The DOE JGI’s Community Science Program (CSP) is now accepting Letters of Intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE Biological and Environmental Research (BER) missions in sustainable biofuel production, global carbon cycling, and biogeochemistry. While applications will be accepted that address any aspect of the DOE mission areas, special consideration will be given to projects that address the following areas of emphasis and exploit the diversity of DOE JGI capabilities.
I. Plant Functional Genomics and Microbiomes:
The DOE JGI has produced several “flagship plant genomes” including sorghum, Brachypodium, and Physcomitrella and is developing genomes for emerging flagship plant species including switchgrass and Miscanthus. These species 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 for different plant tissues and developmental stages. 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, 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 genomes, and may exceed the 2 Tbp cap but not require more than 10 Tbp of sequencing capacity.
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 user community 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.
II. 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:
a) Investigation of the genomic basis of microbial mutualism and microbe-microbe interactions in stable model communities, e.g. enrichment cultures or synthetic communities.
b) Functional and chemical characterization of secondary metabolites that are involved in inter-organism interactions, leveraging synthetic biology, transcriptomics, and metabolomics.
c) 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.
d) Genomic investigation of viral evolution and host specificity.
III. Microbiology of Extreme Environments
Extreme habitats, including those experiencing extremes of pH, temperature, pressure and other extremes in nutrient availability and geochemical variables, harbor an array of microorganisms thought to represent a vast biomass reservoir and which may impact on natural resource extraction activities. Yet very little is known about microbial phylogenetic and functional diversity in these settings, which may be preferred niches for early life. Investigations of microbial, microeukaryotic and viral lifestyles and interactions in these extreme environments can reveal novel metabolic activities, broaden our understanding of biogeochemistry and contribute to our understanding of early evolution and the limits of life. The DOE JGI encourages proposals with sequencing targets from extreme environments that are not well studied including the deep terrestrial or coastal subsurface.
IV. Microbes and communities involved in elemental cycling in terrestrial and coastal environments
Bacteria, archaea, fungi and algae are important consumers and producers of greenhouse gases in the environment. 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).
CSP projects are expected to generate publicly available data that will answer important questions relevant to the target organism or environment 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 scale and complexity that exceeds the capacity of a single lab, 2) engaging a large group of collaborators, 3) involving more than a single species, and 4) requiring DOE JGI capabilities that reach beyond genome sequencing.
Each proposal must carefully justify the amount of sequencing requested. No single proposal should expect more than 2 Tbp of sequence allocation, except for multi-investigator/-institutional plant resequencing projects (see Ib above), where proposals exceeding 2 Tbp (but not >10 Tbp) will be considered but the proposed sequencing amount should be strongly justified in the Letter of Intent, including a timeline with milestones and decision points.
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.
DOE JGI Capabilities
The DOE JGI employs an evolving suite of sequencing platforms, currently comprised of Illumina HiSeq, NextSeq and MiSeq as well as Pacific Biosciences single molecule long-read sequencing. 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, within the overall 2 Tbp cap, but the 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 for variation detection
- Single-cell genome sequencing, including fluorescence-activated cell sorting and amplification of genomic DNA
- Microbial community shotgun DNA/RNA sequencing, as well as amplicon tag sequencing of 16S, 18S and ITS2 regions.
- Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
- Target-enriched re-sequencing
- Whole genome DNA methylation analysis
- Chromatin analysis including mapping of histone modifications and open chromatin (ChIP-seq, FAIRE, ATAC-seq, etc.)
- 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 call for stand-alone DNA synthesis proposals)
- 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 genome analysis of DOE JGI datasets
- Raman spectroscopy-based single-cell sorting
- Access to high-performance computing at the National Energy Research Scientific Computing Center (NERSC)
Mechanism and Timing of Review
Letters of intent will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/ between February 6 and March 31, 2017. 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 14, 2017, whether to prepare a full proposal. Full proposals will be due May 26. Guidance for submitting full proposals will be included in the email notification to invited applicants.
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 2017.
For questions about the appropriateness of projects, program specifics or application process, please contact Susannah Tringe.
To respond to the annual CSP call, a Letter of Intent (LOI) is required before submitting a proposal. Letters of intent for CSP18 will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/ between February 6 and March 31, 2017. Applicants will be advised by April 14 whether to prepare a full proposal, and full proposals will be due May 26. Guidance for submitting full proposals will be included in the email notification to invited applicants.
The full FY18 schedule is below:
|Calls for proposals issued||February 6, 2017|
|Letters of intent received||March 31, 2017|
|Invitation of proposals||April 14, 2017|
|Proposals received||May 26, 2017|
|Technical and scientific review||July 12, 2017|
|Approval and rejection notices sent||September 15, 2017|
|Prepare user agreements||October 2017|
|Projects start||As soon as user agreement is finalized|