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 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. 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. The 2015 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. Proposals for de novosequencing of new plant genomes will not be considered at this time.
Projects of interest may fall into the following three 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 to be studied and extend functional studies beyond straightforward transcriptomics. 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) 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.
II. Probing functional diversity of microbes: To complement its Genomic Encyclopedia of Bacteria & Archaea and 1000 Fungal Genomes initiatives, the DOE JGI has begun to explore microbial functional diversity. Proposals are now encouraged that extend this effort using high-throughput sequencing and the 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 hypothetical or unknown. Proposals are expected to use one or a combination of the DOE JGI’s (meta-) genome, (meta-) transcriptome, single-cell and isolate sequencing and resequencing pipelines. ENCODE-like projects for functional genomics of bacteria, archaea and fungi that could serve as model organisms for DOE-relevant problems are encouraged and could include new JGI capabilities for genome-wide transcriptomics, including non-coding and small RNAs, and epigenomics, including methylation detection and ChIP-seq.
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 ranging from deserts to wetlands has lagged behind. Proposals are encouraged that will provide insight into global carbon (including methane) and nitrogen 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. Discovery and expression of natural product pathways relevant to energy-related and environmental processes: Bacteria, archaea, fungi, and plants are important producers of natural products (NPs), many of which are relevant to energy and environmental processes of interest to DOE. The DOE JGI has developed a platform that enables the discovery of novel NPs based on technology combining computational genomics, pathway refactoring, host engineering, and high-throughput analytics. Proposals are encouraged to exploit this NP platform in order to identify and/or produce novel activities of relevance to DOE missions, e.g. NPs that contribute to plant-microbial interactions, microbial community structure, bioenergy development, carbon processing, or environmental contaminant cycling. Proposers should note that the DOE JGI’s intent is to support the identification and development of energy- or environment-relevant NPs, not the development of NPs for biomedical purposes.
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 but no single proposal should expect more than 2 Tb of sequence allocation.
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 primarily Illumina HiSeq and MiSeq sequencing platforms, with Pacific Biosciences long-read capabilities (3+kb and 10kb) 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, 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
- Target-enriched re-sequencing
- Whole genome DNA methylation analysis
- Chromatin analysis including mapping of histone modifications by ChIP-seq and formaldehyde-assisted isolation of regulatory elements (FAIRE)
- 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 pipelines for the datasets above
The 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 of genomic DNA
- Transposon mutagenesis of bacteria
- Custom genome analysis of generated 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 13 and April 10, 2014. 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 April 24, 2014, whether to prepare a full proposal. Full proposals will be due June 5. 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 October 2014.