CSP Annual Call

CSP FY2022

The 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 JGI capabilities.

I.  Genes to Function

Today’s ability to generate sequence data far outpaces the rate at which gene functions can be validated. Gene annotation tools are becoming more sophisticated but still rely on the provenance of previously generated information for comparative analyses. Proposals building a broader understanding of gene function in plants and microorganisms are encouraged to improve gene and genome annotations for energy and environment applications. Characterizations of metabolic and functional capabilities of candidate phyla are of particular interest. Projects may include:

• Annotation of gene function 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
• Characterization of secondary metabolite biosynthetic gene clusters and their products that spans (meta)genome mining, computational predictive analyses, and expression and/or determining produced metabolites using metabolomic approaches
• Function-driven microbial 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

II. Plant Functional Genomics

The JGI has produced several “flagship plant genomes” across plant nodes of interest including Brachypodium, Chlamydomonas, Physcomitrella, Miscanthus, Populus, Setaria, Glycine, Sorghum, and Panicum. These genera are of special interest as potential biofuel feedstocks or as comparators to provide insight into feedstock evolution and phenotype; 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 three categories:

a) High quality de novo genomes & pan-genomes – We invite proposals for whole genome sequencing of species using our advanced pipelines. The scientific focus can include comparative or evolutionary genomics studies with the JGI flagship species or clusters of comparative plant species that would inform fundamental plant biology and lead to new insights into plant gene function. Examples of projects might include multi-genotype, high quality pan-genomes for comparison to diversity resources, drought- or salt-tolerant species, secondary metabolite producers, or a concentration of genomes in an under-sampled area of the plant phylogeny with compelling biology that is relevant for DOE’s mission. For proposals that include non-flagship species the relevance and application to BER plant science should be clearly demonstrated.

b) Large-scale germplasm resequencing – We invite germplasm resequencing projects aimed at 1) understanding natural population variation of relevant genus/species, 2) creating a foundation for large scale GWAS projects for gene discovery, or 3) developing views of the pan and core genomes to determine a complete picture of gene content within a relevant genus/species.

c) Comparative transcriptomes and functional assays – The JGI is sequencing flagship plant transcriptomes under a variety of experimental conditions with an emphasis on plant stress response. New proposals are encouraged that expand experimental conditions or the range of plants to be studied and extend functional studies beyond straightforward transcriptomics (e.g. metabolomics). This can include proposals for genome-wide annotation of gene regulatory sequences to understand gene function across evolutionary time in areas such as: abiotic stress, development patterning, or signaling systems (See core capabilities below for available assays).

III. Inter-organismal interactions:

A key focus for the JGI is understanding the mutualistic, competitive, or antagonistic interactions among bacteria, archaea, fungi, protozoa, plants, and viruses, as these in turn impact global biogeochemical cycles of carbon and other nutrients, as well as plant health. 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. We encourage applicants to consider using the DOE Systems Biology Knowledgebase (KBase) to model interactions. Projects that could address this focus include:

• Plant or algal microbiomes to study interactions associated with BER mission-relevant host systems
• Omics-enabled interrogations of aquatic symbioses (non-animal associated) involving microorganisms from freshwater, estuarine and inter-tidal environments
• Investigation of the genomic basis of microbial mutualism and microbe-microbe interactions in stable model communities, e.g. enrichment cultures or synthetic communities
• Investigations using EcoFAB devices (https://eco-fab.org/) supplied by the JGI to conduct experiments to uncover the mechanisms underlying the interactions between plants and their root microbiomes
• Chemical ecology of secondary metabolites: Integration of large-scale genome sequencing, genome mining and predictive analyses, with functional activation and exometabolomic analysis of secondary metabolites to infer function in inter-organismal interactions, including mechanisms of resource competition and cross-feeding
• Genomic investigation of coupled viral and microbial dynamics, activity, and/or evolution
• Exploration of viral molecular mechanisms for host cell take-over and metabolic reprogramming

IV. Microbes and communities involved in elemental cycling in terrestrial, freshwater, estuarine and inter-tidal environments

Bacteria, archaea, fungi, algae, protozoa and viruses 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 and coastal environments has lagged behind. Proposals are encouraged that will provide insight into microbial activities controlling global cycles of carbon, nitrogen, phosphorus, sulfur and metals from a broad range of terrestrial, freshwater, estuarine and inter-tidal 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 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 and the National Microbiome Data Collaborative (NMDC).

