How to Propose a CSP Project

How do I submit my proposal?

Proposals for bacterial and archaeal isolates, resequencing and RNA-seq projects (12 isolates or fewer) may be submitted at any time as brief white papers and will be reviewed every three months. Deadline for submission is 30 days prior to the review date.

For all other project types, a letter of intent is required to submit a proposal to the CSP. Submitters whose letters of intent/proposals are approved will receive further instructions via email.

Submit microbial white papers (anytime), letters of intent (during the submission period) and full proposals (if invited) using the Work Initiation Process (WIP) interface.

>> View the proposal schedule

What kind of proposals can be submitted?

JGI’s Community Sequencing Program (CSP) is now accepting letters of intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in alternative fuels, global carbon cycling, and biogeochemistry. While applications will be accepted that address any aspect of these mission areas, up to 50% of capacity for this call will be allocated for projects that address the following areas of special emphasis, and exploit the diversity of JGI capabilities.

Plant and plant-microbe interactions: Plant phenotypes are likely to be strongly influenced by their associated microbes. Proposals are encouraged that explore the interaction of plants with their rhizosphere communities and other plant-associated microbes or fungi that affect bioenergy-relevant plant phenotypes. Plant resequencing or transcriptomic projects are of interest but whole-genome de novo plant sequencing projects are discouraged for this CSP call. Plant phenotypes of interest might include, but are not limited to: drought or salt tolerance, nutrient use, primary productivity, biomass composition or yield or recalcitrance.

Microbial emission and capture of greenhouse gases: Bacteria, archaea, fungi, and algae are important consumers and producers of greenhouse gases in the environment. Proposals are encouraged that will provide insight into global carbon, nitrogen, and methane cycles, and/or suggest novel strategies for carbon capture, nitrogen processing, or methane reduction from environmental sources.

Metagenomics: Most microbes live in complex communities in oftentimes dynamic environments where the impact of changing environmental parameters on community structure and function are largely unknown. Proposals are encouraged that couple metagenomic analyses with measures of the active component of microbial populations and associated environmental biogeochemistry to explore dynamic changes in the active community composition and expressed metabolism of microbial communities in DOE mission-relevant areas. Such areas may include: bioenergy-related plant-microbe interactions, carbon/nitrogen cycling and/or carbon sequestration processes in soils and sediments, and biogeochemical processes contributing to contaminant biotransformation and/or immobilization.

Single-cell Genomics: As many microbes inhabiting environments of central importance to DOE missions cannot be grown in culture, acquisition of genomes from isolated single cells has proven to be an important adjunct to metagenome sequencing. JGI has an expanding capability for the isolation, whole genome amplification, sequencing and assembly of single cells, expected to approach 1,000 in FY13. Most single-cell genome projects are anticipated to be part of a larger metagenome or isolate sequencing proposal.

DNA Synthesis: Sequence data from genomes, metagenomes and single cells allow the prediction of millions of novel genes as well as higher-level functions such as carbon-source utilization, secondary metabolite production, stress response, photosynthesis, or nitrogen fixation. DNA synthesis proposals are encouraged that address the re-factoring, screening and functional characterization of multi-gene pathways involved in DOE mission-relevant areas, both in microbes and eukaryotes. Particular focus areas of this call are projects that involve functional prospecting of diverse species/metagenomes, require the construction of large DNA molecules (> 10Kb), and exploit coupling to high-throughput screening technologies. Small-scale DNA synthesis requests that could be easily performed by commercial providers are discouraged.

Project Structure: CSP projects are expected to generate publicly available data that will answer important questions relevant to the organism or environment being sequenced, as well as providing the 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 significant scale, 2) large DNA/RNA sequencing need on the order of hundreds of gigabases or exceeding a terabase, 3) engaging a large group of collaborators, 4) involving more than a single species, and 5) requiring JGI capabilities in addition to genome sequencing.

Overall JGI sequencing capacity is expected to be about 90 Terabases (Tb) in FY13, of which as much as half may be available for this CSP. Each proposal must carefully justify the amount of sequencing requested but no single proposal should expect more than a maximum of 2 Tb.

JGI DNA synthesis capacity for FY2013 is expected to be 4 Mb, of which up to 1.5 Mb will be available for this CSP. Individual projects are expected to require up to 250 Kb of sequence although larger requests may be considered. Additional JGI capabilities including data mining, vector engineering, and construct design can also be included within synthesis proposals.

For the CSP Microbial quarterly call, the JGI is targeting the following project types:

Bacterial and archaeal isolates and single cells
Proposed organisms should broaden phylogenetic representation among sequenced representatives or participate in processes directly relevant to DOE missions. After approval, at an established time prior to project initiation, the proposer will be asked to prepare DNA according to JGI's standard procedures with the goal of having received DNA within two months of approval. For single-cell sequencing projects, MDA products of single amplified genomes should be in hand at the time of proposal submission. DNA of insufficient quality or quantity will delay or potentially defer approval for sequencing. Up to 12 isolates or single-cell genomes may be proposed. For projects with >12 genomes, please refer to the CSP 2013 annual call.

