DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

News & Publications
Home › News Releases › The Book Opens on the First Tree Genome

September 21, 2004

The Book Opens on the First Tree Genome

treetopsWALNUT 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

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases, Poplar

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.

Tracing the Evolution of Shiitake Mushrooms

A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.

JGI announces final round of 2022 Functional Genomics awardees

Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI at 25: Mapping Switchgrass Traits with Common Gardens

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California