DOE Joint Genome Institute

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Our Science
In Hot Spring Microbial Mat, Viruses Ride “Piggyback”
In The ISME Journal, scientists have used sequencing methods for the first time to comprehensively characterize viral-host interactions.
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Effects of Polar Light Cycle on Microbial Food Web
While microbial populations in other Antarctic lakes and the nearby Southern Ocean shift from phototrophs to archaea when sunlight becomes scant, Ace Lake’s bacteria instead go through a boom and bust cycle aligned with light availability.
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Gene Expression: From On-Off Switch to Dial
Scientists have developed a more nuanced library approach to tuning gene expression in metabolic pathways, allowing researchers to identify variations of essential genes in metabolic networks that were missed using traditional approaches.
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Our Projects
Gene Atlas of a Nitrogen-Fixing Legume Symbiont
Understanding how bacterial communities produce biofuels or to remediate contaminated environments is limited due to a lack of knowledge of the functional properties of microbes and their genes. A high-throughput approach will help fill-in these gaps in knowledge, laying a solid foundation for researchers hoping to engineer bacteria with improved or novel traits.
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Role of Fungal Endosymbionts in Host Reproduction
This project focuses on endosymbionts and fungal reproduction, expanding knowledge on the complexities of microbiome interactions. These fungi are industrially important because they produce valuable lipid products.
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Scaling Microbial Traits From Genomes to Watersheds
Using remote sensing, metagenomics and machine learning, researchers are building new ways to predict of how plant and microbial metabolism interact to influence biogeochemistry across watersheds in the headwaters of the Colorado River.
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Data & Tools
- IMG
- Genome Portal
- MycoCosm
- PhycoCosm
- Phytozome
- GOLD
Computationally Classifying Fungal Lifestyles
Machine learning methods were applied on sequenced fungal genomes, generated in part through the 1000 Fungal Genomes Project, to classify them by lifestyles.
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Here, There and Everywhere: Large and Giant Viruses Abound Globally
In Nature, a JGI-led team uncovered a broad diversity of large and giant viruses that belong to the nucleocytoplasmic large DNA viruses (NCLDV) supergroup. The expansion of the diversity for large and giant viruses offered the researchers insights into how they might interact with their hosts.
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Expanding Virophage Diversity
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.
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User Programs
CSP New Investigator Proposal Call
Proposals may be submitted at any time for the CSP New Investigator Call, and will be reviewed every six months.
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JGI Engagement: Accessing Functional Genomics Capabilities Webinar
Hear how researchers have availed of JGI resources and capabilities to advance their science through the year-round Community Science Program’s Functional Genomics call for proposals.
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How to Target a Microbial Needle within a Community Haystack
Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.
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News & Publications
The More the Merrier: Making the Case for Plant Pan-genomes
Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.
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Picking Up Threads of Cotton Genomics
High quality genomes of the five major cotton lineages have been assembled by a multi-institutional team and are available for comparative analysis on JGI’s plant data portal Phytozome. “The goal has been for all this new cotton work, and even the original cotton project was to try to bring in molecular methods of breeding into cotton,” said JGI Plant Program head Jeremy Schmutz.
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Inspiring STEM Careers Through a Hands-on Everglades Microbiome Study
The pilot project between JGI and a Boca Raton Community High School class in Palm Beach County, Florida has led to a data report published in the journal Environmental Microbiome. The class focused on microbial communities in the Arthur R. Marshall Loxahatchee National Wildlife Refuge, a 226-square mile area of the northern Everglades.
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User Programs

https://jgi.doe.gov/kelly-wrighton-colorado-state-university/

Views from Our User Community: Kelly Wrighton

https://jgi.doe.gov/tobias-erb-max-planck-institute-for-terrestrial-microbiology/

Tobias Erb, Max Planck Institute for Terrestrial Microbiology

https://jgi.doe.gov/colleen-hansel-woods-hole-oceanographic-institute/

Colleen Hansel, Woods Hole Oceanographic Institute

https://jgi.doe.gov/j-chris-pires-university-of-missouri/

J. Chris Pires, University of Missouri

https://jgi.doe.gov/cat-adams-university-of-california-berkeley/

Cat Adams, University of California, Berkeley

https://jgi.doe.gov/c-titus-brown-university-of-california-davis/

Views from Our User Community: C. Titus Brown

Views from Our User Community: Jill Banfield

Views from Our User Community: Jill Banfield

https://jgi.doe.gov/rod-wing-arizona-genomics-institute/

Views from Our User Community: Rod Wing

Views from Our User Community: Brian Hedlund

Views from Our User Community: Brian Hedlund

Views from Our User Community: Matt Sullivan

Views from Our User Community: Matt Sullivan

Views from Our User Community: Steven Hallam

Views from Our User Community: Steven Hallam

Views from Our User Community: Mary Ann Moran

Views from Our User Community: Mary Ann Moran

Views from Our User Community: Jeff Dangl

Views from Our User Community: Jeff Dangl

Views from Our User Community: Trina McMahon

Views from Our User Community: Trina McMahon

Keep apprised of the status of JGI’s operations during the limited onsite access due to the COVID-19 pandemic.

Calls for User Proposals:

The Community Science Program (CSP)
Facilities Integrating Collaborations for User Science (FICUS)

User Resources:

Submit a Proposal
Contacts for Users (Project Managers)
Data Release and Publication Policies
User Agreement
Your Partner for Integrative Genome Science brochure
JGI Data Science & Informatics brochure

How do we support user science?

DOE Mission Relevance

Projects with relevance to DOE missions have the best chance for selection.

How to propose a project

Types of Projects accepted, information to include in a proposal, and how to submit.

User Support and Project Management

Discover the services we provide our users to facilitate world-class science.

Approved User Proposals

Learn what types of projects have been supported by JGI’s annual calls for proposals.

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