Bacterial and archaeal resequencing
JGI also seeks proposals centered on resequencing of bacterial and archaeal isolates for which a reference genome exists. Projects may focus on bacterial community structure, understanding gene function in bacteria under selective pressure or in mutagenized strains. We will also consider collections of highly related strains from nature that display differences in phenotypes related to DOE missions, e.g. lignocellulose degradation, fermentation of sugar substrates or metabolism of environmental toxins. Up to 12 isolates may be proposed. For projects with >12 isolates, please refer to the CSP 2013 annual call.

Bacterial and archaeal RNA sequencing
JGI solicits smaller scale RNA sequencing projects for bacterial and archaeal isolates, for which a reference genome is available. RNA-seq data may be used for improvement of genome annotation or for transcript counting applications (ie. gene expression profiling during growth on an array of cellulosic substrates to decipher degradation pathways). Projects should be directly relevant to DOE missions.. Up to 12 RNA samples may be proposed. For projects with >12 samples, please refer to the CSP 2013 annual call.

What are JGI’s capabilities?

JGI employs almost exclusively next generation short read sequencing platforms, with very limited longer-read capabilities. The capabilities available for this call are listed below. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals but if longer read sequencing is needed, the burden is on the submitter to justify the request. Successful projects frequently exploit a combination of capabilities:

Core Capabilities Include:

De novo sequencing of fungal, bacterial, and archaeal genomes
Resequencing for variation detection
Metagenomic DNA/RNA sequencing
RNA-Seq for genome annotation
RNA-Seq for reference gene sets
RNA-Seq for gene counting
Analysis pipelines for the datasets above

JGI also has limited capacity for the following developing capabilities:

3rd generation single-molecule sequencing
Fluorescent Activated Cell Sorting
Micro-manipulator isolation of single cells
Single cell DNA sequencing
Multiplex emulsion PCR amplicon sequencing
Limited DNA/gene synthesis
Custom genome analysis of generated datasets

Mechanism & Timing of Review

Letters of intent will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/ between March 1- April 12, 2012. Applicants will be advised whether to prepare a full proposal within two weeks, and full proposals will be due June 13. Proposals will be independently peer-reviewed and ranked. Final decisions based on ranking will be made by JGI senior management with final approval given by DOE program management. For questions about the appropriateness of projects, program specifics or application process, please contact Jim Bristow.

What information should I include in my CSP proposal?

For small-scale microbial isolate and resequencing proposals, a letter of intent and full proposal are not needed. Instead, use the Work Initiation Process (WIP) form to submit the white paper. These can be submitted at any time.

For all other project types, proposals are submitted annually in response to a call for proposals. A letter of intent (LOI), informing us that you plan to submit a proposal for consideration in the next round, must be sent to JGI before the submission of a proposal. The LOI should be submitted using the web-based Work Initiation Process (WIP) form and should include proposal title, focus area (based on the project types requested in the CSP call), description, justification, sequence utilization, community interest and DOE mission relevance. The LOI helps us to plan for review and allows us to help you with the details of your proposal. Submitters whose letters of intent are approved will receive further instructions via email.

Proposals will be reviewed on the basis of scientific impact, technical demands on JGI resources, and pertinence to DOE missions in bioenergy, biogeochemistry, and carbon sequestration. Human or animal disease-causing organisms will NOT be considered under this Program. Only plant pathogens of relevance to bioenergy-related crops or plants will be considered.

In the application, JGI requests that applicants focus primarily on describing the science that will be enabled by completion of the project rather than the technical details of how sequencing will be carried out, because the former is the primary criterion and the latter is subject to change.

Additional information about proposals

Proposals that Require Gap Closure
The JGI's capacity for draft sequencing is far greater than for finishing. By producing sequences from Illumina libraries, the JGI can produce draft sequence assemblies with contiguity and accuracy sufficient for most projects. However, some projects requiring an additional effort for gap closure will also be accepted.

For genomes larger than 50 Mb, requests for gap closure finishing will be accepted only after the draft sequence is complete.

For genomes less than 50 Mb, you can choose whether to include finishing in the project proposal. Unless you specify finishing as a strict project requirement, it will be considered separately from the rest of the proposal. This will ensure that the JGI proceeds with the draft sequencing process without delays associated with other resource contingencies.

Projects Contingent on Additional Funding
In some cases, a project that involves a large sequencing effort might not be approved without additional funding to accomplish other necessary studies. At the applicant's request, projects can be selected provisionally, contingent on acquiring additional funds from other sources. With no additional funding, these projects will expire two years after being approved for sequencing.

Important note about DNA preparation
The preparation of high quality DNA for sequencing is frequently a bottleneck for large projects. The success of large-scale projects depends on the community’s ability to deliver 50-150 mcg of high quality DNA on a negotiated schedule that will allow timely turnaround of sequence data. Applicants should address the community’s strategy for preparing and delivering DNA to JGI in a timely fashion. Inability to deliver DNA when expected will result in projects receiving a lower priority for sequencing that may result in substantial delay.

Proposal template for the CSP2013 call