DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    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.

    More

    (PXFuel)
    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.

    More

    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.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    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.

    More

    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.

    More

    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.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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.”

    More

    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.

    More

    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.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    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.

    Read more

    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.

    More

    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.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    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.

    More

    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.

    More

User Programs
Home › User Programs › User Program Info › CSP Overview › CSP Functional Genomics

CSP Functional Genomics

About This Call

The CSP Functional Genomics call is to enable users to perform state-of-the-art functional genomics research and to help them translate genomic information into biological function. The emphasis is on projects leveraging JGI’s DNA synthesis and ‘omics capabilities to enhance understanding of gene and genome function, particularly those not readily achievable without the capabilities and expertise available at the JGI.

Proposals to this call may be submitted to the JGI at any time using a simple web-based form (begin a new proposal document at proposals.jgi.doe.gov to see the proposal format) and are reviewed twice a year. All proposals will undergo an internal pre-review to ensure technical feasibility and alignment with JGI and DOE missions. Screened proposals will be reviewed for scientific merit, DOE relevance, feasibility and impact.  Applicants are encouraged to review the Synthetic Biology Internal Review Process guidelines, as insufficient information will delay or potentially defer approval for the proposal.

570 JGI functional genomics webinar

For accepted proposals, sequencing, synthesis, metabolomics and analysis will be paid for by the Department of Energy’s funding of the JGI. There is no cost to the user and no granting of funds.

For questions about whether your project is appropriate, or for program specifics or technical guidance, please contact Yasuo Yoshikuni (DNA synthesis program head), Trent Northen (metabolomics group lead), Tanja Woyke, Deputy for User Programs, or Miranda Harmon-Smith (project manager).  For questions about the application process, please contact Miranda Harmon-Smith.

Watch the  JGI Engagement: Accessing Functional Genomics Capabilities Webinar hosted by the DNA Synthesis Science group. The webinar invites researchers to submit white papers to the Community Science Program’s Functional Genomics call for proposals. 

Current Call (OPEN)

The current call for proposals offers multiple capabilities, as described below:

1) Synthesis of genes and pathways for functional characterization. A single proposal can request a total of 100 to 500 kb of DNA synthesis capacity per proposal. A consortium (with co-PIs from at least 3 different institutions) can request up to 1,500 kb. All constructs are synthesized and assembled into user-defined plasmids, sequence validated, and transformed into an E. coli strain before shipment to users. The products are delivered to users as glycerol stocks. Projects requiring specific nucleotide sequences (such as those required for homology-based recombination) may experience lower successful assemblies due to difficulties in synthesizing precise DNA sequences in the absence of refactoring. Therefore, we may have to adjust the scope of the project depending on the complexity of the sequence constraints. Prospective users are encouraged to contact JGI staff to discuss.

2) Synthesis of combinatorial pathway libraries for fast-track metabolic engineering. Each proposal may request up to 500 kb of DNA de novo synthesis capacity to produce millions of basepairs of combinatorial variants. The JGI will also help identify a panel of each pathway component and design final constructs. All constructs are assembled using type II restriction-enzyme-based technologies (e.g., golden gate assembly) into user-defined plasmids and are transformed into E. coli strains before shipment to users; no sequencing validations will be performed for the constructs. The products are delivered to users as glycerol stocks.

3) Synthesis of sgRNA libraries.  Each proposal may request up to six libraries comprising up to 12,000 sgRNA sequences per library, or more than six libraries with less degree of variants per library. The JGI can help design sgRNA sequences based on the genome sequences of targeted microbes. All sgRNA constructs are synthesized, cloned into user-defined plasmids, and transformed into an E. coli strain as pools. The quality of these libraries is evaluated with sequencing-based analysis using MiSeq before shipment to users. The JGI will deliver the libraries to users as glycerol stocks.  The subsequent transformation into the targeted microbes and functional screenings will be performed by users. The JGI can further evaluate enriched sgRNA libraries with sequencing-based analysis using MiSeq.

4) Strain Engineering: Genomic Integration of Synthetic Constructs into a Set of Bacterial Strains.  JGI is offering a limited capacity of Chassis-independent recombinase-assisted genome engineering (CRAGE) to users. This technology enables integration of large, complex genetic constructs directly into the chromosomes of diverse gamma-proteobacteria with high accuracy and efficiency. Proposals may request up to 96 constructs to be cloned into a CRAGE compatible vector under the control of a T7 promoter and conjugated into a maximum of 5 gamma-proteobacteria hosts.  We currently do not offer domestication of new strains to users. 

