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 › Closed Calls › CSP FY20

CSP FY20

CSP FY2020 (Status: CLOSED)

The DOE JGI’s Community Science Program (CSP) is now accepting Letters of Intent for large-scale genomic science projects that address the following areas of emphasis and exploit the diversity of DOE JGI capabilities.

I. Genes to Function

Today’s ability to generate sequence data far outpaces assigning validated function to genes. Gene annotation tools are becoming more sophisticated but still rely on the provenance of previously generated information for comparative analyses. Building a broader understanding of gene function will enable the development of new biosynthetic routes for biofuels and bioproducts. Projects of interest may include:

  • Development and deployment of hierarchical annotation pipelines using advanced computational analyses, functional genomics, DNA synthesis and/or metabolomics.
  • Generation of genome-wide CRISPR gRNA libraries that enable gene function characterization.
  • Coupling genetic information with protein structure and function by combining sequence-based methods with structural or imaging data.
  • High-throughput enzyme characterization that spans genome mining to expression to determining enzyme function through mass spectrometry or targeted analytics.

II. Plant Functional Genomics and Microbiomes

The DOE JGI has produced several “flagship plant genomes” including Brachypodium, sorghum, Setaria, switchgrass, miscanthus, and poplar. These taxa are of special interest as potential biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype, and projects that directly relate to these genomes are encouraged. For all plant proposals, priority will be given to multi-organism proposals that 1) seek to compare among plants and/or analyze plant-microbiome interactions, and/or 2) are of a large, collaborative nature with multiple participating investigators. Projects of interest may fall into one of the following four categories:

a) Gene Atlas and ENCODE-like projects – The DOE JGI is currently committed to sequencing flagship plant transcriptomes under a variety of experimental conditions with an emphasis on plant stress response. New proposals are encouraged that expand the experimental conditions or plants to be studied and extend functional studies beyond straightforward transcriptomics. This includes proposals aimed at the generation of genome-wide annotation of gene regulatory sequences or other DNA functional elements, similar to the NIH-funded ENCODE encyclopedia of DNA elements in the human genome (See core capabilities below for available assays).

b) Large-scale germplasm resequencing – We invite germplasm resequencing projects aimed at 1) understanding natural population structure of the genus/species, 2) creating a foundation for large scale GWAS projects for gene discovery, or 3) developing pan and core genomes to determine a complete picture of gene content within the genus/species. Studies must target mission-relevant plants with existing high quality genome sequences.

c) High quality or comparative grade de novo genomes – We invite proposals for whole genome sequencing of species that can be used for comparative genomics studies with the DOE JGI flagship species. Proposals should justify the relevance as comparators, including enabling the identification of conserved and selected DNA elements and increasing our ability to infer gene function across plant phylogenetic space. Requests for high quality genomes must clearly indicate the size of the existing and potential future user communities and what BER mission-related science will be enabled above and beyond what could be accomplished with a comparative grade draft.

d) Plant microbiomes – We encourage projects to study the microbiomes of BER mission relevant plants. Proposals aimed at characterizing secondary metabolite biosynthetic pathways in plants and/or associated microbes are specifically encouraged, as are hypothesis-driven projects deciphering functional and phylogenetic changes of natural or synthetic communities upon manipulation of the host and/or host environment. JGI has established exometabolomic workflows that can be used to characterize root exudates and infer metabolite exchange in the rhizosphere (see Section III).  We encourage proposal submitters to consider using the DOE Systems Biology Knowledgebase (KBase) to model these interactions.

III. Inter-organismal interactions:

A key focus for DOE JGI is understanding the mutualistic, competitive or antagonistic interactions among microorganisms, macroorganisms, and viruses. Projects that could address this focus include:

  • Investigation of the genomic basis of microbial mutualism and microbe-microbe interactions in stable model communities, e.g. enrichment cultures or synthetic communities.
  • Genome-guided functional activation and exometabolomic analysis of secondary metabolites.
  • Function-driven single-cell genomics and metagenomics, e.g. sequencing of stable isotope-labeled DNA or selectively sorted single cells to assign functional roles to populations within communities.
  • Genomic investigation of viral evolution and host specificity.
  • Exometabolomic analysis of the production and depletion of metabolites to infer mechanisms of resource competition and cross-feeding.

