DOE Joint Genome Institute

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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    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.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    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.

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    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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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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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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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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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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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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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

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