WALNUT CREEK, CA–An international consortium including the U.S. Department of Energy (DOE), Genome Canada, and the Umeå Plant Science Centre in Sweden has released the first complete DNA sequence of a tree, Populus trichocarpa, the Black Cottonwood or poplar, one member of the most ecologically and commercially valuable group of trees in North America. The sequencing was completed at the DOE Joint Genome Institute Production Genomics Facility.
“By helping to lead this international collaboration to sequence the first tree genome, DOE once again is pioneering discovery-class science that promises to yield important societal benefits,” said Secretary of Energy Spencer Abraham. “The poplar genome sequence will provide researchers with a critical resource to develop faster growing trees, trees that produce more biomass that can be converted to fuels, and trees that can sequester more carbon from the atmosphere or be used to clean up waste sites. Just as DOE earlier played a leading role in mapping the human genome and making possible advances in human health, we now are pleased to build on that success and help deliver the poplar’s parts list–and the clean energy and cleaner environment that scientists will produce using the genetic sequence of the poplar in the future.”
“Forest genomics is rapidly shaping how we do sustainable, intensive forestry,” said David L. Emerson, Canada’s Minister of Industry. “The complete poplar code provides us with the starting material for understanding factors that control the essential traits of trees that fuel our forest economy. It will help us farm trees with desired growth and wood quality characteristics while protecting our forests from pests and diseases through the development of tools for early detection, diagnosis, and control, allowing for more vigilant conservation and forest management.”
The Biological and Environmental Research program in the Department of Energy’s Office of Science has provided a total of $12 million for the poplar initiative, including $8 million for sequencing and $4 million for associated research. The two-year project was coordinated out of the DOE’s Oak Ridge National Laboratory (ORNL) in Tennessee and powered by the sequencing engine of the DOE Joint Genome Institute. The partnership includes Genome Canada, through Genome British Columbia and the University of British Columbia, and the BC Cancer Agency Michael Smith Genome Sciences Centre, which jointly implemented vital DNA mapping, sequencing, and fingerprinting strategies. Genome Canada and Genome BC have invested a total of $10.8 million CDN in the British Columbia Forestry Genomics project, of which $2 million CDN were dedicated to the poplar initiative. The primary European partner, Sweden’s Umeå Plant Science Centre, collected an expressed sequence tag (EST) resource necessary for accurate gene prediction. The total investment in the Swedish Populus program exceeds $10 million, $3 million of which is directly connected to the genome sequencing effort. Stanford University served as an integral part of JGI’s sequence finishing and quality control operation. Ghent University (Belgium) played an increasing role in annotating the sequence that has been generated.
With a genome consisting of more than 480 million letters of genetic code, Populus trichocarpa was sequenced eight times over to attain the highest quality standards. Poplar was chosen as the first tree DNA sequence decoded because of its relatively compact genetic complement, some 40 times smaller than the genome of pine, making the poplar an ideal model system for trees. The poplar genome, divided into 19 chromosomes, is four times larger than the genome of the first plant sequenced four years ago, Arabidopsis thaliana, the tiny workhorse for plant molecular geneticists.
“Although we’re still in the early stages of analyzing the poplar genome, in our first pass we found more than 40,000 genes, most with significant relatedness to genes in other plants,” said Daniel Rokhsar, JGI computational genomics department head. “The trick will be in figuring out how these similar gene sets have been customized and redeployed in poplar to generate a large woody plant instead of a small weed. We’re currently comparing the poplar sequence with the genomes of rice and Arabidopsis to shed light on the evolution of these genes to see how they are differentially regulated in these diverse plants,” Rokhsar said. The poplar consortium researchers plan to publish the results of their analysis early next year.
