DOE Joint Genome Institute
DOE Mission Areas
Bioenergy Research Centers
Fishing for Novel Cellulose Degraders
JGI researchers developed a function-driven, single-cell screen that they described as a “hook and bait” approach to isolate cellulose-degrading microbes. While the screen caught several microbes from known cellulose-degrading groups, the researchers also hooked and were able to reconstruct a high-quality draft co-assembled genome for a new genus level member of the novel candidate phylum Goldbacteria. The work appeared in The ISME Journal.
Dealing with Drought: Uncovering Sorghum’s Secrets
Sorghum bicolor (L.) Moench is an African grass that adroitly handles droughts, floods and poor soils. This is the first paper that describes sorghum’s response to drought, from a large-scale field experiment led by a multi-institutional consortium to uncover the mechanisms behind sorghum’s capacity to produce high yields despite drought conditions.
Making a Lichen Together
Despite a century-and-a-half of lichen research, many details of lichen symbiosis remain unclear. For the first time, a team has analyzed in parallel the genomes and transcriptomes of both partners to better understand lichen.
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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
Expanding Virophage Diversity
Virophages are small viruses with double-stranded DNA genomes that co-infect eukaryotic cells along with giant viruses. In Microbiome, JGI researchers provided a global analysis of the diversity, distribution, and evolution of virophages - and in doing so, increased the number of known high quality virophage genome sequences 10-fold through computational approaches.
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.
Calls for User Proposals
Special Initiatives & Programs
Submit a Proposal
CSP Functional Genomics Call Ongoing
The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by January 31, 2020 will be part of the next review.
CSP New Investigator Call Ongoing
The CSP New Investigator call targets investigators and research initiatives new to the JGI. Proposals submitted by March 2, 2020 will be part of the next review.
What Happens Underground Influences Global Nutrient Cycles
Through the Facilities Integrating Collaborations for User Science (FICUS) program, the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (JGI) have selected 11 proposals for support from 53 received through a joint research call.
News & Publications
Honey Bee Gut Microbiota Divvy Up Dinner
Honey bees rely on their gut microbiota to produce these enzymes to break down polysaccharides. An international team of researchers has identified the major metabolic roles of constituent microbes, publishing their findings in PNAS.
JGI on the 2019 Highly Cited Researchers List
Clarivate Analytics' 2019 list of Highly Cited Researchers includes 10 affiliated with the JGI . The 2019 list focused on Highly Cited Papers, defined in the Methodology section as “those that rank in the top 1% by citations for papers published and cited between 2008-2018.” Less than 6,300 Highly Cited science and social science researchers in one or more of 21 fields appear on the 2019 list.
Mindfully Moving JGI
The process of moving 250 people and their equipment from 4 single-story buildings to a new 4-story building 20 miles away in another city and county began more than three years ago. Staff sorted through the stuff accumulated in offices, labs, lockers, and other storage spaces in Walnut Creek and then designated materials as Keep or else sorted them into multiple waste streams.
March 16, 2017