International project maps salmon genome

New genetic database holds huge potential for fisheries science and conservation

Salmon—they’re tasty and nutritious to eat, many livelihoods depend on them and they’re crucial to the health of coastal ecosystems.

Turns out they’re also a goldmine of information for geneticists and molecular biologists.

In the coming years we’ll find out how rich that goldmine is now that an international research team co-led by a University of Victoria biologist has “mapped” the three billion bits of genetic code—known as the genome—that define what it is to be an Atlantic salmon.

“Just as mapping the human genome has fundamentally changed medical science, sequencing this genome is going to have a tremendous impact on fisheries science and conservation,” says Ben Koop, who studies how living things adapt and change over time.

The Atlantic salmon is one of 68 members of the salmonid family of fish, which also includes trout, grayling and char. Many of these fish are of great economic, ecological and societal importance to coastal communities and the fishing, aquaculture and tourism industries.

“All of the salmonids are about 92 per cent similar at the general DNA-genome level,” says Koop. “That similarity allows us to take information from one species—in this case the Atlantic salmon—and loosely apply it to all the salmonids.

“It will lead to a better understanding of how salmonids react to a changing environment and identify adaptations that will improve survival, whether they’re swimming in the open ocean or in an aquaculture pen.”

The international consortium of scientists and funding organizations—in Canada, Norway and Chile—has spent more than four years and $10 million to map the Atlantic salmon’s entire DNA sequence. They announced its completion this summer.

It was no simple task. For one thing, the salmon genome is two to three times larger than in most other vertebrates. In fact, it’s roughly the same size as the human genome—about 50,000 genes.

Why does a fish have just as much genetic information as we do? It’s all about adaptability—the ability of an organism to adapt to different or changing environments.

“Genomes are very dynamic systems,” explains Koop. “Fifty per cent of the human genome, for example, is made up of virus-like elements that don’t code for genes. They float around the genome doing their own thing and if one of them jumps into the middle of a gene, it’s bad news for the gene.”

In salmonids, about 60 per cent of the genome is made up of these rogue elements. They often cause problems, but they can also lead to variability. That’s essential for salmon, which to survive must adapt to multiple environments—freshwater, saltwater, brackish water, tiny streams, big streams, the ocean, and so on.

“It’s that complexity and variability that allows us all to survive in new environments,” says Koop. “If we had just one strand of DNA with no variability it wouldn’t take long for us to go extinct.”

There’s another distinctive feature of the salmon genome—about 90 million years ago it created a complete backup copy of itself.

“A duplication has massive effects,” Koop explains. “You have the potential for evolutionary innovation and that allows for adaptation to completely new environments.”

Genome duplication is nothing new. An ancient duplication 400-500 years ago gave rise to the huge diversity of vertebrates we see today—birds, amphibians, reptiles and mammals, including us.

But in evolutionary terms, the salmonid duplication is recent—and therefore very intriguing for scientists like Koop who study the molecular mechanisms of evolution. “It’s a rare event that allows us to look at how DNA evolution gives rise to radically diverse animals.”

Having two copies of everything also doubled the challenge for the genome mappers. “It’s been an extremely difficult genome to complete,” says Koop, “but we’ve now got it to a point where we’re very happy with its accuracy.”

Koop, who is also the Canada Research Chair in Genomics and Molecular Biology, was one of three founders of the project. His lab did a lot of computational work for the early gene assemblies and much of the gene identification.

The fully mapped genome is openly available to fisheries managers, aquaculture managers and scientists around the world. It can be applied to a wide range of management issues affecting salmonids, including disease, nutrition and growth, stock conservation and climate change.

The project was funded by Genome BC, with contributions from the Natural Sciences and Engineering Research Council, the Canada Research Chairs program and Compute Canada.