“Carbon management issues are overwhelming, but poplar trees could play a significant role in the solution,” said Gerald Tuskan, whose team at the ORNL leads the poplar research effort. “Trees have a built-in mechanism for storing captured carbon dioxide in their leaves, branches, stems, and roots. This natural process of carbon sequestration suggests opportunities to further clean up the air by engineering trees so that they would more effectively shuttle and store more carbon below ground in their roots and the soil.” Joining Tuskan on the ORNL poplar team are Steve DiFazio, Tongming Yin, Frank Larimer, Lee Gunter, Gwo-Liang Chen, and Phil Locascio. JGI contributors include Daniel Rokhsar, Nik Putman, Igor Grigoriev, Paul Richardson, and Susan Lucas, who manages JGI’s production sequencing operation.
“This achievement will have a huge impact on research far beyond the field of forestry,” said Stefan Jansson at Umeå Plant Science Centre. Plant scientists throughout the world now have a tree model system to work with in addition to the already established models of Arabidopsis and rice. The many unique properties of trees, for example wood formation, longevity, seasonal growth, and hardiness patterns, mean that Populus now can be used to study many fundamental biological questions.” Joining Jansson in leading the Swedish poplar team are Jan Karlsson, Goeran Sandberg, and Fredrik Sterky.
“The sequencing is extremely valuable because attributes found in the poplar model will also be applicable to other trees,” added Don Riddle, Chief Scientific Officer of Genome British Columbia, on behalf of the four principal investigators of the Canadian component of the research. “Forestry is an integral part of Canada’s economy–for industry, ecology, and recreation. Despite increasing pressure on forestry resources through human demand, pest outbreaks, and global climate change, tree breeding for improved yield, quality, and pest resistance is still in its infancy. This research will help provide a solid base in tree genomics to advance biological knowledge and aid breeding programs.” The Canadian research team was led by Carl Douglas, Kermit Ritland, Joerg Bohlmann, and Brian Ellis from the University of British Columbia.
The genome browser, developed by JGI and accessible at http://www.jgi.doe.gov/poplar, is the repository for all the poplar sequence information. As a complement, a Swedish database with Populus gene expression information is also made available and can be accessed at www.populus.db.umu.se.
On September 22, Stefan Jansson from the Umeå Plant Science Centre will highlight the poplar work at the third Plant Genomics European Meeting, in Lyon, France.
On October 11, the poplar genome resource will be introduced to an international community of plant geneticists and ecologists. Consortium members Steve DiFazio and Pierre Rouzeé will present at the symposium “Functional Genomics of Environmental Adaptation in Populus” in Gatlinburg, Tennessee, cosponsored by DOE and Phytologist Trust.
In December, the JGI will host a “Poplar Annotation Jamboree” that will assemble the international community tasked with extracting the particular functions of the annotated gene set and highlighting other valuable motifs to further populate the publicly-accessible poplar database. A tutorial can be arranged on the use of the poplar genome browser through the contact below*.
See the backgrounder for facts about forest trees.
For additional information about the major poplar genome partners, see the following:
The International Populus Genome Consortium: http://www.ornl.gov/sci/ipgc/
Contact: Gerald Tuskan, 865-576-8141; gtk@ornl.gov
Oak Ridge National Laboratory: http://www.ornl.gov
Ron Walli, 865-576-0226; wallira@ornl.gov
DOE Joint Genome Institute: http://www.jgi.doe.gov
*Contact: David Gilbert, 925-296-5643; gilbert21@llnl.gov
Genome Canada: http://www.genomecanada.ca/
Contact: Anie Perrault, 613-751-4460, ext. 13; aperrault@GENOMECANADA.CA
Genome British Columbia: http://www.genomebc.ca/
Contact: Linda Bartz, 604-637-4373; lbartz@genomebc.ca
Umeå Plant Science Centre
Contact: Stefan Jansson, +46-90-7865354; stefan.jansson@plantphys.umu.se
Stanford Human Genome Center: http://www-shgc.stanford.edu
Contact: Ruthann Richter, 650-725-3900; richter1@stanford.edu
Department of Plant Systems Biology and INRA-associated laboratory at Ghent University: http://www.psb.ugent.be/
Contact: Yves Van de Peer, +32 (0)9-331-3807; yves.vandepeer@psb.ugent.be
Contact: Pierre Rouzé, +32 476 638 304; pierre.rouze@psb.ugent.be