DOE Joint Genome Institute

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    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

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    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    screencap long reads webinar_ Metagenome Program
    Utilizing long-read sequencing for metagenomics and DNA modification detection webinar
    Watch the webinar on how the JGI employs single-molecule, long-read DNA sequences to aid with genome assembly and transcriptome analysis of microbial, fungal, and plant research projects.

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    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

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    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

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    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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Our Science
Home › Our Science › DOE Mission Areas

DOE Mission Areas

The US Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, is managed by DOE’s Office of Biological and Environmental Research (BER). JGI provides high-throughput DNA sequencing, synthesis and analysis services to the user community in support of BER’s bioenergy and environmental missions. These missions mirror DOE’s and national priorities to develop renewable and sustainable sources of biofuels and bioproducts from plant biomass, to understand the biological processes controlling greenhouse gas accumulation in the atmosphere (especially carbon dioxide and methane, key factors in global climate change), and to gain insights into biogeochemical processes controlling the cycling of key nutrients in environments for sustainable bioenergy production or the mobility of heavy metals and radionuclides at contaminated sites for which DOE has stewardship responsibilities. Projects with direct relevance in these areas will have the best chance for selection. Projects focused on organisms for comparative purposes, on model systems for microbe-microbe or plant-microbe interactions, or on development of improved sequencing-based technologies are also welcomed but the applicant should clearly outline how the proposed work will advance BER-mission relevant science. Projects primarily focused on human health, food/animal agriculture, wastewater treatment, or bioremediation of organics will not be considered. Projects targeting marine systems must clearly demonstrate relevance and translatability to freshwater, coastal or terrestrial systems.

Additional information about DOE’s Biological and Environmental Research program mission can be found at http://science.energy.gov/ber/.

Bioenergy

The United States is one of the world’s largest consumers of petroleum, most of which is used for transportation and industry. Petroleum is also the starting material for the production of almost all plastics. This drives the DOE’s focus on developing lignocellulosic biomass as a clean, renewable and sustainable alternative source for biofuels and bioproducts. Such biofuels would ideally offer energy content on par with gasoline while being compatible with our existing fuel distribution infrastructure. Sequencing projects at the JGI that contribute to meeting this goal focus on one of three categories: terrestrial plants that can be used as feedstocks for biofuel and bioproduct production and their associated microbiomes; fungi, microbes and microbial communities that can break down the lignin and cellulose in plant walls; and organisms that can convert lignocellulosic-derived sugars or lignols into biofuels or other bioproducts currently produced from petroleum (excluding pharmaceutical, cosmetic, and food products).

Environmental Microbiome Processes

Microbes constitute the largest reservoir of biodiversity on Earth. Their activities and interactions are at the core of many environmental processes, and the genetic makeup of microbial species and communities forms the basis of their behavior in the environment. The JGI sequences the genomes of microbes and microbial communities that significantly contribute to element and nutrient cycling, particularly those found in less well-understood terrestrial, subsurface, and terrestrial-aquatic interface ecosystems. JGI also focuses on projects that aim to understand biogenic contributions to the global carbon cycle as well as atmospheric particle formation and evolution. Data from such studies is expected to contribute to better predictive models of global climate. They may also provide a basic understanding of the roles microbiomes play in determining the behavior of the physical environment and provide opportunities for biologically-based mitigation strategies.

The JGI seeks to support projects that will foster a genome-enabled understanding of microbial behavior with an impact on the physical, chemical, and geochemical processes that control the environmental fate of key elements with an impact on BER’s energy and environmental mission objectives. Microbes and microbial communities of interest to the JGI as sequencing targets include: those involved in elemental and nutrient cycles, those that impact sustainable bioenergy crop growth or global carbon cycling, and those involved in the cycling of elements that mediate the transformation or are energetically coupled to contaminants such as heavy metals or radionuclides in soils, freshwater, coastal sediments, and the subsurface.

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

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