SA scientists find plant barcode

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Janine Erasmus

For years scientists have been trying to find a gene that can be reliably used to identify members of the plant kingdom, using the fast-developing technique of DNA barcoding. Now a group of experts from South Africa’s University of Johannesburg (UJ), working with colleagues from the University of Costa Rica and Imperial College London, have opened that door with the discovery that a segment of the matK (megakaryocyte-associated tyrosine kinase) gene can fulfil this purpose.

This discovery is of great significance to the world of botany, as DNA barcoding has many potential uses. Using snippets of DNA code for quick, cheap, easy and accurate identification, barcoding will make it possible to identify existing species from tiny pieces of plant material or from specimens taken from different stages in the plant’s life cycle, while data for new specimens will be submitted to the database on the spot.

The same ease of identification has forensic, ecological and medicinal implications. Officials at ports and airports will instantly be able to identify plants in transit, even if obvious identifying features such as leaves or flowers have been stripped away – helping clamp down on the smuggling of endangered plant species. It will also take only minutes to identify plant ingredients in traditional medicines or specimens at crime scenes, even if they have degraded.

Dr Michelle van der Bank, senior lecturer in UJ’s Department of Botany and Plant Biotechnology, led the South African contingent in the group. Her overseas colleagues were headed by Dr Vincent Savolainen of both the Royal Botanic Gardens and Imperial College London’s Department of Life Sciences, and Diego Bogarin of the Lankester Botanical Garden at the University of Costa Rica.

Their results were published in the 7 February 2008 edition of the Proceedings of the National Academy of Sciences.

Animal barcoding already in progress

The barcoding process is already widely carried out with animals, using the genetic sequence for the enzyme known as cytochrome c oxidase 1 (CO1 or cox1). But this gene is not suitable for the same purpose in plants because evolution rates in higher plants are much slower than in animals, with the result that there is often no DNA sequence variation between species. For this reason cox1 – the animal standard – cannot be used to distinguish between plants at species level.

The distinguished group of scientists have now found that the matK gene can be used to identify plants reliably, as the gene’s DNA sequences are almost identical between plants of the same species, but differ between species. This means that the matK gene can provide scientists with a way of distinguishing between different plants, even though they may look identical.

Neither the matK nor cox1 genes are found within the nucleus of the cell – matK is found in the chloroplast, the area of the plant cell involved in photosynthesis, while cox1 is found in the mitochondrion, the powerhouse of the animal cell.

Studies in Africa and South America

The researchers, led by Savolainen, carried out two large-scale field studies: one in Costa Rica and one in South Africa. Both sites were chosen for their exceptional diversity of plant life.

Costa Rica, with its wealth of orchid species, was illuminating – the matK technique proved that a particular orchid that was thought to be a single species was actually two distinct species that relied on different insects for pollination. As Van der Bank says, it is difficult to identify an orchid that is not in bloom, but in total some 1 600 distinct species of orchids were catalogued during the study.

Costa Rica’s national flower is in fact an orchid – the Guaria Morada (Cattleya skinneri).

Meanwhile, in South Africa, the trees and shrubs of the Kruger National Park (KNP) also came under scrutiny. The KNP provided an ideal environment for research because it is one of the largest protected areas in Africa – around the size of Wales. It is now part of the Great Limpopo Transfrontier Park, itself a part of the Kruger to Canyons biosphere which has been designated by Unesco as an international man and biosphere reserve.

The KNP encompasses at least 16 recognised ecozones, each with its own vegetation, geology, rainfall, soil and temperature.

With Van der Bank at the helm, the project was initiated in 2005 and to date more than 2 000 plant specimens have been collected. Although the matK gene on its own identified more than 90% of the species, it was suggested that a combination of barcodes be used for identification of some of the plants in this area where matK alone could not suffice.

This will only be the case in the remaining 10% of plant species, and the reason is hybridisation, or cross-breeding of species, which occurs much more readily in the plant kingdom than among animals. In these cases, the genome – the complete set of genetic material contained in an organism, including chromosomes, genes and DNA – has been altered and therefore it becomes necessary to make use of additional DNA references.

UJ has set up a DNA bank that holds the results of the study. The team is now working to create a matK database of all the plant samples from South Africa and Costa Rica. This will be expanded to include plant samples from all over the world.

The barcode of life

DNA barcoding refers to the technique that uses a short DNA sequence from a standardised locus as a species identification tool. In genetics, the locus is a fixed position on a chromosome, where a specific gene, or DNA sequence within a gene, is located.

Since identification is one of the first strategies in discovery, research and monitoring, it is vital that fast, inexpensive and accurate methods are available. Existing methods can be cumbersome to use, often rely on detailed examination of specific physical features, typically require interpretation by trained experts and are also limited to certain stages of life – but because DNA does not change as the organism grows it can be used at any stage.

DNA barcoding is analogous with the process used to identify manufactured goods and as such, is considered to be a practical tool for the identification of the estimated 10 million species on the planet. Scientists expect that it will also help reveal the evolutionary history of life on earth.

In addition, says the Canadian Centre for DNA Barcoding, because DNA barcoding quickly distinguishes new species, it will greatly accelerate the rate of their discovery. The fact that it has taken 250 years to scientifically describe roughly 15% of life’s diversity and that this diversity is now being lost at an alarming rate – often before there is even time to properly identify it – proves that DNA barcoding has arrived at a critical time.

Furthermore, a hand-held scanner linked to a database can perform the identification in the field in seconds – the person using the scanner does not even have to possess scientific knowledge. This means that people living in inaccessible or little-studied parts of the world, such as central Africa, can use scanners to submit new samples to the database even as they go about their daily lives. The device does not yet exist but it is one of the goals of the project.

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