DOE Joint Genome Institute

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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Past Events
Home › Past Events › CSP 2012 PI Workshop

CSP 2012 PI Workshop

Walnut Creek, California

The DOE-JGI is organizing a two-day workshop for Principal Investigators on successful CSP 2012 proposals in the focus areas of “plant-microbe interactions” and “terrestrial greenhouse gas emissions and capture” to be held at the JGI in Walnut Creek, CA, on January 23-24, 2012.

Attendance to this workshop is by invitation only

List of Projects

  • Dangl et al., Plant associated metagenomes–Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems.
  • Schadt et al., Defining the Populus Microbiome: Role of Genotype by Environment Interactions in Shaping the Rhizosphere Microbiome of Populus trichocarpa Gross et al., The Agave Microbiome: Exploring the role of microbial communities in plant adaptations to desert environments
  • Bucking et al., Exploring the transcriptome of perennial grasses in association with beneficial microorganisms to increase biomass production and environmental sustainability of bioenergy production
  • Laplaze et al., Transcriptome Analysis of Salt Tolerance in Casuarina trees
  • Fierer et al., Cross-site metagenomic analyses to assess the impacts of experimental nitrogen additions on belowground carbon dynamics
  • Brodie et al., Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.
  • Pester et al., Targeted metagenomics and metatranscriptomics of a sulfate-reducing rare biosphere member and potentially novel sulfate reducers that impact methane emission from peatlands
  • Rodrigues et al., Profiling metagenomic consequences of Amazon deforestation at different spatial scales
  • Martin et al., Metatranscriptomics of Soil Forest Ecosystems
  • DeAngelis et al., Microbial ecology and genomics of carbon-storing bacteria in rhizosphere soils
  • Mohn et al., Metagenomic and metatranscriptomic analysis of forest soil communities across North America

 

  • 2017 Microbial and Plant Systems Modulated by Secondary Metabolites Meeting
  • 2016 Microbial and Plant Systems Modulated by Secondary Metabolites Meeting
  • NeLLi 2017: From New Lineages of Life To New Functions
  • Program Meetings and Workshops
  • CSP 2012 PI Workshop
  • Bay Area Plant Microbe Interaction Symposium II
  • Microbial Genome Reannotation Workshop
  • Application of High Performance Computing to the DOE Joint Genomic Institute’s Data Challenges

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