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

JGI@25

JGI’s 25th Anniversary

The year 2022 marks the JGI’s 25th anniversary. During this year we’ll revisit a number of notable achievements that showcase our collaborations and capabilities to enable great science that will help solve energy and environmental challenges. 

Notable stories from the past 25 years

 

JGI contributions detailed in DOE Human Genome Project poster The Human Genome Project, or the JGI’s Origin Story

In 1997, the U.S. Department of Energy (DOE) united the people and resources from three national labs to work on the Human Genome Project. The JGI contributed ~12% of the total human genome.

 A man stands at a podium with a mural in the background

Historical perspectives on JGI’s 25 years 

At the 2022 JGI Annual Meeting, speakers shed light on how the JGI was established, all that it has contributed, and what they’re excited about in the JGI’s future.

A plantation of poplar trees. (David Gilbert) Poplar, The Bioenergy Tree

In 2006, JGI collaborated on the first tree genome, Populus trichocarpa. The genome offers exciting opportunities beyond just a bioenergy feedstock crop.

Jennifer Doudna Pioneering Metagenomics Research Paves Path for Nobel

A conversation on extremophiles elements with a longtime JGI collaborator piqued the interest of  Jennifer Doudna, leading to her 2020 Nobel Prize for co-developing CRISPR-Cas9  technology.

Laccaria bicolor Roots of a Mutualist Relationship

The genome sequence of Laccaria bicolor, a forest fungus in symbiosis with poplar, was published in 2008. Today ~2,000 mycorrhizal fungal genomes are publicly available on the fungal portal MycoCosm.

Artistic rendering of a microbial genome layered over a dark forest. (Composition by Zosia Rostomian/Berkeley Lab)

A Single Cell, Myriad Microbial Discoveries

Single cell genomics offers a way for researchers to study the planet’s microbial diversity, much of which remains unknown and uncultured.

An assortment of sorghum varieties. (Roy Kaltschmidt, LBNL) Studying Sorghum’s Survival Skills

Since publishing the sorghum reference genome, the JGI continues collaborating to better understand its toughness and energy storage.

The oil slick in the Gulf of Mexico from the Deepwater Horizon oil spill as seen on April 29, 2010. (NASA Earth Observatory image created by Jesse Allen, using data provided courtesy of the University of Wisconsin’s Space Science and Engineering Center MODIS Direct Broadcast system) Solving the Mystery of the Missing Oil

Working with Berkeley Lab  researchers, the JGI’s single cell genomics and metagenomics capabilities were harnessed for a systems biology approach to the Deepwater Horizon oil spill.

Chlamydomonas is an insightful little alga that holds clues to leveraging other organisms for sustainable biofuel production. [Image: MPI-CBG, Dresden]

The Little Alga That Could

The reference Chlamydomonas genome is cited in roughly 10% of all since-released publications on green algae.

The common bean (Phaseolus vulgaris) includes pinto beans, kidney beans, black beans, navy beans and more. (Image Credit: TK) Building a Better Bean

The common bean genome has fueled further research into disease tolerance in crops, stressors and  nitrogen fixation.

An image of Robert Hungate set against a blue background with white bacteria images Fueling investigation into methane-making microbes

Supporting studies involving methane-making microbes in ruminants to drive solutions for stemming methane-emissions.

A white bowl of beige soybeans is set against a black background. On top of the individual beans is a pea pod. Strengthening Soybean

Aside from supporting work on the soybean plant, the JGI has also helped researchers understand a fungus threatening these crops.

 

JGI25 intern alumni video screencap

Stories from Intern Alumni 

Former JGI interns share how these experiences have influenced their career journeys.

Cow Rumen and the Early Days of Metagenomics 

A 2011 Science paper has led to a hands-on undergraduate research course at four  universities.

 

  • 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