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DNA Barcoding

DNA Barcode of Acacia trees DNA barcoding quickly became one of the buzzwords in biology. The goal of this international effort is to establish an easy and cost-effective way of species identification, by reading a standardized region of DNA in a biological sample. The idea is not new, of course. For the past several decades, scientists have been using DNA sequences to construct evolutionary history of animals and plants, or identifying pathogens. However, the DNA regions that they have been using are chosen to optimize the resolution for their specific experimental purposes. What makes the DNA barcoding radically different lies in the standardization of the DNA region for all the species in nature, or at least for major taxa such as kingdoms. There is a lot of appeal to it, but the story is not as simple as it appears.

Significance of Barcoding the DNAs

DNA barcoding can potentially change the way people identify species and biological products derived from them. Barcoding requires a very small piece of sample. It can identify species by sampling a small quantity of market products, such as fish meat, which may be illegally caught, or herb mixture which may not have any medicinal value. Another advantage is that barcoding makes the identification easy and accurate for any non taxonomist. For example, many look-alike mosquitoes exist, but only certain species can cause malaria. This will aid epidemiological studies and eradication efforts. For animals and fungi, a consensus has been reached that a 648-bp region that code for the mitochondrial cytochrome c oxidase subunit I (COI) is most suitable for barcoding.

Plant DNA Barcoding

Acacia Trees The COI DNA region, that works well as a barcode for animal and fungal species, lacks variability in plants to identify samples accurately at the species level. As an alternative, the combination of rbcL and matK regions were proposed as a standard barcode for plant species (CBOL Plant Working Group, 2009¹). However, it is not clear whether this combination provides that resolution required to identify most plants to the species. Additional regions may be necessary for certain taxa of plants.

¹CBOL Plant Working Group (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences, USA 106:12794-12797.

DNA Barcoding Project at IIAR

Acacia Trees A DNA barcoding project was initiated at the Indian Institute of Advanced Research for several reasons. First, it is a new institute established in 2006 and it needed a project that does not require an established infrastructure, and yet that can be a pioneering work in modern biology. Second, after the barcoding standard for acacia species is established, the expertise can be applied to the identification of medicinal and aromatic plants. India is home to the biodiversity of these herbs and has a long history of utilizing these plants in traditional folk medicine, such as ayurveda. However, adulteration of medicines by contaminating cryptic (morphologically indistinguishable) species has been a problem. DNA barcoding may be a cost-effective solution for the problem.

We chose acacia species for the barcoding project, considering its importance in local ecology and economy. To collect acacia samples, we travel to various locations in Gujarat, although so far, we have covered only the locations around Gandhinagar. We first spot acacia trees and tag each tree with metal plate with a sample number, and then collect leaves, flowers, and pods. The specimens are preserved for later deposition in herbaria, and at the same time, genomic DNA is extracted from them. The DNA samples are used for PCR with primers proposed internationally for barcoding and the products are sequenced and analyzed. Dr. Rajani Nadgauda, who is the group leader of the Plant Science Department of the institute, has been very supportive of the project and undertook all the logistics and business part of the work. The initial stage of the project was carried out by Drs. Neeraj Jain and Soni Gupta, whom you can see in some of the pictures.