How to Propose a CSP Project
How do I submit my proposal?
Proposals for small-scale microbial and metagenome projects 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/metagenome white papers (anytime), letters of intent (during the submission period) and full proposals (if invited) using the Work Initiation Process (WIP) interface.
What kind of proposals can be submitted?
For the CSP14 annual call (this is now closed, the next call for proposals is expected to be issued in Spring, 2014)
The DOE 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, priority for this call will be given to projects that address the following areas of special emphasis, and exploit the diversity of DOE JGI capabilities.
I. DOE JGI Plant Flagship Genomes: DOE JGI has produced several “flagship” genomes genome.jgi.doe.gov/programs/plants/flagship_genomes.jsf) that are of special interest as biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype. The 2014 call will focus on projects that directly relate to these genomes. Projects may fall into the following four categories:
a) Gene Atlas & ENCODE-like projects- DOE JGI is currently committed to sequencing flagship transcriptomes under a variety of experimental conditions and for different plant tissues and developmental stages. New proposals are encouraged that expand the experimental conditions to be studied and that extend functional studies beyond transcriptomes. Genome-wide epigenetic and microRNA studies that will contribute to understanding important phenotypes of flagship plant species are specifically encouraged. In addition studies that make use of DOE JGI’s DNA synthesis capacity to modify flagship genomes in order to understand gene function are also encouraged.
b) Large-scale resequencing projects- Projects aimed at characterizing the genetic variation of species or populations by large-scale resequencing are encouraged. Preference will be given to species or populations that are relevant to plant flagship genomes. These could be natural populations or structured populations (mapping populations, recombinant inbred lines, etc.) targeted at exploiting variation for some trait or traits of interest.
c) De novo sequencing of flagship comparators- Nominations of species for whole genome shotgun sequencing for use as "comparators" for plant flagships are encouraged. Proposers must have demonstrated the ability to produce high quality genomic DNA for sequencing of the proposed species at the time of proposal and commit to providing DNA to DOE JGI in a timely fashion. Proposals must provide an estimate of sequence divergence from flagship genomes and describe why one or more proposed species would be useful as a comparator or as a secondary model in its own right.
d) Plant microbiomes- DOE JGI encourages projects to study the plant microbiomes of plant flagship genomes. Proposals aimed at studying microbial communities throughout various plant tissues are specifically encouraged, as are hypothesis-driven projects deciphering functional and phylogenetic community changes upon manipulation of the host and/or host environment.
II. Probing functional diversity of microbes: Through its Genomic Encyclopedia of Bacteria & Archaea (http://www.jgi.doe.gov/programs/GEBA/) and 1000 Fungal Genomes (http://1000.fungalgenomes.org/home/) initiatives, DOE JGI has begun to explore microbial phylogenetic diversity. Proposals are now encouraged that extend this effort using high-throughput sequencing, and DOE JGI’s DNA synthesis capabilities, to identify novel activities of relevance to DOE missions or to provide new annotations to genes whose functions are presently unknown. Proposals are expected to use one or a combination of DOE JGI’s metagenome, metatranscriptome, single-cell and isolate sequencing pipelines. Studies of the functional importance of DNA methylation in bacteria and archaea are particularly encouraged.
III. Microbial emission and capture of greenhouse gases in terrestrial systems: Bacteria, archaea and fungi are important consumers and producers of greenhouse gases in the environment. While a nascent understanding of carbon cycling in marine environments exists, our understanding of these processes in terrestrial systems has lagged behind. 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 through gene/genome engineering. Preference will be given to proposals focused on terrestrial environments.
IV. Exploratory Collaborations between the Environmental Molecular Sciences Laboratory and Joint Genome Institute: Applications are now being accepted for pilot projects that integrate DOE JGI and EMSL capabilities to address the following:
- Biofuels production -- Projects that explore plant, fungal and microbial physiology and that enable improved production of biofuel and chemical intermediates.
