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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.

    Read more

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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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    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 › User Program Info › CSP Overview › CSP New Investigator

CSP New Investigator

About This Call

The CSP New Investigator call seeks to target investigators and research initiatives new to the JGI, with an emphasis on providing pilot data to assess feasibility of a novel approach or form the foundation for a large-scale CSP proposal submission.  Projects must be independent of ongoing JGI proposals, and lead PIs cannot have been lead PI on any previously accepted JGI CSP or FICUS proposal.  Sequence requests should not exceed 500 Gbp in total.

Proposals for this call may be submitted at any time as brief white papers and will be reviewed every six months.  Applicants may submit up to two proposals per cycle (but may be listed as co-PI on an unlimited number of proposals).  Proposals must be submitted using the web form available at  (begin a new proposal document at http://proposals.jgi.doe.gov/ to see the proposal format).

All proposals will undergo an internal pre-review to ensure technical feasibility and alignment with JGI and DOE missions.  Screened proposals will then be reviewed for scientific merit, DOE relevance, proposed data usage by the applicant/community, and track record of the applicant. It is highly recommended that samples meeting JGI’s sample requirements be in-hand at the time of proposal submission.  Samples that are not immediately available, or are of insufficient quality or quantity, may delay or potentially defer approval for sequencing.

For details on JGI product offerings see https://jgi.doe.gov/user-program-info/product-offerings/.  For questions about the appropriateness of projects, program specifics or application process, please contact us.

Get tips on how to submit an effective New Investigator proposal: https://jgi.doe.gov/webinar-successfully-apply-for-csp-proposal/

Current Call (OPEN)

Bacterial and archaeal isolates and single cell draft genomes

The JGI will accept proposals for sequencing of collections of bacterial and archaeal genomes from cultivated isolates or physically isolated single cells. Proposed organisms should broaden phylogenetic representation among sequenced representatives or participate in processes directly relevant to DOE missions. Type strains, including proposed strains prior to publication, are highly encouraged. Between 48 and 184 isolates may be proposed.  For single-cell sequencing projects, JGI will sort up to 8 samples and sequence up to 384 single particle sorts (unverified by 16s) per proposal.  For projects with larger numbers of genomes, please refer to the CSP Annual Call.

Genome resequencing

The JGI seeks proposals centered on resequencing of bacterial, archaeal, fungal, algal and plant isolates for which a reference genome exists. Projects may focus on natural population structure, understanding gene function under selective pressure or in mutagenized strains, or developing pan and core genomes. We will also consider collections of highly related strains from nature that display differences in phenotypes related to DOE missions, e.g. lignocellulose decomposition, fermentation of sugar substrates or degradation of environmental toxins for bacteria and fungi or biomass composition for plants. Between 36 and 72 samples may be proposed for bacteria or fungi; up to 12 samples for plants or algae. For projects with larger numbers of samples, please refer to the CSP Annual Call.

Plant/algal genome size estimation

Proposals will be considered for low-pass short-read sequencing of plant and algal genomes to assess genome size and complexity in preparation for large-scale genome sequencing projects.  PacBio may not be requested.  Between 1-6 samples may be proposed.  For larger number of samples, please refer to the CSP Annual Call.

RNA sequencing

The JGI solicits RNA sequencing projects for bacterial, archaeal, fungal, algal and plant genomes for which a reference genome is available. RNA-seq data may be used for improvement of genome annotation or for transcript counting applications (e.g. gene expression profiling of a bacterium during growth on an array of cellulosic substrates to decipher degradation pathways). Projects should be directly relevant to DOE missions; for plants, projects using the standard conditions defined by the Plant Gene Atlas are specifically encouraged. Between 36 and 54 samples (including replicates) may be proposed. For projects with >54 samples, please refer to the CSP Annual Call.

Bacterial and archaeal epigenomes and high-quality draft genomes

Single molecule real time sequencing enables greater genome contiguity as well as assessment of DNA base modifications (6mA, 5mC, 4mC and others) of potential importance in host defense and gene regulation. The JGI will accept proposals including up to 12 samples for improved draft or epigenome sequencing. For projects with >12 samples, please refer to the CSP Annual Call.

Metagenomes and metatranscriptomes

Due to a large backlog of metagenome projects, JGI will not be accepting proposals requesting metagenomes or metatranscriptomes for the current cycle (deadline March 1, 2021).

However, the JGI does have limited capacity (≤8 samples; 24 sequencing libs) for targeted sorting and metagenomic analysis of specific populations that can be fluorescently labeled, e.g. naturally pigmented cells, cells labeled with Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT), etc. This ‘mini-metagenomic’ approach does not require whole genome amplification assuming >10,000 target cells can be recovered, and target populations should be >1% of cells.

DNA synthesis for functional assays

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. (Use of this capability is encouraged, but synthesis-only projects should be directed to the Functional Genomics call). JGI is accepting proposals for synthesis of up to 500 kb.

Metabolomics based functional analyses

Targeted and untargeted 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. JGI is accepting proposals for up to 50 polar metabolite sample analyses or 150 non-polar metabolite sample analyses.

Proposal Schedule

Proposals are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Deadline for submission is 60 days prior to the review date. This call replaces the “Small Scale Microbial CSP call” which is no longer active.

Upcoming submission deadlines/review dates:

March 1, 2021/May 2021

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