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Checkbiotech: The book opens on the first tree genome
Posted by: DR. RAUPP & madora (IP Logged)
Date: September 23, 2004 07:14AM

www.czu.cz ; www.raupp.info

An international consortium including the U.S. Department of Energy (DOE),
Genome Canada, and the Ume? 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, September 2004
.

"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 Ume? 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 Ume? 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
[www.jgi.doe.gov], 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 Ume? 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 Rouzeť will present at the symposium
"Functional Genomics of Environmental Adaptation in Populus" in Gatlinburg,
Tennessee, cosponsored by DOE and Phytologist Trust. For more information
about the meeting see [www.newphytologist.org] .

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: [www.ornl.gov]
Contact: Gerald Tuskan, 865-576-8141; gtk@ornl.gov
Oak Ridge National Laboratory: [www.ornl.gov]
Ron Walli, 865-576-0226; wallira@ornl.gov
DOE Joint Genome Institute: [www.jgi.doe.gov]
*Contact: David Gilbert, 925-296-5643; gilbert21@llnl.gov
Genome Canada: [www.genomecanada.ca]
Contact: Anie Perrault, 613-751-4460, ext. 13; aperrault@GENOMECANADA.CA
Genome British Columbia: [www.genomebc.ca]
Contact: Linda Bartz, 604-637-4373; lbartz@genomebc.ca
Ume? Plant Science Centre: [www.upsc.nu]
Contact: Stefan Jansson, +46-90-7865354; stefan.jansson@plantphys.umu.se
Stanford Human Genome Center: [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: [www.psb.ugent.be]
Contact: Yves Van de Peer, +32 (0)9-331-3807; yves.vandepeer@psb.ugent.be
Contact: Pierre Rouzť, +32 476 638 304; pierre.rouze@psb.ugent.be

[www.jgi.doe.gov]

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