DNA

Research Project led by Professor Vincent Savolainen

DNA barcoding

Summary

Taxonomy is of key relevance to the environment, agriculture, food production, and human health. However, describing all living organisms is such a daunting task that it calls for new approaches. A DNA-based system for species identification, called 'DNA Barcoding', is one such solution. The implementation of such a system requires the standardisation of specific genetic markers (i.e. 'DNA barcodes'). Imperial researchers identified DNA barcodes for plants in 2008, which have since been endorsed by the Consortium for the Barcoding of Life and have led to multiple applications ranging from helping authentication of material for trade control (herbal medicine), facilitating biodiversity inventories or combating invasives.

The Challenge

A DNA-based system for species discovery, identification and delimitation could complement, or even substitute, the existing centuries-old taxonomic system. It would 'democratise' species identification even for non-specialists, while being applicable to all life stages and partially preserved specimens. This approach - either called DNA Barcoding or DNA Taxonomy - requires a reference sequence database at species level to ultimately catalogue and provide identifications for the estimated 10 million species on Earth. The implementation of such a system requires the discovery of suitable genetic markers for species identification (i.e. 'DNA Barcodes'), biologically meaningful methods for defining species entities, and a proof-of-principle of the methods in complex ecosystems.

Insights

My research, and that of key colleagues in the Department of Life Sciences at Imperial College London, has been instrumental in designing and trialling a DNA-based taxonomic approach. My research led to the development of a universal DNA barcode for plants, a particularly challenging problem - e.g., as reported in Science: ‘Wanted: a DNA barcode for Plants’ (318:190, 2007). Specifically, I combined results from research in Costa Rica and Africa and demonstrated the feasibility of DNA barcoding plants using the matK locus. I found that this genetic marker exhibited the necessary 'barcoding gap', that is, it is well conserved within a plant species but varies extensively between them. This DNA barcode was then trialed in (sub)tropical plant communities, leading to the discovery of a new species of orchids and demonstrating its use for identifying taxa covered by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) regulations.

Impact

My research, and that of key colleagues in the Department of Life Sciences at Imperial College London, has been instrumental in designing and trialling a DNA-based taxonomic approach. My research led to the development of a universal DNA barcode for plants, a particularly challenging problem - e.g., as reported in Science: ‘Wanted: a DNA barcode for Plants’ (318:190, 2007). Specifically, I combined results from research in Costa Rica and Africa and demonstrated the feasibility of DNA barcoding plants using the matK locus. I found that this genetic marker exhibited the necessary 'barcoding gap', that is, it is well conserved within a plant species but varies extensively between them. This DNA barcode was then trialed in (sub)tropical plant communities, leading to the discovery of a new species of orchids and demonstrating its use for identifying taxa covered by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) regulations.

Some references

[1] Lahaye R., van der Bank M., Bogarin D., Warner J., Pupulin F., Gigot G., Maurin O., Duthoit S., Barraclough T. G., Savolainen V., ‘DNA barcoding the floras of Biodiversity hotspots’, PNAS 105: 2923-2928 (2008).

[2] CBOL Plant Working Group (incl. Savolainen V.), ‘A DNA barcode for land plants’, PNAS 106:12794-12797 (2009).

[3] Dunning, L.T., Savolainen, V., ‘Broad-scale amplification of matK for DNA barcoding plants, a technical note’, Bot. J. Linn. Soc. Vol 164:1 1-9 (2010).