CSP Annual Call

The DOE JGI’s Community Science Program (CSP) is now accepting Letters of Intent for large-scale genomic science projects that address the following areas of emphasis and exploit the diversity of DOE JGI capabilities.

I. Genes to Function

Today’s ability to generate sequence data far outpaces assigning validated function to genes. Gene annotation tools are becoming more sophisticated but still rely on the provenance of previously generated information for comparative analyses. Building a broader understanding of gene function will enable the development of new biosynthetic routes for biofuels and bioproducts. Projects of interest may include:

• Development and deployment of hierarchical annotation pipelines using advanced computational analyses, functional genomics, DNA synthesis and/or metabolomics.
• Generation of genome-wide CRISPR gRNA libraries that enable gene function characterization.
• Coupling genetic information with protein structure and function by combining sequence-based methods with structural or imaging data.
• High-throughput enzyme characterization that spans genome mining to expression to determining enzyme function through mass spectrometry or targeted analytics.

II. Plant Functional Genomics and Microbiomes

The DOE JGI has produced several “flagship plant genomes” including Brachypodium, sorghum, Setaria, switchgrass, miscanthus, and poplar. These taxa 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 with an emphasis on plant stress response. 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 or other DNA functional elements, 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 genome sequences.

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 existing and potential future user communities 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. JGI has established exometabolomic workflows that can be used to characterize root exudates and infer metabolite exchange in the rhizosphere (see Section III).  We encourage proposal submitters to consider using the DOE Systems Biology Knowledgebase (KBase) to model these interactions.

III. 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:

• Investigation of the genomic basis of microbial mutualism and microbe-microbe interactions in stable model communities, e.g. enrichment cultures or synthetic communities.
• Genome-guided functional activation and exometabolomic analysis of secondary metabolites.
• 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.
• Genomic investigation of viral evolution and host specificity.
• Exometabolomic analysis of the production and depletion of metabolites to infer mechanisms of resource competition and cross-feeding.

IV. Microbes and communities involved in elemental cycling in terrestrial and coastal environments

Bacteria, archaea, fungi and algae are important participants in earth’s biogeochemical cycles. 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). In addition, developing multi-omics datasets to enable modeling of regulatory and metabolic processing of these elements in model microbes and microbial systems is encouraged.

V. Algal genomics

Algae are important primary producers with tremendous diversity, long evolutionary history, and exceptional potential for DOE science and applications. Significant and rapid advances in the fundamental knowledge of algal biology, the entire biomass-to-bioenergy supply chain, and algal cultivation strategies are dependent on genetic, biochemical and phenotypic information which is currently lacking. Proposals are encouraged that will expand genomic knowledge across algal diversity, that will build fundamental knowledge of algal metabolism and physiology, and which will provide insights into algal associations with other microbes and viruses.

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 provide a 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) requiring DOE JGI capabilities that reach beyond genome sequencing, 4) generating data of high value to the scientific community, and 5) plans to analyze and distribute data and results through KBase.

All proposals may request up to 2.5 Tbp of sequence data. For multi-PI projects generating data of broad utility to the scientific community, requests of up to 10 Tbp will be considered.  Larger Tbp totals (up to 40 Tbp) will be considered for shotgun Illumina DNA sequencing only (i.e. plant resequencing and metagenome sequencing), but such proposals will be evaluated separately with the anticipation that only 1 or 2 would be approved.

Requests for Pacific Biosciences long read sequencing are capped at 25 Gbp, while requests of up to 50-100 Gbp will be considered for multi-PI projects of high value to the scientific community.

If coupled with sequencing, proposals may request DNA synthesis up to 500 kbp of synthesized DNA, and 1 Mbp of DNA constructs.

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. Users are encouraged to consider and describe in their proposal how KBase may be used or extended to meet these needs.

DOE JGI Capabilities

All proposals should justify why JGI capabilities are critical to success. The DOE JGI employs an evolving suite of sequencing platforms, currently comprised of short read Illumina as well as single molecule long-read Pacific Biosciences technology. The capabilities available for this call are listed below. While individual proposals may draw from one or more of these capabilities as needed to fulfill project goals, within the overall cap, the final 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 and target-enriched resequencing for variation detection
• Microbial community shotgun DNA/RNA sequencing (not amplicon sequencing, which is no longer offered)
• Whole genome DNA methylation analysis
• Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
• Fluorescence activated cell sorting for targeted metagenomics and single-cell genomics
• 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, and generation of whole-genome CRISPR-based libraries. (Use of this capability is encouraged, but synthesis-only projects should be directed to the call for stand-alone DNA synthesis proposals)
• Chassis-independent recombinase assisted genome engineering (CRAGE) of novel expression hosts.
• 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 analysis of DOE JGI datasets
• Chromatin analysis including mapping of histone modifications by Chromatin Immunoprecipitation (ChIP-seq), and open chromatin by Assay for Transposase-Accessible Chromatin (ATAC-seq).
• In vitro transcription factor binding site mapping by DNA affinity purification sequencing (DAP-seq). DNA/gene synthesis should also be requested for construction of affinity-tagged transcription factor clones used in the assay.
• Flow cytometric sorting and genomic analysis of metabolically active microbes labeled via Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT)
• Density centrifugation and fraction collection for stable isotope probing (SIP) metagenomic studies
• Access to high-performance computing at the National Energy Research Scientific Computing Center (NERSC)
• Developing new applications and extending capabilities in KBase

Mechanism and Timing of Review

Letters of intent will only be accepted electronically and should be submitted at https://proposals.jgi.doe.gov/ between February 4 and April 11, 2019. 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 29, 2019, whether to prepare a full proposal. Full proposals will be due June 11, 2019. Guidance for submitting full proposals will be included in the email notification to invited applicants.  A full schedule is below.

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 2019.

For questions about the appropriateness of projects, program specifics or application process, please contact Susannah Tringe.

Proposal Schedule

To respond to the annual CSP call, a Letter of Intent is required before submitting a proposal. Letters of intent for CSP20 will only be accepted electronically and should be submitted at https://proposals.jgi.doe.gov/ between February 4 and April 11, 2019. Applicants will be advised by April 29 whether to prepare a full proposal, and full proposals will be due June 11. Guidance for submitting full proposals will be included in the email notification to invited applicants.

The full FY20 schedule is below:

Calls for proposals issued	February 4, 2019
Letters of intent received	April 11, 2019
Invitation of proposals	April 29, 2019
Proposals received	June 11, 2019
Technical and scientific review	August 2018
Approval and rejection notices sent	by September 16, 2019
Prepare user agreements	September 2019
Projects start	As soon as user agreement is finalized