This work was published in August 2009 in PNAS with the recommendation of rbcL+matK as a standard land plant barcode. This recommendation is now being assessed by the Consortium for the Barcode of Life. See the CBOL PWG pages for more information:
Barcoding the British liverwort flora
Liverwort species can be difficult to identify using morphological characters, cryptic species frequently occur, and there is a shortage of taxonomic experts. DNA barcoding can thus be used as a tool for species identification and taxonomic clarification. In collaboration with RBGE's bryologist David Long, we are using the British liverwort flora (ca 300 species) as a model to evaluate the performance of DNA barcoding in liverworts.
General evaluation of the performance of DNA barcoding techniques
Sequencing a small number of plastid regions will not provide species level resolution in all plant groups. Recent diversification and hybridisation will result in the sharing of haplotypes among species. We are interested in establishing how often plastid barcoding provides species level resolution in different plant groups, and conversely in which groups additional assays are required.
Protocol development for DNA barcoding
We are currently working on protocol development to improve amplification strategies for matK in DNA barcoding studies. This involves design of primers and primer cocktails aiming to improve the amplification efficiency of the proposed barcoding region from angiosperms and other land-plant groups.
For more information on DNA barcoding at the Royal Botanic Garden Edinburgh, contact Pete Hollingsworth
Recent DNA barcoding publications:
- CBOL Plant Working Group (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences, USA, 106: 12794-12797
- Hollingsworth ML, Clark A, Forrest LL, Richardson JE, Pennington RT, Long D, 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 Molecular Ecology Resources 9: 439-457
- Hollingsworth PM. (2008) DNA barcoding plants in biodiversity hot spots: progress and outstanding questions. Heredity 101: 1-2
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Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madrinan S, Petersen G, Seberg O, Jorgsensen T, Cameron KM, Carine M, Pedersen N, Hedderson TAJ, Conrad F, Salazar GA, Richardson JE, Hollingsworth ML, Barraclough TG, Kelly L and Wilkinson M. (2007) A proposal for a standard protocol to barcode all land plants. Taxon 56: 295-299.
- Hollingsworth PM. (2007) DNA barcoding: potential users. Genomics Society and Policy 3: 44-47.
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Long DG, Paton JA, Squirrell J, Woodhead M, Hollingsworth PM. (2006) Morphological, ecological and genetic evidence for two species in one: Anastrophyllum joergensenii Schiffn. and A. alpinum Steph. (Hepaticae; Lophoziaceae). Journal of Bryology 28: 108-117.
RBGE staff involved in DNA barcoding
Pete Hollingsworth
Michelle Hollingsworth (Science and Technical Services Group)
James Richardson (Tropical Biology Group)
Laura Kelly
Alan Forrest
Kath Evans (Diatom barcoding)
David Mann (Cryptogamic group)
David Long (Cryptogamic group)