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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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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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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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  • Data & Tools
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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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  • User Programs
    • Calls for User Proposals
    • Special Initiatives & Programs
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    • Submit a Proposal
    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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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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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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User Programs
Home › User Programs › Special Initiatives & Programs

Special Initiatives & Programs

Partnerships Development Team (PDT)

The vast majority of the JGI’s over 1,800 Users come from the public sector – academic and government institutions. As such, the capabilities and expertise of the JGI are largely unknown and underutilized by industry. With the arrival of JGI Director Nigel Mouncey, who joined the JGI with 20 years of industry experience in 2017, an opportunity emerged to expand JGI’s portfolio of user companies by establishing a Partnerships Development Team (PDT). Other targets of PDT’s activities include other academic, governmental, and non-governmental institutions that have not yet partnered with the JGI. Learn more about the PDT.

Biological and Environmental Research Support Science (BERSS):

Overview

JGI provides sequencing, synthesis, and targeted metabolomics support for DOE-BER funded awards, including awards funded through BER Funding Opportunity Announcements, Science Focus Areas (SFA) opportunities, and the Office of Science Early Career Research Program.

Available Resources

Eligible product types include those listed here:  https://jgi.doe.gov/our-science/product-offerings/

Proposals may not exceed 3 Tbp sequencing, 500 kbp synthesis, and 200 polar/500 nonpolar metabolomics samples, and should generally conform to the guidelines for current annual Community Science Program proposals.

Process

Proposals may be submitted at any time.  Support is limited to work included in the BER-funded proposal, and PIs must provide an award number and contact information for their DOE program officer. Submitters should contact JGI scientific staff to determine general feasibility prior to submitting a BER proposal that includes a JGI request.  Proposals whose scope was not negotiated with the JGI will only be accepted pending technical review and scope negotiation at JGI.

Investigators with grants funded by DOE-BER requiring support from JGI capabilities may submit proposals here.

Investigators preparing grant applications to DOE-BER and requesting an optional letter of feasibility to accompany their proposal may contact Tanja Woyke (twoyke@lbl.gov), Interim Deputy for User Programs, with a proposed scope.

Investigators wishing to expand on their DOE-BER funded work with additional sequencing, synthesis, or metabolomics should apply to one of the JGI’s calls for user proposals.

Emerging Technologies Opportunity Program (ETOP)

The ETOP identifies and funds partnerships to develop new technical capabilities that could be provided to JGI users.  Projects targeted for 2018 include development of methods for rapid prototyping of gene and pathway function targeting organisms found in natural environments:

  • High-throughput cell-based systems for biological and metabolic characterization
  • Cell-free technologies that enable scaleable in vitro gene and pathway functional analyses
  • Sensor-based technologies, biological or non-biological, that enable in vivo reporting of metabolic activity and/or activity-based cell sorting

Deadline for proposal submission has passed. For more information, check out the solicitation.

See a list of previously supported projects.

Visiting Scientist Program

The JGI Visiting Scientist Program (VSP) provides an opportunity for faculty-level scientists who are seeking to build upon their line of scientific inquiry by leveraging JGI experimental, computational, and personnel resources for genomic research and sequence-based science. Projects include de novo generation of genome data, assistance in interpreting and/or building on an existing data set, or the refining of new technology (e.g., single-cell genomics; metagenomics, etc.). Length of stay depends on complexity of the project being considered and availability of data and other resources. Investigators, postdocs, and graduate students participating in approved JGI User Projects are also invited to apply for on-site access to JGI resources and capabilities. For more information, contact Tanja Woyke (twoyke@lbl.gov), Interim Deputy for User Programs.

  • Partnerships Development Team (PDT)

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