DOE Joint Genome Institute
DOE Mission Areas
Bioenergy Research Centers
Building Sphagnum Genomic Resources
Sphagnum’s impact on global carbon cycling and climate is estimated to be larger than any other single plant genus. Researchers estimate that the peatlands hold about 25 percent of the world’s soil carbon. Enabled by the JGI’s Community Science Program (CSP), researchers are developing a number of resources to build up Sphagnum as a plant model system focused on carbon cycling studies.
Iron-rich Microbial Mats’ Main Players: Marsarchaeota
Through a combination of sequencing tools and techniques applied to samples collected from acidic iron-oxide microbial mats in Yellowstone National Park over time, researchers have discovered and characterized a novel phylum-level lineage of archaea with at least two major subgroups dubbed Marsarchaeota.
The fungus that made itself at home
Due to its aggressive capacity to damage the wood in homes, bioenergy researchers have been interested in harnessing the brown rot Serpula lacrymans towards breaking down plant mass for conversion to sustainable, alternative biofuels and bioproducts. In The ISME Journal, insights on how the fungus has responded to manmade changes in its ecological habitat, adapting to thrive in built environments.
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Approved User Proposals
Comparative and Population Genomics of Xylariaceae
A genomic survey of the Xylariaceae, one of the largest and most diverse families of fungi made up of endophytic, pathogenic, and saprotrophic (including wood degrading) species.
Gene Atlases of Grass-Microbe Interactions
This proposal seeks to build comprehensive gene atlas maps for diverse bioenergy grass-microbe interactions, including pathogenic and beneficial interactions in two grass models, Brachypodium and Setaria.
Quantifying Cyanobacteria Interactions
The long term objective is to quantify dynamic interactions between phototrophs and their virus predators. This will help to build quantitative, dynamic and predictive models of host-viral interactions and the effect on carbon and nutrient cycling.
Data & Tools
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.
DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform
In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers.
Benchmark Study for Improving Microbial Community Profiling
Researchers used synthetic and natural microbial lake communities to compare the microbial community profiles generated from high throughput short-read sequencing and high throughput long-read sequencing approaches.
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Calls for User Proposals
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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.
Meet a JGI User: Tobias Erb
"The JGI has been crucial for our research because it has provided the scientific community with a tremendous amount of gene sequences over the last couple of years. These gene sequences have become a true treasure grove for synthetic biologists like us."
Meet a JGI User: Colleen Hansel
"We have been working on genomic and transcriptome studies of a unique group of manganese (Mn) oxidizing Ascomycete fungi that were isolated from coal mine drainage treatment systems and metal-laden freshwater ponds. The staff and facilities at the JGI were critical for conducting this research. "
News & Publications
Freedom and Flexibility: Thinking Outside the Cell for Functional Genomics
The latest proposal approved through the JGI’s Emerging Technologies Opportunity Program (ETOP) aims to develop an optimized cell-free platform that will enable researchers to speed up the “build” and “test” portion of the design-build-test-analyze cycle in synthetic biology.
A Reference Catalog for the Rumen Microbiome
In Nature Biotechnology, an international team presents one of the largest targeted cultivation and sequencing projects to date: a reference catalog of rumen microbial genomes and isolates cultivated and sequenced from the Hungate1000 collection produced through the coordinated efforts of rumen microbiology researchers worldwide.
Tracking Microbial Diversity Through the Terrestrial Subsurface
In Nature Microbiology, JGI researchers collaborated with a team led by longtime collaborator Jill Banfield of the University of California, Berkeley and Cathy Ryan of the University of Calgary in Canada, investigating samples collected at Utah's Crystal Geyser over one of the its complex, five-day eruption cycles.
› Recent Fungal Genome Releases
Recent Fungal Genome Releases