Joint Genome Institute accepting letters of intent for large-scale sequence-based genomic projects; focus on alternative fuels, global carbon cycling and biogeochemistry

The US Department of Energy’s (DOE) Joint Genome Institute’s (JGI) Community Sequencing 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 alternative fuels, global carbon cycling and biogeochemistry.

While applications will be accepted that address any aspect of these mission areas, up to 50% of capacity for this call will be allocated for projects that address the following areas of special emphasis, and exploit the diversity of JGI capabilities:

  • Plant and Plant-Microbe interactions: Plant phenotypes are likely to be strongly influenced by their associated microbes. Studies are encouraged that explore the interaction of plants with their rhizosphere communities and other microbes or fungi that affect bioenergy-relevant plant phenotypes. Plant resequencing or transcriptomic projects are of interest but whole-genome de novo plant sequencing projects are discouraged for this CSP call. Plant phenotypes of interest might include drought or salt tolerance, nutrient use, primary productivity, biomass composition or yield or recalcitrance.

  • Microbial emission and capture of greenhouse gases: Bacteria, archaea, fungi, and algae are important consumers and producers of greenhouse gases in the environment. Studies are sought that will provide insight into global carbon, nitrogen, and methane cycles, and/or suggest novel strategies for carbon capture, nitrogen processing, or methane reduction from environmental sources.

  • Metagenomics: Most microbes live in complex communities in oftentimes dynamic environments where the impact of changing environmental parameters on community structure and function are largely unknown. Proposals are encouraged that couple metagenomic analyses with measures of the active component of microbial populations and associated environmental biogeochemistry to explore dynamic changes in the active community composition and expressed metabolism of microbial communities in DOE mission-relevant areas. Such areas may include: Bioenergy-related plant-microbe interactions, carbon/nitrogen cycling and/or carbon sequestration processes in soils and sediments, and biogeochemical processes contributing to contaminant biotransformation and/or immobilization.

CSP projects are expected to generate publicly available data that will answer important questions relevant to the organism/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 involving combinations of the following features: a significant scale, large DNA/RNA sequencing need (100s of gigabases to terabases), engaging a large group of collaborators, involving more than a single species and requiring JGI capabilities in addition to genome sequencing.

Overall JGI capacity is expected to be about 15 Terabases (Tb) of which as much as 10 Tb may be available for this CSP. Each proposal must carefully justify the amount of sequencing requested but no single proposal should expect more than a maximum of 1 Tb.

JGI Capabilities. JGI employs almost exclusively next-generation short-read sequencing platforms, with very limited longer-read capabilities. 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 if longer read sequencing is needed, the burden is on the submitter to justify the request. Successful projects frequently exploit a combination of capabilities:

Core Products Include:

  • De Novo Sequencing of Fungal, Bacterial, and Archaeal Genomes
  • Resequencing for Variation Detection
  • Metagenomic DNA/RNA Sequencing
  • RNA-Seq for Genome Annotation
  • RNA-Seq for Reference Gene Sets
  • RNA-Seq for Gene Counting
  • Analysis pipelines for the datasets above

JGI also has limited capacity for the following developing capabilities:

  • 3rd Generation Single-Molecule Sequencing
  • Fluorescent Activated Cell Sorting
  • Micro-Manipulator Isolation of Single Cells
  • Single Cell DNA Sequencing
  • Multiplex Emulsion PCR Amplicon Sequencing
  • Limited DNA/Gene Synthesis
  • Custom Genome Analysis of Generated Datasets

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