CSP FY17

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 or other BER mission relevant genomes. These species should enable the identification of conserved and selected DNA elements and increase our ability to infer gene function across plant phylogenetic space, and requests for high quality genomes must clearly indicate the size of the user community and what 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 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 and to suggest roles for organisms whose lifestyles are 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) ENCODE-like projects for functional genomics of bacteria, archaea and fungi that could serve as model organisms for DOE-relevant problems.

c) Investigation of the genomic basis of microbial mutualism and microbe-microbe interactions in stable model communities, e.g. enrichment cultures or synthetic communities.

d) Functional characterization of secondary metabolites that are involved in microbe-microbe interactions, leveraging synthetic biology, transcriptomics, and metabolomics

III. Extreme Environments Including the Deep Subsurface

Extreme habitats, including the deep subsurface biosphere, harbor an array of microorganisms thought to represent a vast biomass reservoir, yet very little is known about microbial phylogenetic and functional diversity in 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. Similarly, investigations of microbial lifestyles in these extreme environments can reveal novel metabolic activities, broaden our understanding of biogeochemistry and provide insights into 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. Sequencing library preparation protocols are available at the DOE JGI for samples in which large-scale DNA/RNA extraction poses a challenge. In addition, single-cell sorting of environmental cell material is available, including for low biomass samples. Samples with high abundances of bacterial and archaeal candidate phyla are strongly encouraged.

IV. Microbes and communities involved in carbon cycling and related nitrogen, phosphorus and sulfur (N, P, S) cycling in terrestrial and coastal environments

Bacteria, archaea and fungi are important consumers and producers of greenhouse gases in the environment. While a nascent understanding of carbon and 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 (e.g. peat bogs/wetlands, tundra, hyporheic zones).

Project Structure

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 Tb of sequence allocation, except for multi-investigator/-institutional plant projects, where 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 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 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 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)
• 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
• Mass spectrometry-based metabolomics analysis of primary and secondary metabolites from plants and microorganisms
• 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 19 and April 7, 2016. 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 21, 2016, whether to prepare a full proposal. Full proposals will be due June 9. 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 2016.

For questions about the appropriateness of projects, program specifics or application process, please contact Susannah Tringe ([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 CSP17 will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/ between Feb 19 and April 7, 2016. Applicants will be advised by April 21 whether to prepare a full proposal, and full proposals will be due June 9. Guidance for submitting full proposals will be included in the email notification to invited applicants.

The full FY17 schedule is below:

Calls for proposals issued	February 19, 2016
Letters of intent received	April 7, 2016
Invitation of proposals	April 21, 2016
Proposals received	June 9, 2016
Technical and scientific review	August 1, 2016
Approval and rejection notices sent	September 15, 2016
Prepare user agreements	October 2016
Projects start	As soon as user agreement is finalized