Using DNA bar codes to tell friend from foe

Canadians in many parts of the country have become all too familiar with the damage that invasive alien species can do. Insects such as the emerald ash borer and the Asian longhorn beetle that have arrived here in shipments of goods from other countries have led to the destruction of millions of trees in cities, towns and rural areas in Ontario

Invasive alien plants are just as bad. The Eurasian milfoil is expanding its range in Canada, covering the surface of lakes and rivers with an impenetrable mat of weed, stealing light and nutrients that native aquatic plants and fish need to survive. Purple loosestrife chokes out native species in wetlands.

With few or no natural enemies in this country, controlling the spread of these invaders is exceptionally difficult and costly. The best defence is to stop them at the border — but it is not always easy to tell a potentially destructive new arrival from a perfectly harmless native species.

A painstaking process

As Agriculture and Agri-Food Canada (AAFC) research scientist Dr. André Lévesque explains, "Different species of insects, for example, can look remarkably alike. In some cases, there might only be one or two people in the whole country who can look through a microscope and say whether a particular insect spotted on a shipment of fruit from overseas is a foreigner or a native Canadian."

The job is even more difficult when microscopic pathogens are involved. Pathogens such as the potato wart fungus can lead to embargoes of our potato exports. Others cause diseases that affect fish and other wildlife. Dr. Lévesque says it can be exceptionally difficult to tell these pathogens apart. "It can take days to determine whether a pathogen found in a shipment of perishable goods poses a threat," he says. "Even if the pathogen is found to be harmless, it may be too late to recover any value from the goods."

The bar code approach

Thanks to the science of genomics, the time required to make such an identification is getting much shorter. Today, scientists can sequence a specific, small section of DNA from an organism in as little as 24 hours. New technologies on the horizon could reduce that even further, allowing this kind of sequencing to be done in minutes.

"No two sequences from that part of the genome are the same," says Dr. Lévesque. "So you can read them the same way the scanner in the supermarket reads the bar code on a box of crackers. You feed the sequence into a computer, it compares them to the sequences from known organisms in your database, and within seconds, it tells you exactly what you're dealing with."

While he looks forward to the possibilities of ever-faster DNA sequencing technologies, Dr. Lévesque says the big challenge at the moment is developing the database that will make those fast comparisons possible. As he points out, "If you have nothing to compare your sample to, it's not going to help you."

"We have about 20 million specimens — insects, pathogenic fungi, plants — in our collections at AAFC alone," says Dr. Lévesque. "Obviously, we don't have to sequence all of them — we are focused on the high-risk organisms — but along with our colleagues in other departments, Fisheries and Ocean Canada, for example, we are adding many thousands of these DNA bar codes to a database that will be accessible to agencies all over the world."

Protecting jobs and growth

As well as helping to identify and protect Canada from potentially harmful alien species, the research — led by a team of researchers from different departments — will also help to protect Canada's exports. "With this information, we can assure other countries that the products they are buying from us don't contain anything they shouldn't," says Dr. Lévesque. "We'll be able to quickly identify any organisms or microorganism that may be present in an export shipment and if they are something that might cause a problem, take steps to manage any risk."

In 2012, for example, Canada exported some $13.5 billion in grains and oilseeds. Dr. Tom Gräfenhan, a research scientist with the Canadian Grain Commission, says Dr. Lévesque's growing database will play a role in assuring international markets that Canadian grain is safe. "There will always be a variety of microorganisms present in natural products like wheat," says Dr. Gräfenhan."It's important to know exactly what those microorganisms are, and the faster we can identify them, the better."

The project is funded by the Government of Canada's Genomics Research and Development Initiative (GRDI). In addition to building the DNA bar code database, Dr. Lévesque says GRDI has allowed the multidepartmental team to make progress in a number of key areas that will contribute to more effective genomics research in Canada in the future. "For example, thanks to the GRDI funding, we've been able to try out several different 'kits' for extracting the DNA we need, and we've identified the ones that work best," he says. "We're able to process a hundred samples at a time, some from specimens that are more than 100 years old."

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