DOE Joint Genome Institute

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    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.

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    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.

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    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

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    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.

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    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.

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    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

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    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.”

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

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News & Publications
Home › News Releases
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July 11, 2006

Energy-rich Portfolio of New Genome Sequencing Targets for DOE JGI

WALNUT CREEK, CA–Bioenergy crop plants switchgrass and cassava, other important agricultural commodities such as cotton, and microbes geared to break down plant material to render biofuels, round out the roster of more than 40 projects to be tackled by the U.S. Department of Energy Joint Genome Institute (DOE JGI) over the next year. Drawing submissions… [Read More]

June 27, 2006

DOE JGI Releases IMG 1.5 with Curated Archaeal Genomes

WALNUT CREEK, CA–Version 1.5 of the Integrated Microbial Genomes (IMG) data management system of the U.S. Department of Energy Joint Genome Institute (DOE JGI) has been released to the public. IMG 1.5 now contains a total of 741 genomes (435 bacterial, 32 archaeal, 15 eukaryotic genomes and 259 bacterial phages) of which 602 are finished… [Read More]

May 23, 2006

DOE JGI Finishes 100th Microbial Genome

ORLANDO, Florida — Microbes, thriving in even the world’s most extreme environments, are capable of performing myriad biological functions, learned over the billions of years they have inhabited the planet. Those lessons, and how they can be captured to render clean renewable sources of energy and to repair damaged environments, are among the many secrets… [Read More]

April 21, 2006

DOE JGI to Host Microbial Genomics Workshop for Educators in Recognition of Earth Day & National DNA Day

WALNUT CREEK, CA–The DOE Joint Genome Institute (DOE JGI) every year reveals the wonders of DNA sequencing to thousands of avid students, teachers, researchers, and community members drawn through the portal of its Walnut Creek, Calif., Production Genomics Facility. Visitors often ask the question: what becomes of those billions of letters of genetic information churning… [Read More]

March 30, 2006

DOE JGI Releases Experimental Metagenomics Data Management & Analysis System

WALNUT CREEK, CA–To tackle the computational challenges of analyzing the complex world of microbial communities, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released to the worldwide research community IMG/M, an experimental metagenome data management and analysis system. IMG/M integrates aggregate genome (also known as metagenome) data from diverse environmental microbial communities… [Read More]

January 10, 2006

Report Highlights DOE Joint Genome Institute Achievements

WALNUT CREEK, CA–The U.S. Department of Energy investment in large-scale genome sequencing is paying dividends with powerful implications for the nation’s energy and environmental clean-up needs, according to a report just released by the DOE Joint Genome Institute. As the leading national user facility targeting microbes and microbial communities, plants, and aquatic organisms, DOE JGI… [Read More]

December 22, 2005

DOE Joint Genome Institute Issues New Call for Large-Scale Sequencing Proposals

WALNUT CREEK, CA–Responding to the escalating demand for genome sequencing to unlock the potential of plants and microbes as fuel for the nation’s energy needs, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has announced the call for 2007 Community Sequencing Program (CSP) proposals. The applications for the CSP capacity have been doubling… [Read More]

December 1, 2005

DOE JGI Releases Fourth Version of IMG in 2005

WALNUT CREEK, CA–The fourth version of the Integrated Microbial Genomes (IMG) data management system of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has been made available to the public. The new version, IMG 1.3, contains 42 additional genomes sequenced by other institutions and 20 new genomes sequenced by DOE JGI, bringing the… [Read More]

September 1, 2005

DOE JGI Releases Latest Version of IMG

WALNUT CREEK, CA–An enhanced version of the Integrated Microbial Genomes (IMG) data management system of the U.S. Department of Energy (DOE) Joint Genome Institute (DOE JGI) has been made available to the public. The new version, IMG 1.2, contains 270 additional public genomes and nine (four finished, five draft) new JGI genomes, bringing the total… [Read More]

June 2, 2005

DOE JGI Sequences DNA from Extinct Cave Bear

WALNUT CREEK, CA–The genomic DNA sequencing of an extinct Pleistocene cave bear species–the kind of stuff once reserved for science fiction–has been logged into scientific literature thanks to investigators from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI).  This study, published in the June 2 online edition of the journal Science, has set… [Read More]
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