Dubliner Colin Kellegher has been collaborating in Canada with a team of international experts on tracing tree genomes, writes Dick Ahlstrom
An Irish scientist has helped to produce the first genome sequence of a tree. While the human genome is six and a half times larger, the wild poplar may have almost twice as many genes.
Dublin-born Colin Kelleher spent the last few years in Canada working on an international collaboration involving the US Department of Energy, Genome Canada, the Umea Plant Science Centre in Sweden and Belgian researchers in Ghent. The goal was to provide a sequence for the wild poplar, Populus trichocarpa.
The choice of the poplar for the world's first tree genome was a relatively haphazard affair, says Kelleher. "They were looking for a tree genome and could have chosen any number of species." Something in favour of the poplar however was a great deal of associated research into its fundamental biology, biochemistry and other studies.
"It wasn't just going into a new organism," says Kelleher. "There were a lot of things to back up information coming from the sequence." In the end the poplar won out and the sequence emerged late last year after more than two year's work.
Kelleher studied in University College Dublin, then did a Masters in Bangor, Wales. His PhD was at Trinity, looking in particular at population genetics in the oak. His partner was also involved in research and they decided to spend some time abroad, finally choosing the University of British Columbia, Vancouver.
Canada seemed a natural place to study trees. "Canada has 10 per cent of the world's forests so it is really big here," he says. "I came over directly for the project. It had been going about six months and they needed someone to work in several areas, particularly in poplar genomics."
He joined the university's "Treenomix Group". "It is made up of four main PIs (principle investigators), nine research associates (such as himself) and 10 research technicians." It is an interdisciplinary group involving botany, forestry and biotechnology.
Delivering the first tree genome is no small accomplishment, and is important for fields as diverse as forestry, climate change and molecular genetics, he says.
"Trees are fantastic things, completely different to regular plants. They have to live in the same space for a long time and have to survive climatic and biotic factors."
They cannot escape from exposure to sun, wind and snow, nor run from diseases or pests. "They have to have a huge chemical resource to survive against these things."
This may provide a reason for the apparently high number of genes in the poplar. Its genome is about 485 million sequence steps or base pairs, small compared to a human's 3,200 million. Early analysis suggests it may have 58,000 genes, the genetic components that produce protein chemicals, compared to 25,000 to 30,000 in a human.
"They are only predictive gene models for the poplar," he acknowledges. The final count might be lower. Notwithstanding, the genome will provide a valuable information resource.
"We are using the genome to develop specific assays for gene variants to try to match up physical traits to these genes," Kelleher says. The goal is to find single or groups of genes associated with things such as wood quality, shape and grain.
The genome should also be important for climate change research, in the removal of carbon dioxide from the atmosphere via carbon sequestration. "Trees are harnessing a large amount of carbon. If you have a tree that is harnessing much more carbon, it could be used on plantations to balance greenhouse gas emissions."
Genome Canada was a key funder of the University of BC group. It is a Canadian government-backed agency that supports all of that country's genome projects.
The US participants at the Joint Genome Institute did the main sequencing, using a now familiar method. Leaves provided the DNA, which in turn was "chopped up using specialised cleaving enzymes and then amplified using polymerase chain reaction (PCR) technology. "The problem is these pieces are tiny and you need a larger framework to order them. That is where we came it," says Kelleher.
The sequence elements from the US were at most 800 base pairs long, but the Canadian sequence "map" is built using large chunks of DNA about 100,000 base pairs long.
The map was created using a form of DNA fingerprinting. It gives a broad outline, a kind of scaffold of the genome. This in turn provided a base onto which the smaller elements could be lined up in their proper order to produce the genome. "We had to add information and add specific markers in a very targeted way," says Kelleher.
Kelleher finishes working with the Treenomix Group this autumn when he hopes to return to Ireland and resume his research career at home.