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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)
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    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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    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 › User Support › Project Management Office (PMO)

Project Management Office (PMO)

The Project Management Office (PMO) Team:

Christa Pennacchio Special Projects
Christa Pennacchio, PMO Lead, Metabolomics Program
Kerrie Barry Plant and Fungal Genomics Programs
Kerrie Barry, Plant and Algal Genomics
Natasha Brown, Supply Chain Manager
Natasha Brown, Supply Chain Manager
Tijana Glavina del Rio Metagenomics Program
Tijana Glavina del Rio, Metagenomics
Danielle Graham, Workflow Project Manager

Nancy Hammon, Workflow Planning Manager
Miranda Harmon-Smith DNA Synthesis and Single-Cell Genomics
Miranda Harmon-Smith, DNA Synthesis and Single-Cell Genomics
Vivian Ng Project Manager
Vivian Ng, Fungal Genomics
Nicole Shapiro Microbial Genomics Program
Nicole Shapiro, Microbial Genomics

How PMO Works

JGI Project Managers work with users and JGI scientists and technical staff to prepare a Statement of Work (SOW) document that defines the scope of sequencing and analysis and lays out roles and responsibilities. The SOW includes the following items:

  • Defined source, protocols, and timeline for the provision of DNA/RNA material, libraries, and any other resources needed to initiate the project, including required ancillary documentation (e.g., experimental data supporting genome size estimates, community resources, etc.).
  • Platform and approximate quantity of JGI sequencing to address the scientific goals of the project, and timeline for the generation of this data, including responsibilities for analysis of pilot sample data to assess sequence for contamination, uniformity, and other quality control checks at the initial stages of the project. If contamination is a problem at this stage, the project may be suspended until suitable materials are available.
  • Defined plan for maintaining regular communication between the JGI and collaborators through the duration of the project.
  • Defined responsibilities for collaborators and the JGI after the completion of sequencing, including genome assembly, automated and/or manual annotation, and other analyses, and initial plan for experimental and/or computational studies needed to address the specific scientific aims of the project.
  • The initial publication plan, including a provisional timeline and anticipated authorship. To the extent that JGI scientists contribute scientific and/or technical expertise or leadership to the project, it is expected that they will participate in the publication.
  • Acknowledgment of JGI Data Release policies, and affirmation that the project will conform to applicable safety regulations, including regulations that govern organisms that are pathogenic or could potentially be used as bioweapons.

Additionally, before work can begin, users must sign a formal User Agreement that defines legal responsibilities of the JGI and the User.   Depending on the type of project, additional agreements may be needed.

Once a proposal has been approved through the review process, and the Statement of Work and User Agreement documents (if applicable) have been signed, the project may begin. Essential elements of the project are entered into JGI’s LIMS (Integrated Tracking System, or ITS) to allow staff to understand the requirements, history and status of any JGI project.  Active project management involves the following considerations:

  • Designation of a Project Manager within the JGI.
  • Designation of a principal collaborator or “Project Representative,” not necessarily the original applicant, who will be the JGI’s main point of contact throughout the duration of the sequencing project.
  • The collaborator will provide DNA or RNA, libraries, and other materials as described in the Statement of Work. Detailed guidelines for DNA/RNA submission are available. All materials described in the project proposal must be available with the appropriate documentation and should be submitted to the JGI as specified by the Project Manager. Failure to provide materials described in the proposal in a timely fashion may lead to cancellation of the project and/or return of the proposal to the review panels.
  • All source materials must pass the JGI QC process. Work will not commence on a new or resubmitted project component until the source material has passed the QC process.
  • The JGI’s Project Manager will communicate with the Project Representative to confirm, in a timely manner, when the initial sample data is of appropriate quality, free of contamination, etc.
  • Samples from approved projects will enter the production queue. This queue is managed primarily on a first-in/first-out basis, so it can take weeks or months for actual production to begin on a project, depending on the current workload and the length of time required to prepare and quality control representative libraries. Scheduling of the sequencing will be at the discretion of the JGI, given the overall production sequencing queue and the need to optimize available resources.

The post-sequencing analysis and publication plans must be coordinated and scheduled as specified in the Statement of Work.

  • Institutional User Agreements
  • Sequencing Sample Overview
  • Sequence Submission Requirements - DNA Synthesis Program
  • Project Management Office (PMO)
  • Project Management FAQ
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