The current list of preferred microbial species offered through this call include:    

Pseudomonas putida KT2440    

Pantoea agglomerans ATCC 13460 (Eh1087 (ICMP 13301))

Dickeya solani DSM 28711

Yersinia aldovae DSM 18303

Aeromonas piscicola LMG 24783

Photorhabdus luminescens laumondii TTO1

Shewanella oneidensis MR-1

Photobacterium halotolerans DSM 18316           

Reference: CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria https://www.nature.com/articles/s41564-019-0573-8

For additional information (literature citations, video), see this CRAGE blog post.

Applicants are also invited to request one or more other JGI functional genomics capabilities listed below.

5) Sequence data mining. The JGI’s genome portals IMG, Mycocosm and Phytozome contain a wealth of genomic data from microbes, fungi, plants and microbiomes.  Proposals may request assistance with database searches for the selection of target genes and pathways for synthesis. However, capacity for analyzing search results and aiding in target selection is very limited; users needing assistance with these tasks should contact JGI in advance to discuss feasibility.

6) Metabolomics based functional analyses. Metabolomic technologies at JGI enable users to examine diverse polar and non-polar metabolites from plants, microbes, and environments. In addition, users may request targeted analysis of stable isotope labeling for specific metabolites. Proposals should clearly indicate how the data obtained will be linked to gene function, and may request up to 50 polar metabolite sample analyses or 150 non-polar metabolite sample analyses.

7) Mapping of transcription factor binding sites (DAP-seq). High-throughput mapping of putative transcription binding sites enables large-scale characterization of gene regulatory networks in a selected species. Proposals can request in vitro transcription factor binding site mapping by DNA affinity purification sequencing (DAP-seq) for between 70-92 transcription factors. DNA/gene synthesis should also be requested for construction of affinity-tagged transcription factor clones used in the assay.

8) RNA-seq. Transcriptional profiling can aid in characterizing gene regulatory pathways activated in response to perturbations or environmental stimuli.  Proposals may request RNA sequencing of between 22 and 92 samples (including replicates) from plants, algae, fungi, or microbes for the purpose of testing gene function or elucidating regulatory networks.

9) EcoFAB pilot projects. The JGI can provide up to 50 EcoFAB devices (https://eco-fab.org/) to study plant-microbiome interactions. These devices allow for non-destructive root imaging and sampling of the growth media while maintaining a sterile environment. In addition, the JGI can provide a standardized defined microbial community that colonizes plant roots and Brachypodium germplasm, if desired. Users would conduct experiments using these resources and return samples to the JGI for analysis by existing JGI capabilities e.g. metabolomics and transcriptomics.

Proposal Schedule

CSP Functional Genomics proposals are accepted on a continuous basis and will be reviewed twice a year. Submission deadline for reach review process is listed below. Letters of intent are not required.

Submission deadlines:

  • July 31, 2023
  • January 29, 2024

Proposal Review Process

All proposals undergo scientific review as described at https://jgi.doe.gov/user-programs/program-info/csp-review-process-and-contract-documents/.  In addition, proposals requesting DNA synthesis that are tentatively approved will undergo an additional review of potential impacts as described below prior to project initiation.

Proposals requesting DNA synthesis are evaluated by at least three external reviewers in a process known as Synthetic Biology Internal Review (SBIR). SBIR encourages investigators to extensively consider broader aspects of their research (e.g., biosafety, biosecurity, bio-containment and environmental issues) to evaluate both positive and negative impacts and to propose strategies to mitigate concerns. If issues are not sufficiently addressed, users will be asked to modify their proposal. If issues are not resolved, the proposal may be rejected. SBIR generally takes three weeks.

Investigators should not merely write “None” or “All research will be conducted in a safe manner according to Federal regulations” in the broader implications statement, as this will lead to requests for proposal modifications, incurring delays of three weeks or longer.

Investigators must explicitly state whether their proposed research would:

  • Demonstrate how to make a vaccine ineffective
  • Confer resistance to antibiotics or antiviral agents
  • Enhance a pathogen’s virulence or make a non-virulent microbe virulent
  • Increase transmissibility of a pathogen
  • Alter the host range of a pathogen
  • Enable a pathogen’s ability to evade diagnostic or detection modalities
  • Enable the weaponization of a biological agent or toxin

 

  • Calls for User Proposals
  • CSP Overview
    • CSP Annual Call
    • CSP New Investigator
    • CSP Functional Genomics
  • FICUS Overview
  • Closed Calls
  • Review Process and Scoring Criteria
  • DOE Mission Relevance
  • FAQ

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
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

© 1997-2023 The Regents of the University of California