By Cat Robinson
Canadian researcher Paul Herbert and his team from the University of Guelph in Ontario first proposed the DNA barcoding system in a paper (Biological identifications through DNA barcodes) in 2003. Their aim was to use a short section of DNA in a standardised section of the genome which could be used as a unique identifier for a particular species. Herbert thought of the idea in a supermarket in the late 1990’s: “It occurred to me that if the retail industry can use a few numbers to represent a vast array of products, why can’t we look at DNA the same way?”
It is estimated that there may be up to 100 million different species on Earth, and before the DNA barcoding initiative, fewer than two million of these had been catalogued. In traditional taxonomy, a few keys and features are used by specialist taxonomists to identify a particular specimen, and even a very experienced researcher may not be able to identify a species if the specimen is damaged or still in a juvenile phase of development. Because DNA is the same at every stage of growth and can be taken from a miniscule sample of an organism, it provides the fastest and most accurate may of identifying existing species and cataloguing new discoveries correctly. And of course, you wouldn’t need years of study and experience to use it, and it would be far less expensive.
Delegates from 25 countries therefore gathered in Guelph in 2007 to discuss creating a barcode library for all multi-cellular organisms which could be added to and accessed internationally in a global collaborative effort. Funding requests and organisational work began in 2009, and finally in October of 2010 the International Barcode of Life project was formally activated.
The standard section of the chromosome used for DNA barcoding in animals is named the CO1 region, which contains 648 base-pairs, whereas gene regions in the chloroplast are used for plants – these are known as the matK and rbcL regions. Because each strand of DNA is composed of four nucleotides: adenine, guanine, thymine and cytosine (A, G, T and C) – these can be given a colour allocation (adenine=green, guanine=black, thymine=red and cytosine=blue) and shown in sequence to create that particular species’ “barcode” – which comes out looking surprisingly like their retail barcode counterparts!
The International Barcode of Life project collects specimens from all over the world – either directly from collectors in the field, museums, and botanical gardens amongst many others. South Africa has our own sector of IBOL which has been running through a steering committee of several academic institutions since 2010, and runs many DNA barcoding projects throughout the country through the various universities and from overseas scientists, amongst others.
Once samples reach the laboratory, a tiny piece of the specimen is used to extract the organism’s DNA. Through a process known as PCR amplification, the region of the DNA strand used for barcoding is replicated and sequenced, and can then be filed in a database. The largest global database is housed at the Barcode of Life Database (BOLD) and currently has over 1.5million records which are publicly accessible. These records contain immensely valuable information about where and when the specimen was collected, which research team made the collection and who the team leader was, and of course genus, family and species information.
For example, this author looked up her favourite animal – the orca or killer whale, orcinus orca – and the first data entry brings up the following nucleotide sequence:
One of the main benefits of DNA barcoding is in the identification of smuggled animals such as in the illegal bush meat trades and the smuggling of highly endangered species. By being able to identify an animal (even from eggs in the case of birds and reptiles) as endangered and illegal to transport, authorities can confidently and quickly make arrests. Another major benefit could be for public health initiatives such as the control of diseases such as malaria and other insect-carried diseases. At present, projects are operating in the collection of specimens of mosquitoes in India, black flies in South America which transmit river blindness, and parasites which afflict livestock in Central America and Mexico. More case studies can be found in this news article from NBC.
Other potential benefits include food safety regulation, ecosystem monitoring for conservation and climate change research, resource management, and control of alien and invader species. It is hoped that large-scale, automated monitoring across oceans, inland water, and reserves will soon become routine.
EAN and UPC barcodes revolutionised the retail sector and how worldwide trade was conducted – hopefully DNA barcodes can do the same for science and conservation!
Further reading and sources: