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Our Science
Evolution of a Fungal Gene Expression Regulator
The abundance of fungal genomes underscores the need for a more comprehensive exploration of genomic DNA modifications (epigenome). In Nature Ecology & Evolution, a team conducted the largest analysis to date of 5mC, an important piece of the epigenome, across the fungal tree of life.
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Waiting to Respire
UC Berkeley and JGI researchers joined forces and data sets to describe bacterial genomes for related (“sibling”) lineages that diverged from the bacterial tree before Cyanobacteria and its contemporaries. The information was then used to predict the metabolic strategies applied by a common ancestor to all five lineages.
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A Model System for Perennial Grasses
The DOE supports research programs for developing methods for converting plant biomass into sustainable fuels for cars and jets. By studying a close relative model species like Panicum hallii, researchers can develop crop improvement techniques that could be applied to the candidate bioenergy feedstock switchgrass.
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Our Projects
Methane Flux in the Amazon
Wetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.
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Infections and Host-Pathogen Interactions of Chlorella
The non-photosynthetic, predatory cyanobacterium Vampirovibrio chlorellavorus is a globally important obligate pathogen of Chlorella species/strains, which are of interest as biofuel feedstocks.
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Insights into Functional Diversity in Neurospora
This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.
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Data & Tools
- IMG
- Genome Portal
- MycoCosm
- Phytozome
- GOLD
Mining IMG/M for CRISPR-Associated Proteins
Researchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.
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DAS Tool for Genome Reconstruction from Metagenomes
Through the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published in Nature Microbiology.
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New Software Tools Streamline DNA Sequence Design-and-Build Process
Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows.
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User Programs
CSP Synthesis Science Call Ongoing
DNA Synthesis Science proposals are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Proposals submitted by July 31, 2019 will be part of the next review.
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CSP Annual Call Ongoing
Letters of Intent are due April 11, 2019, for large-scale genomic science projects that address the specific areas of special emphasis that are listed in the call, and exploit the diversity of JGI technical and analytical capabilities.
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JGI-EMSL FICUS Call Ongoing
Letters of Intent (LOI) are due March 20, 2019, for collaborative research applications with the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL). Combine the power of genomics and molecular characterization in a single research project.
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News & Publications
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Hidden Giants in Forest Soils
In Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.
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Symbiosis a Driver of Truffle Diversity
Truffles are the fruiting bodies of the ectomycorrhizal (ECM) fungal symbionts residing on host plant roots. In Nature Ecology & Evolution, an international team sought insights into the ECM lifestyle of truffle-forming species. They conducted a comparative analysis of eight Pezizomycete fungi, including four species prized as delicacies.
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Expanding Fungal Diversity, One Cell at a Time
In Nature Microbiology, a team led by JGI researchers has developed a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated fungal species representing early diverging fungi.
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December 9, 2013

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