DNA Barcoding Basics

The Sixth International Barcode of Life (held at the University of Guelph) has just wrapped up and the abstracts and information gathered are being spread all over the internet for professionals and enthusiastic amateurs alike. For those who are not obsessed with the sheer world of awesome inherit in the topic of genetics, DNA Barcoding was an idea created by Paul Herbert as a way to identify species using DNA. This might seem like a no-bainer but in reality comparing the entire DNA of one individual against another’s is time consuming and expensive. The possibilities of being able to identify species through comparison of a small,  specific genetic area (though those areas are different in plants and animals) exploded onto the scene in a big way. Canadians led the charge into a new area of genetics and biotechnology that is still being enthusiastically pursued. The idea is to use the same genetic area of every living being as a point of comparison. To that end, a lot of the work done so far has involved creating large databases with as many barcodes as possible. Some of these archives are used for medical work, others for conservation, along with a whole host of other interesting projects.

Below is a longer run-down on DNA Barcoding 101:

DNA Representation  -Andy Leppard

DNA Representation -Andy Leppard


DNA Barcoding

DNA barcoding is a process by which a standardized region of DNA is used to identify specimens and discover new species. This process has revolutionized not just taxonomy, but biosurveillance as a whole. This POSTnote summarizes the process and its current uses, the economic and trade implications, and the current policies and ethical issues surrounding DNA barcoding.

Background

The traditional method of determining new species through morphological differences is severely hampered by the difficulty of identifying,  recalling, and describing these differences. The estimated number of species on Earth is between 10 to 100 million; over 100,000 taxonomists would be needed just to sustain the ability to recognize Earth’s species. In 2003 Dr. Paul Herbert and his research team published a paper that suggested a method for creating a universal barcode for identification of species. DNA barcoding removes the need for specialists and allows for the identification of samples that people would previously have been unable to use due to damage or age.

Overview

  • DNA barcoding is a universal method for species identification and discovery.
  • Created by a research team in Canada, a global effort has been made to identify all life on Earth through the International Barcode of Life (iBOL) project. Currently 26 nations are involved.
  • The new process and accompanying technology has decreased the cost and increased the speed and accuracy of taxonomy and biosurveillance.
  • DNA barcoding is now being used in several countries for related fields that include: healthcare, conservation, market regulation, pest control, forensics, and resource management.
  • There are ongoing discussions about the intellectual property rights of participants, data management and equitable access and benefits sharing, and compliance and enforcement policies.

The DNA Barcode

The specific region used for barcoding almost all animal groups is called COI (a 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene). While highly effective, it is not an efficient region for plants because it does not evolve fast enough. Two regions in the chloroplast,  the matK and rbcL, have recently been approved as barcode regions for land plants. All approved barcoding regions were chosen because they are both short enough to be sequenced quickly and cheaply, yet long enough to identify species variations.

The Process

Live specimens are not required, DNA barcoding can be done with preserved specimens or damaged samples that contain DNA. A lab technician gathers a small piece of tissue, from which the COI region is isolated and then replicated through the common process of PCR amplification. Afterwards it is sequenced. The sequence is represented by four letters (ATCG) that represent the four nucleic acids that form the entirety of all DNA – cytosine, adenine, thymine, guanine. The sequence would therefore look like this:

GTACCCAATGTGACGCGTA

Once a barcode has been sequenced for a species it is placed in the Barcode of Life Data Systems (BOLD) database. This database is used to identify unknown specimens. BOLD stores specimen data, images, sequences, and trace files. BOLD promotes the use of its data and analytical programs for Visualization, Interpretation, Identification, Browsing, Sharing, and Publishing.

International Barcode of Life project (iBOL)

After exploring the potential of DNA barcoding, 25 countries sent delegates to Guelph to discuss the proposal for a “United Nations of barcoding” – a global collaboration to create a reference library for all multi-cellular life. A committee was created in each country to gather participant researchers and funding. 2009 saw the finalization of  the International Barcode of Life project (iBOL), a Canadian not-for-profit corporation.

Currently iBOL research spans 26 nations, varying in levels of investment and responsibility. Canada has a central role in iBOL due to its initial early development of DNA barcoding. The Biodiversity Institute of Ontario (BIO) employs over 100 geneticists, informaticians and taxonomists that work as “iBOL’s scientific hub.” They operate the sequencing processors, maintain the central digital platform and host the largest scientific team working on iBOL.

Mission

The main goal of iBOL is to coordinate their network to create a reference library of sequenced barcodes for all life on Earth; and to develop technology for gathering and using this information. This requires proper data management, ability for community access, and the creation of new technology to allow for global access. Within 5 years iBOL aims to have five million species barcodes, to provide an excellent identification system “for economically, socially or environmentally important species” [1].

