DOE Joint Genome Institute

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From Competition to Cooperation
By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.
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A Grass Model to Help Improve Giant Miscanthus
The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.
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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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Our Projects
Podcast: Xiaohan Yang on A Plantiful Future
Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.
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Synthesizing Microbial Expansins with Unusual Activities
Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.
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Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.
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Data & Tools
- IMG
- Genome Portal
- MycoCosm
- PhycoCosm
- Phytozome
- GOLD
Podcast: A Primer on Genome Mining
In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.
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From Life at the Extremes to Editing Genomes
For the past few years, Jennifer Doudna's lab has partnered with JGI’s Microbiome Data Science group to mine the IMG/M system for novel Cas genes and CRISPR systems.
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Accelerating Metagenomics Discoveries with Deep Learning
Notes from a workshop aimed at showcasing how researchers are utilizing deep learning to automatically generate insights from metagenomic data.
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User Programs
Learn About the Approved 2021 Large-Scale CSP Proposals
A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.
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How to Successfully Apply for a CSP Proposal
Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.
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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
Uncovering Novel Genomes from Earth’s Microbiomes
A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .
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Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.
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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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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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