IV. Microbes and communities involved in elemental cycling in terrestrial and coastal environments

Bacteria, archaea, fungi and algae are important participants in earth’s biogeochemical cycles. While a nascent understanding of nutrient cycling in marine environments exists, our understanding of these complex processes in natural terrestrial environments has lagged behind. Proposals are encouraged that will provide insight into microbial activities controlling global cycles of carbon, nitrogen, phosphorus, and sulfur from a broad range of terrestrial and coastal environments (including terrestrial-aquatic interfaces such as peat bogs, marshes, and hyporheic zones). In addition, developing multi-omics datasets to enable modeling of regulatory and metabolic processing of these elements in model microbes and microbial systems is encouraged.

V. Algal genomics

Algae are important primary producers with tremendous diversity, long evolutionary history, and exceptional potential for DOE science and applications. Significant and rapid advances in the fundamental knowledge of algal biology, the entire biomass-to-bioenergy supply chain, and algal cultivation strategies are dependent on genetic, biochemical and phenotypic information which is currently lacking. Proposals are encouraged that will expand genomic knowledge across algal diversity, that will build fundamental knowledge of algal metabolism and physiology, and which will provide insights into algal associations with other microbes and viruses.

Project Structure

CSP projects are expected to generate publicly available data that will answer important questions relevant to the target organism or environment as well as provide a substrate for broader use by the DOE research community. CSP projects have historically provided a means for user communities to assemble and interact in collaborative ways. Proposals are encouraged that involve some or all of the following features: 1) a scale and complexity that exceeds the capacity of a single lab, 2) engaging a large group of collaborators, 3) requiring DOE JGI capabilities that reach beyond genome sequencing, 4) generating data of high value to the scientific community, and 5) plans to analyze and distribute data and results through KBase.

All proposals may request up to 2.5 Tbp of sequence data. For multi-PI projects generating data of broad utility to the scientific community, requests of up to 10 Tbp will be considered.  Larger Tbp totals (up to 40 Tbp) will be considered for shotgun Illumina DNA sequencing only (i.e. plant resequencing and metagenome sequencing), but such proposals will be evaluated separately with the anticipation that only 1 or 2 would be approved.

Requests for Pacific Biosciences long read sequencing are capped at 25 Gbp, while requests of up to 50-100 Gbp will be considered for multi-PI projects of high value to the scientific community.

If coupled with sequencing, proposals may request DNA synthesis up to 500 kbp of synthesized DNA, and 1 Mbp of DNA constructs.

Requests for metabolomics are capped at 200 samples for polar analysis and 500 samples for nonpolar analysis.

The DOE JGI provides extensive data analysis pipelines. Applicants should present a plan for all data analysis that may be required beyond these standard pipelines. Users are encouraged to consider and describe in their proposal how KBase may be used or extended to meet these needs.

DOE JGI Capabilities

All proposals should justify why JGI capabilities are critical to success. The DOE JGI employs an evolving suite of sequencing platforms, currently comprised of short read Illumina as well as single molecule long-read Pacific Biosciences technology. The capabilities available for this call are listed below. While individual proposals may draw from one or more of these capabilities as needed to fulfill project goals, within the overall cap, the final scope is ultimately at the discretion of the DOE JGI. Successful projects frequently utilize a combination of capabilities.

