(status: CLOSED for new Letters of Intent)
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 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 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. Functional Genomics and Microbiomes of DOE JGI Flagship Plants:
The DOE JGI has produced several “flagship plant genomes” including Poplar, Sorghum, Brachypodium, Chlamydomonas, Soybean, Foxtail millet, and Physcomitrella. Additional emerging flagship plant species include Switchgrass, Miscanthus, and Hall’s panicgrass. These species are of special interest as biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype. This call will focus on projects that directly relate to these genomes. For all plant proposals, multi-organism proposals will be given priority that 1) seek to compare among plants and/or analyze plant-microbiome interactions, and 2) large, collaborative, multi-investigator projects. Projects of interest may fall into one of the following four categories related to JGI flagship plants, as well as one special focus area aimed at functional genomics of algae:
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 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. Genome-wide methylation, RNA-seq (including low-template RNA-seq), non-coding RNAs, small RNAs, histone binding assays, and other epigenomic assays are encouraged to address important mission-related phenotypes and other aspects of plant biology in flagship plant species. In addition, studies that make use of the DOE JGI’s DNA synthesis capacity to modify flagship organisms in order to understand gene function are 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 flagship plant genomes. These can be natural populations or structured populations (mapping populations, recombinant inbred lines, etc.), suitable for linking genome variation to traits of interest.
c) Comparative grade de novo genomes – Whole genome sequencing of species that can be used for comparative genomics studies with the JGI flagship species. These species should enable the identification of conserved and selected DNA elements and increase our ability to infer gene function across plant phylogenetic space.
d) Plant microbiomes – The DOE JGI encourages projects to study the microbiomes of flagship plants. Proposals aimed at studying microbial communities associated with 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.
e) Algal functional genomics (Special Focus Area) – Algae are important for DOE bioenergy interests but sequencing their genomes remains technically challenging and resource-intensive. At this time, the DOE JGI invites proposals for functional genomic experiments on algal organisms with previously sequenced genomes, while exploring the sequencing of selected new algal genomes in the future. In this cycle, proposals are encouraged that include targeted functional assays that leverage focused sequencing, e.g., transcriptomics, epigenomics or population diversity surveys, that will add to our understanding of the functions of algal species to facilitate the exploration of organisms of importance for the development of algal biofuels.
II. Function-driven Microbial Genomics:
A key focus area for DOE JGI is the exploration of microbial functional diversity, especially to provide new annotations to genes whose functions are presently hypothetical or unknown. Proposals are encouraged that extend this effort in the areas of:
a) Function-driven single-cell genomics and metagenomics, e.g. sequencing of stable isotope-labeled DNA or selectively sorted single cells.
b) High-throughput experimental annotation, e.g. transposon mutagenesis and sequencing.
c) ENCODE-like projects for functional genomics of bacteria, archaea and fungi that could serve as model organisms for DOE-relevant problems.
d) Investigation of the genomic basis of microbial mutualism in stable model communities, e.g. co-cultures and enrichment cultures.
III. Extreme Environments Including Deep Subsurface:
Extreme habitats, including the deep subsurface biosphere, harbor an array of microorganisms and are thought to represent vast biomass reservoirs, yet very little is known about microbial phylogenetic and functional diversity under these settings. As deep subsurface environments may be preferred niches for early life, genome and metagenome sequences from these environments are likely to contribute to our understanding of early evolution. Investigations of microbial lifestyles in these extreme environments can reveal novel metabolic activities and broaden our understanding of the limits of life. The DOE JGI encourages proposals with sequencing targets from extreme habitats, including the deep subsurface. Low template sequencing library protocols are available at the JGI for samples, for which large-scale DNA/RNA extraction poses a challenge. In addition, single-cell sorting of environmental cell material is available, including low biomass samples. Samples with high abundances of bacterial and archaeal candidate phyla are strongly encouraged.
IV. DNA Synthesis Projects:
Projects that contain DNA synthesis as a follow-on to DNA sequencing being proposed are encouraged, especially if the synthesis component is focused on understanding gene function. Projects that contain requests for DNA synthesis only are not responsive to this call and should be submitted to JGI’s twice-annual DNA synthesis call.
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 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 Tb of sequence allocation. For multi-investigator/-institutional plant projects, proposals exceeding 2 Tb will be considered but the proposed sequencing amount should be strongly justified in the Letter of Intent.
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 primarily of Illumina HiSeq and MiSeq. In addition, the DOE JGI uses Pacific Biosciences instruments with long-read capabilities for specific applications. 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 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, bacterial, archaeal, and plant genomes
- Resequencing for variation detection
- Single-cell DNA sequencing, including fluorescence-activated cell sorting and amplification of genomic DNA
- Microbial community DNA/RNA sequencing
- 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 (note that there is a separate call for stand-alone DNA synthesis, gene and pathway synthesis available
- Analysis support for the datasets above
The DOE JGI also has limited capacity for the following developing capabilities:
- Transposon mutagenesis of bacteria
- Custom genome analysis of JGI datasets
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 5 and April 16, 2015. The CSP Call is open to anyone with the understanding that CSP data is made publicly available immediately, without exception. Applicants will be advised by May 7, 2015, whether to prepare a full proposal. Full proposals will be due July 2. 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 2015.
For questions about the appropriateness of projects, program specifics or application process, please contact Axel Visel ([email protected]).
Proposal Schedule
To respond to the annual CSP call, a Letter of Intent (LOI) is required before submitting a proposal. Letters of intent for CSP16 will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/ between Feb 5 and April 16, 2015. Applicants will be advised by May 7 whether to prepare a full proposal, and full proposals will be due July 2. Guidance for submitting full proposals will be included in the email notification to invited applicants.
The full FY16 schedule is below:
| Calls for proposals issued | February 5, 2015 |
|---|---|
| Letters of intent received | April 16, 2015 |
| Invitation of proposals | May 7, 2015 |
| Proposals received | July 2, 2015 |
| Technical and scientific review | August 28, 2015 |
| Approval and rejection notices sent | October 8, 2015 |
| Prepare user agreements | October 2015 |
| Projects start | As soon as user agreement is finalized |