Earth is currently experiencing a mass extinction driven by human activity. Loss of biodiversity threatens critical ecosystem services such as pollination, nutrient cycling, natural products, etc. These services have an estimated value of over 500 billion [3].There is economic loss and societal repercussions associated with issues that come from loss of biodiversity, such as increase in pests and diseases that affect crops, livestock, and people. It’s impossible to calculate exact amount of knowledge and economic services lost when so much of life is still unknown.

Economic Benefits

DNA barcoding  has created an revolution in the time, effort and cost of biosurveillance, and the economic benefits are large. Once fully implemented this system will have impacts in a variety of areas. The application of the barcode process and technology will act as a solution or aid for: forensics, conservation, marketplace regulation, control of pests and diseases, ecosystem monitoring, food production and safety, resource management, conservation, research, education, and recreation.

It has large implications for identification and regulation in international trade. Increased globalization of trade and climate change means increased exposure to invasive species. DNA barcoding will allow for rapid identification and eradication, with both a decrease in cost and increase in success rate. It will aid in optimal control choice for pest and disease agents. DNA barcoding will also play a critical role in regulating trade in endangered or protected species, and products; as well as identifying counterfeit products and unapproved commodities. As the technologies become more efficient and available, and the barcode library larger, sophisticated environmental monitoring will become possible. Living organisms can be used as indicators of environmental change and early warnings of any environmental issues. The goal is to establish large scale, automated monitoring of species presence and abundance in the oceans, agro-ecosystems, plantations, etc.

Canadian Funding

Canada has invested a lot of money in the development of barcoding initiatives. The initial startup funds for iBOL came from Genome Canada’s International Consortium Initiative (ICI) program. Canadian funders that have contributed more than $100,000 are: Canada Foundation for Innovation; Environment Canada; Genome Canada; International Development Research Centre; New Brunswick Innovation Foundation; Natural Sciences and Engineering Research Council of Canada; Ontario Genomics Institute; Ontario Ministry of Economic Development and Innovation; and the University of Guelph.

Current Implementation

In Canada, BOLD is now used extensively by Health

Canada, Parks Canada, and Agricultural and Agri-Food Canada. The United States’ Food and Drug Administration uses barcoding for identifying seafood; the Environmental Protection Agency uses it to monitor freshwater invertebrates that are reliable environmental indicators; and the Department of Agriculture along with the Animal and Plant Health Inspection Service use barcoding to identify pests. New Zealand uses barcoding for monitoring invasive species.

Several international bodies and ministers that regulate trade are working with iBOL to create universal standards for using barcoding as a regulatory tool for international trade. The current national uses of barcoding lend support to its efficiency and provide opportunities to improve protocols that can then be expanded for international trade.

 Ethics

There are always concerns regarding the distributions of the benefits of science in large projects, especially international ones such as iBOL that require access and aid from a variety of genetic resources, and local and indigenous knowledge. The protection of indigenous values is important.

The collection of genetic material can be seen as very problematic if benefits sharing is not ensured. The “Draft Nagoya Protocol on Access and Benefit Sharing”  made by the Secretariat of the CBD (Convention on Biological Diversity) is being used by iBOL. It designates access to genetic resources to all members, and it promotes each party to create a national focal point and competent national authority. There is the additional problem of iBOL’s ability to monitor uses of genetic material; work is ongoing to create compliance and enforcement policies that everyone can agree to.

All biotechnological applications, including non-commercial applications, are subject to the access and benefits sharing. The GE3LS team reviews international and national treaties, laws, regulations and procedures that are relevant and ensure that “iBOL’s data, intellectual property and materials transfer policies compared with those of other interested stakeholders such as policy makers, funders, industry, NGOs and indigenous peoples” [1].

Education

Educational resources need to be created in order to begin public engagement with DNA barcoding. The three main focuses are educational modules for students, public perception and media and the engagement of scientific journalists. The educational barcoding module for students is being made in collaboration with Let’s Talk Science, a not-for-profit organization dedicated to improving scientific literacy.

It is important to know how both the science and the technology related to this science is perceived. At the moment DNA barcoding is not really in the public eye, but barcoding will be directly and indirectly impacting consumers, offering a variety of benefits and the science and technology behind DNA barcoding needs to be effectively communicated. iBOL is working with the Science Media Centre of Canada (SMCC) to develop a communication strategy directed at the media, the public, and the policy makers in government.

Citations:

[1]  International Barcode of Life <http://ibol.org&gt;

[2] “Memorandum of Understanding.” International Barcode of Life. <http://ibol.org/about-us/how-ibol-works&gt;

[3] Anielski, Mark, and Sara Wilson. (2009)”Counting Canada’s Natural Capital: Assessing the Real Value of Canada’s Boreal Ecosystem.” Canadian Boral Initiative. <http://www.borealcanada.ca/documents/BorealBook_CCNC_09_enFINAL.pdf&gt;

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