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Brown Trout genome sequencing a game-changer for wildlife conservation

The genome sequencing of the wild Brown Trout – a significant milestone in conservation biology – has been completed by an international team of scientists, including from the Institute for Global Food Security

The task – part of an ambitious project to track the DNA of tens of thousands of lifeforms in the UK – was led by scientists at the Cambridge-based Wellcome Sanger Institute and collaborators, including fish-genetics expert Professor Paulo Prodöhl, from IGFS.

The research will help paint a picture of how UK species are responding to environmental pressures including climate change, and what secrets they hold in their genetics that enables them to flourish, or flounder.

It turns out that the humble brown trout (Salmo Trutta) is one of the most genetically diverse group of vertebrates. Indeed, based mainly on appearance, from three to 50 species are currently recognised in what is commonly referred to as brown trout. Scientists agree that trout taxonomy is still far from resolved.

But the DNA sequencing will help settle a longstanding debate about whether the physically varied brown trout is better recognised as a single species or several. This will enable conservation efforts targeted at specific populations during a period of rapid climatic change.

The newly-sequenced DNA will also help to explain the mythical ‘superpowers’ of the iconic brown trout by facilitating the identification of unique genetic adaptations. For instance, different populations have adapted to exploit particular biological niches, with some living their whole lives within a 200-metre stretch of freshwater stream while others migrate from the stream to the open sea.

As a result of this trait, brown trout were one of the first species to recolonise previously frozen freshwater areas from the sea at the end of the last Ice Age.

Professor Prodöhl explained: “Pinpointing genetic variations that allow some Scottish loch brown trout to adapt to living in relatively acidic waters may be useful in guiding conservation efforts to protect populations affected by increasing acidity in rivers and oceans as a result of climate change.

“Much European conservation legislation is still based only on species, in spite of many arguments to the contrary. If it is shown that diversity does not fit into conventional categories, then a move to more population-based conservation would be mandated, as is already the case for related salmonid species in North America.

“And while genes are known to be involved in determining both whether migration takes place or not, and the destination of the migrants, the individual genes responsible have yet to be identified. This will now be much easier with full sequence information.”

Due to the genetic complexity and diversity of the brown trout, which has 38 to 40 chromosomes and multiple copies of those chromosomes within its genome, specimens with only one set of chromosomes were specially bred by Norway’s Institute of Marine Research. Scientists at Wellcome Sanger Institute extracted DNA from these specimens and used PacBio SMRT Sequencing technology to generate the first, high-quality brown trout reference genome.

The brown trout is one of the 25 UK species to have been sequenced as part of the Sanger Institute’s 25th anniversary 25 Genomes Project. The 25 Genomes Project includes species such as grey and red squirrels, golden eagle, blackberry and robin. The project has laid the groundwork for the ambitious Darwin Tree of Life programme, which will sequence all 60,000 complex species in the UK.

Principal scientist Tom Hansen, of the Institute of Marine Research in Norway, who bred the fish used in the genome sequencing, said: “Given the variability of brown trout in the wild, it was important that we could create a number of genetically identical individuals to build the reference genome. Now that we have the genome, we can begin to learn more about how trout adapt to different conditions, helping the management of wild and farmed fish stocks in future.”

Professor Mark Blaxter, Programme Lead for the Darwin Tree of Life Project, said: “It’s fantastic that we can contribute the genome of such an interesting species as the brown trout to our growing store of knowledge. It will help scientists and conservationists the world over to discover the genetic secrets that make this species so unique. With every species we sequence, we’re learning lessons that will help us step up to the challenge of creating genomes for all complex species in the UK.”

The 25 Genomes project and Tree of Life programme at the Wellcome Sanger Institute are supported by Wellcome.