DOE Joint Genome Institute
DOE Mission Areas
Bioenergy Research Centers
Better Genome Editing for Bioenergy
CRISPR-Cas9 is a powerful, high-throughput gene-editing tool that can help scientists engineer organisms for bioenergy applications. Cas9 needs guide RNA to lead it to the correct sequence to snip—but not all guides are effective. Researchers created a set of guide RNAs that were effective against 94 percent of the genes in a lipid-prolific yeast.
Cultivating Symbiotic Antarctic Microbes
In the Proceedings of the National Academy of Sciences, researchers employed multiple microbiology and ‘omics techniques to experimentally determine that Nanohaloarchaeota are not free-living archaea but rather symbionts.
Developing Switchgrass for Biomass Production
To better understand the genetic basis of local adaptation, researchers established community gardens of switchgrass plants in 10 different field sites on a north-south gradient across the United States. Early results from these large-scale field tests conducted over two years reveal fewer tradeoffs in plant fitness and adaptation than expected.
Search JGI Project List
Approved User Proposals
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.
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.
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.
Data & Tools
Improving the Cacao Genome and Phytozome
An updated reference genome for Theobroma cacao Matina 1-6 has now been completed and released by HudsonAlpha scientists, with the help of Mars Wrigley funding. The annotated genome has been updated to a high quality modern standard and includes RNA-seq data. The improved genome is available for comparative purposes on the latest version of the JGI plant portal Phytozome (phytozome-next.JGI.doe.gov).
Expanding Universe of Methane Metabolisms in Archaea
In Nature Microbiology, researchers mined the Integrated Microbial Genomes & Microbiomes (IMG/M) database maintained by the JGI for publicly available metagenome data provided by the other study co-authors, and reconstructed from these 10 metagenome-assembled genomes (MAGs) representing new potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea.
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.
Calls for User Proposals
Special Initiatives & Programs
Submit a Proposal
CSP New Investigator Call Ongoing
The CSP New Investigator call targets investigators and research initiatives new to the JGI. Proposals submitted by September 26, 2019 will be part of the next review.
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.
Next CSP Annual Call: Spring 2020
The Community Science Program (CSP) Annual Call is focused on large-scale genomic science projects that address specific areas of special emphasis, and exploit the diversity of JGI technical and analytical capabilities. To respond to the annual CSP call, a Letter of Intent is required before submitting a proposal.
News & Publications
Learning to Look
Using machine learning, JGI researchers combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes.
JGI Early Career Researchers in mSystems Special Issue
JGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like. In one article, Rex Malmstrom and Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental sample. In a separate article, Simon Roux makes a pitch for readers to get involved in the developing field of virus ecogenomics.
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.