Core Capabilities Include:

  • De novo sequencing of fungal, algal, bacterial, archaeal, viral and plant genomes
  • Resequencing and target-enriched resequencing for variation detection
  • Microbial community shotgun DNA/RNA sequencing (not amplicon sequencing, which is no longer offered)
  • Whole genome DNA methylation analysis
  • Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
  • Fluorescence activated cell sorting for targeted metagenomics and single-cell genomics
  • DNA/gene synthesis linked to sequence data generation, including codon optimization, refactoring, and assembly of biosynthetic pathways into appropriate vector systems for expression in heterologous hosts, and generation of whole-genome CRISPR-based libraries. (Use of this capability is encouraged, but synthesis-only projects should be directed to the call for stand-alone DNA synthesis proposals)
  • Chassis-independent recombinase assisted genome engineering (CRAGE) of novel expression hosts.
  • Mass spectrometry-based metabolomics analysis of primary and secondary metabolites from plants and microorganisms
  • Analysis pipelines for the datasets above

The DOE JGI also has limited capacity for the following developing capabilities, when tightly linked to sequencing or DNA synthesis:

  • Custom analysis of DOE JGI datasets
  • Chromatin analysis including mapping of histone modifications by Chromatin Immunoprecipitation (ChIP-seq), and open chromatin by Assay for Transposase-Accessible Chromatin (ATAC-seq).
  • In vitro transcription factor binding site mapping by DNA affinity purification sequencing (DAP-seq). DNA/gene synthesis should also be requested for construction of affinity-tagged transcription factor clones used in the assay.
  • Flow cytometric sorting and genomic analysis of metabolically active microbes labeled via Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT)
  • Density centrifugation and fraction collection for stable isotope probing (SIP) metagenomic studies
  • Access to high-performance computing at the National Energy Research Scientific Computing Center (NERSC)
  • Developing new applications and extending capabilities in KBase

Mechanism and Timing of Review

Letters of intent will only be accepted electronically and should be submitted at https://proposals.jgi.doe.gov/ between February 4 and April 11, 2019. The CSP Call is open to anyone with the understanding that CSP data are made publicly available immediately, without exception. Applicants will be advised by April 29, 2019, whether to prepare a full proposal. Full proposals will be due June 11, 2019. Guidance for submitting full proposals will be included in the email notification to invited applicants.  A full schedule is below.

Proposals will be independently peer-reviewed and ranked following given review criteria. Final decisions will be made by DOE JGI senior management with final approval given by DOE program management. All projects will begin as soon as User Agreements are finalized, targeted for October 2019.

For questions about the appropriateness of projects, program specifics or application process, please contact Susannah Tringe.

Proposal Schedule

To respond to the annual CSP call, a Letter of Intent is required before submitting a proposal. Letters of intent for CSP20 will only be accepted electronically and should be submitted at https://proposals.jgi.doe.gov/ between February 4 and April 11, 2019. Applicants will be advised by April 29 whether to prepare a full proposal, and full proposals will be due June 11. Guidance for submitting full proposals will be included in the email notification to invited applicants.

The full FY20 schedule is below:

Calls for proposals issued February 4, 2019
Letters of intent received April 11, 2019
Invitation of proposals April 29, 2019
Proposals received June 11, 2019
Technical and scientific review August 16, 2019
Approval and rejection notices sent by September 16, 2019
Prepare user agreements September 2019
Projects start As soon as user agreement is finalized
  • Calls for User Proposals
  • CSP Overview
  • FICUS Overview
  • Closed Calls
    • CSP FY23
    • FICUS JGI-EMSL FY23
    • CSP Small-scale
    • CSP DNA Synthesis
    • CSP FY22
    • CSP FY21
    • CSP FY20
    • CSP FY19
    • CSP FY18
    • CSP FY17
    • CSP FY16
    • CSP FY15
    • FICUS JGI-NERSC-KBase FY19
    • FICUS JGI-EMSL FY22
    • FICUS JGI-EMSL FY21
    • FICUS JGI-EMSL FY20
    • FICUS JGI-EMSL FY19
    • FICUS JGI-EMSL FY18
    • FICUS JGI-NERSC FY17
    • FICUS JGI-EMSL FY17
    • FICUS JGI-EMSL FY16
    • FICUS JGI-EMSL FY15
  • 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