- Carbon cycling -- Projects that enhance our understanding of terrestrial carbon cycling with an emphasis on plant and soil associated fungal and microbial interactions and physiology.
These applications should be modest in scope, focused on high risk/high payoff projects that can be completed in 18 months, and generate datasets unique to these two facilities and beyond what each could generate by itself. An individual application should not request more than 300 Gb of DOE JGI sequencing as well as the EMSL resources necessary for the proposed work. Accepted projects must broadly address DOE/BER missions but proof of concept for the demonstration of a technology that would be applicable to a DOE mission is appropriate.
EMSL houses an unparalleled collection of state-of-the-art capabilities that are used to address scientific challenges relevant to the U.S. Department of Energy and the nation. Details regarding these capabilities and the full schedule and review process for the joint EMSL-DOE JGI call are available at: http://www.emsl.pnnl.gov/access/calls/jgi/.
V. 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, and 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 within this topic area are projects that involve functional prospecting of diverse species/metagenomes, require the construction of large DNA molecules (>10 kb), 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 (i.e larger than the capacity of a single lab, 2) large DNA/RNA sequencing projects 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 DOE JGI capabilities that reach beyond genome sequencing.
Overall DOE JGI sequencing capacity is expected to be about 90 Terabases (Tb) in FY14, of which at least 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.
Large-scale DNA synthesis projects are expected to require up to 250 kb of sequence although larger requests may be considered. Proposals may include both sequencing and DNA synthesis components. Additional DOE JGI capabilities including data mining, vector engineering, and construct design can also be included within synthesis proposals.
Bacterial and archaeal epigenomes
DNA base modifications (6mA, 5mC, 4mC and others) are known to be important in host defense (as part of restriction systems), but may have additional functional roles that have previously been difficult to detect. New technologies now allow direct sequencing of DNA base modifications, providing a first opportunity for genome-wide exploration of bacterial epigenomes. JGI is seeking proposals to examine the possible regulatory roles of DNA base modification in Bacteria and Archaea. Up to 12 isolates may be proposed. For projects with >12 genomes, please refer to the CSP 2014 annual call.
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. Type strains, including proposed strains prior to publication, are highly encouraged. All proposals will be reviewed for scientific merit, DOE relevance, how the data will be used, and track record of the applicant. 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 2014 annual call (released in Spring 2013).
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 genomes, please refer to the CSP 2014 annual call (released in Spring 2013).
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 genomes, please refer to the CSP 2014 annual call (released in Spring 2013).
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. JGI is accepting proposals which include no more than 12 samples, of which up to 6 may be metagenomes. The remaining samples may include bacterial or achaeal isolates or single cells. Metatranscriptome samples should not be included. Up to 92 iTag samples may also be proposed, although iTag-only proposals will not be considered. Proposals must show clear DOE mission relevance in areas such as 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. For projects that fall outside these criteria, please refer to the CSP 2014 annual call (released in Spring 2013).
What are JGI’s capabilities?
DOE JGI employs almost exclusively next-generation short read sequencing platforms, with limited 3rd generation long-read capabilities (3+kb and 10kb). 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 plant, fungal, bacterial, and archaeal genomes
- Resequencing for variation detection
- Single-cell DNA sequencing
- Microbial community DNA/RNA sequencing
- Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
- Laser capture micro-dissection (LCM) coupled RNA-Seq
- Target enriched re-sequencing
- Whole genome DNA methylation analysis
- Chromatin analysis including FAIRE, histone modifications through ChIP-seq
- DNA/gene synthesis
- Analysis pipelines for the datasets above
DOE JGI also has limited capacity for the following developing capabilities:
- 3rd generation single-molecule sequencing
- Fluorescence activated cell sorting, including single-cell sorting and amplification
- Micromanipulation for isolation of single cells
- Multiplex emulsion PCR amplicon sequencing
- Transposon mutagenesis of bacteria
- Custom genome analysis of generated datasets
What information should I include in my CSP proposal?
For small-scale microbial and metagenome 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
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.