All proposals may request up to 3 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 plant Illumina resequencing only, 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 250 Gbp, but larger requests will be considered for multi-PI projects of high value to the scientific community.

Proposals may request DNA synthesis up to 500 kbp of synthesized DNA, and up to 1,500 kbp of synthesized DNA for consortium proposals with co-PIs from at least 3 different institutions. More details on DNA synthesis requests and their scales can be found

Requests for metabolomics are capped at 200 samples for polar analysis and 500 samples for nonpolar analysis of lipids and secondary metabolites. Larger requests may be considered for a very limited number of multi-PI projects of high value to the scientific community, at JGI’s discretion and pending scientific and technical review.

The 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 to advance their analyses and data management/sharing plans. KBase integrates a variety of community data and analysis tools into an easy-to-use platform that leverages scalable computing infrastructure to perform sophisticated systems biology analyses, while also creating reproducible analysis workflows for sharing and publication. Additionally, applicants interested in collaborating with the National Microbiome Data Collaborative (NMDC) to develop project plans aligned with making their data findable, accessible, interoperable, and reusable (FAIR) should indicate so in their proposal.

JGI Capabilities

All proposals should justify why JGI capabilities are critical to success. The JGI employs an evolving suite of sequencing platforms, currently consisting of short read Illumina (NovaSeq) as well as single molecule long-read Pacific Biosciences technology (Sequel II). 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 for variation detection
• Microbial community shotgun DNA/RNA sequencing (not amplicon sequencing of 16S or other genes, 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
• Stable Isotope Probing (SIP) metagenomic studies, including density centrifugation and fraction collection carried out by the JGI
• Fluorescence activated cell sorting for targeted metagenomics, single-cell genomics (bacteria and archaea only) and microbial aggregates
• 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. This also includes synthesis of combinatorial pathway libraries. More details
• Whole-genome or partial-genome CRISPR-based gRNA library construction and QC
• Mass spectrometry-based metabolomics analysis of primary and secondary metabolites from plants, microorganisms, and environmental samples using targeted and untargeted approaches
• Analysis pipelines for the datasets above

The JGI also has limited capacity for the following developing or resource-intensive capabilities.  Since these are emerging technologies, proposed should contact JGI staff for technical details when developing proposals.

• Custom analysis of JGI datasets
• Chromatin analysis including ATAC-seq and ChIP-seq library preparation from User immunoprecipitated DNA
• Target-enriched resequencing
• 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)
• EcoFAB pilot projects. The JGI can provide a limited number of EcoFAB devices (https://eco-fab.org/) to study plant-microbiome interactions. These devices allow for non-destructive root imaging and sampling of the growth media while maintaining a sterile environment. In addition, the JGI can provide a standardized defined microbial community that colonizes plant roots and Brachypodium germplasm, if desired. Users would conduct experiments using these resources and return samples to the JGI for analysis by existing JGI capabilities e.g. metabolomics, transcriptomics and metatranscriptomics.
• Pore-based sequencing with the Oxford Nanopore MinIon or PromethIon
• Access to high-performance computing at the National Energy Research Scientific Computing Center (NERSC)
• Developing new applications and extending capabilities in KBase

Mechanism of Review

Letters of intent will only be accepted electronically and should be submitted at https://proposals.jgi.doe.gov/. The CSP Call is open to anyone with the understanding that CSP data are made publicly available immediately, without exception. Applicants will be advised approximately six weeks prior to the proposal submission deadline whether to prepare a full proposal. 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 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 2021.

Contacts

For general questions, please contact Christa Pennacchio, Project Management Office.  For questions about the appropriateness of projects, program specifics, or experimental design, please contact Tanja Woyke, Deputy for User Programs.

Proposal Schedule

To respond to the annual CSP call, a Letter of Intent is required before submitting a proposal. Letters of intent for CSP22 will only be accepted electronically and should be submitted at https://proposals.jgi.doe.gov/. Guidance for submitting full proposals will be included in the email notification to invited applicants.

The full FY22 schedule is below: