DNA barcoding aims to speed 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.
Current research effort on DNA barcoding includes:
Chairing the Scientific Steering Committee of the International Barcode of Life Project (iBOL).
IBOL is the largest biodiversity genomics project that has been undertaken. Its aim is to generate DNA barcodes from 5 million specimens representing 500K species by 2015, as a tool for species identification and species discovery. Pete Hollingsworth chairs the Scientific Steering Committee (SSC) of iBOL – the committee responsible for scientific direction and coordination of international activities to realise this goal.
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. Further discussion on the process of choosing and using a plant barcode is presented in a 2011 paper in PLOSone.
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:
- Ruhsam M, Rai HS, Mathews S, Ross TG, Graham SW, Raubeson LA, Mei W, Thomas PI, Gardner MF, Ennos RA, HOLLINGSWORTH PM (2015). Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria? Molecular Ecology Resources, DOI: 10.1111/1755-0998.12375.
- Fazekas AJ, Kuzmina M, Newmaster Steven G, HOLLINGSWORTH PM (2012) DNA barcoding methods for land plants. Methods in Molecular Biology 858: 223-252.
- Bell D, DG Long, AD Forrest, ML Hollingsworth, HH Blom and PM Hollingsworth. (2012) DNA barcoding European Herbertus (Marchantiopsida, Herbertaceae) and the discovery and description of a new species. Molecular Ecology Resources 12, 36-47
- Fazekas AJ, M Kuzmina, G Newmaster Steven, and PM Hollingsworth. in press. DNA barcoding methods for land plants. In press. WJ Kress and DL Erickson, editors. DNA Barcodes: Methods and Protocols. Humana Press, New York.
- Hollingsworth, PM (2011) Refining the DNA barcode for land plants. Proceedings of the National Academy of Sciences 108, 19451-19452.
- Hollingsworth PM, Graham SW and Little DP (2011) Choosing and using a plant DNA barcode. PLoSONE 6, e19254
- Kelly L, Hollingsworth PM, Coppins B, Ellis C, Harrold P, Tosh J and Yahr R (2011) DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytologist. 191, 288-300
- Fazekas AJ, Steeves R, Newmaster SG, Hollingsworth PM (2010). Stopping the stutter: Improvements in sequence quality from regions with mononucleotide repeats can increase the usefulness of non-coding regions for DNA barcoding. Taxon. 59, 694-697.
- 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
- 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.
- 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
Michelle Hollingsworth (Science and Technical Services Group)
James Richardson (Tropical Biology Group)
David Mann (Cryptogamic group)
David Long (Cryptogamic group)