DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • 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 › DOE Joint Genome Institute Completes Soybean Genome— Data Released to Advance Biofuel, Food, & Feed Research

December 8, 2008

DOE Joint Genome Institute Completes Soybean Genome— Data Released to Advance Biofuel, Food, & Feed Research

lores_dried_soybean

Dried soybean, courtesy of USDA-ARS

WALNUT CREEK, CA— The U.S. Department of Energy Joint Genome Institute (DOE JGI) has released a complete draft assembly of the soybean (Glycine max) genetic code, making it widely available to the research community to advance new breeding strategies for one of the world’s most valuable plant commodities.  Soybean not only accounts for 70 percent of the world’s edible protein, but also is an emerging feedstock for biodiesel production. Soybean is second only to corn as an agricultural commodity and is the leading U.S. agricultural export.

DOE JGI’s interest in sequencing the soybean centers on its use for biodiesel, a renewable, alternative fuel with the highest energy content of any alternative fuel. According to 2007 U.S. Census data, soybean is estimated to be responsible for more than 80 percent of biodiesel production.

“The genome sequence is the direct result of a memorandum of understanding between DOE and USDA to increase interagency collaboration in plant genomics,” said DOE Under Secretary for Science Dr. Raymond L. Orbach.  “We are proud to support this major scientific breakthrough that will not only advance our knowledge of a key agricultural commodity but also lead to new insights into biodiesel production.”

“Soybeans have been an important food plant providing essential protein to people for hundreds of years,” said USDA Chief Scientist and Under Secretary for Research, Education, and Economics Dr. Gale A. Buchanan.  “Now, with the new knowledge available through this joint DOE/USDA genome sequencing project, researchers everywhere will be able to further enhance important traits that make the soybean such a valuable plant. It’s a great day for agriculture and people everywhere.”

This effort was led by Dan Rokhsar and Jeremy Schmutz of the DOE JGI, Gary Stacey of the University of Missouri-Columbia, Randy Shoemaker of the U.S. Department of Agriculture (USDA)-Agricultural Research Service (USDA-ARS), Scott Jackson of Purdue University, with support from the DOE, the USDA, and the National Science Foundation (NSF). In addition, the United Soybean Board, the North Central Soybean Research Program, and the Gordon and Betty Moore Foundation, have supported the soybean genome effort.

“Soybean is the one of the largest and most complex plant genomes sequenced by the whole genome shotgun strategy,” noted Rokhsar.  The process entails shearing the DNA into small fragments enabling the order of the nucleotides to be read and interpreted. Steven Cannon of the USDA-ARS collaborated with the DOE team to ensure the accuracy of the assembly.

Preliminary scientific details emerging from the sequence analysis will be presented by Schmutz at the International Conference on Legume Genomics and Genetics in Puerto Vallarta, Mexico, December 8, 2008. The soybean genome sequence information can be browsed at http://www.phytozome.net/soybean.

Schmutz and colleagues have begun to analyze the soybean genome, which at one billion nucleotides is roughly one-third the size of the human genome. Preliminary studies suggest as many as 66,000 genes—more than twice the number identified in the human genome sequence, and nearly half-again as many as the poplar genome, sequenced by DOE JGI and published in the journal Science in 2006.

“We have ordered and localized about 5,500 genetic markers on the sequence, which promise to be of particular importance to those researchers seeking to optimize certain qualities in soybean,” said Schmutz. Thousands of these markers were developed by Perry Cregan and colleagues of the USDA-ARS with support of the United Soybean Board. A genetic marker represents a known location on a chromosome that can be associated with a particular gene or trait. Prospective genome pathways of interest are those that directly influence yield, oil and protein content, as well as drought tolerance and resistance to nematodes and diseases such as the water mold Phytophthora sojae, previously sequenced by DOE JGI, which causes stem and root rot of soybean.

In 2007, soybean accounted for 56 percent of the world’s oilseed production.  James Specht, Professor at the University of Nebraska, said that this nitrogen-fixing legume crop offers the dual benefit of a seed high in protein and oil—with room for improvement. “With the advent of low-cost re-sequencing technologies, soybean scientists now have the means to identify sequence differences responsible for yield potential–the most desired of all crop traits, but to date the most intractable.”

“The soybean genome sequence will be a valuable resource for the basic researcher and soybean breeder alike,” said Jim Collins, Assistant Director for the Biology Directorate at the NSF. Collins and Judith St. John of USDA Agricultural Research Service co-chair the Interagency Working Group on Plant Genomes, which oversees the National Plant Genome Initiative.  “The close coordination between the DOE sequencing project and the NSF SoyMap project facilitated through the National Plant Genome Initiative has added value to the sequence and physical map resources for this important crop,” Collins said.

The soybean genome project is already making its mark out in the field.

“It’s tremendous that the soybean genome is out in the public’s hands.” Said Rick Stern, a New Jersey soybean farmer and chair of the Production Research program for the United Soybean Board (USB).  “Now every breeder can go into this valuable library for the information that will help speed up the breeding process.  It should cut traditional breeding time by half from the typical 15 years.”

The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories — Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest — along with the HudsonAlpha Institute for Biotechnology — to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI’s Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

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

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