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The Surprising Structure of a Shrub Willow Sex Chromosome
Shrub willow and its close relative Populus trichocarpa, or the poplar tree, are potential biofuel feedstocks. Understanding the mechanisms by which they reproduce can help guide breeding efforts. For the first time, the sex chromosomes of shrub willow have been sequenced with sufficient resolution to analyze their structure.
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Viruses Reprogram Cells into Different Virocells
If it looks like a duck and quacks like a duck, so the adage goes, it must be a duck. But if the duck gets infected by a virus so that it no longer looks or quacks like one, is it still a duck? For a team led by researchers from The Ohio State University and the University of Michigan studying how virus infections cause significant metabolic changes in marine microbes, the answer is no. They refer to the infected microbial cells as virocells, the name change reflecting the metabolic changes the cells have undergone.
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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.
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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
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, and how those interactions may in turn impact the host communities and their roles in carbon and other nutrient cycles.
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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.
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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).
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User Programs
JGI-enabled User Science Highlights in our Progress Report
Check out some of the JGI-enabled user science from the last year highlighted in the latest JGI Progress Report! Download a copy or request a print copy today!
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Submit Anytime to Our CSP New Investigator Call
The CSP New Investigator call targets investigators and research initiatives new to the JGI, with an emphasis on providing pilot data to assess feasibility of a novel approach or to form the foundation for a large-scale CSP proposal submission.
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CSP Functional Genomics Call Ongoing
The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 30, 2020 will be part of the next review.
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News & Publications
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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, one of the senior authors of the Nature Genetics study.
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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 sought to apply the latest molecular techniques to learn more about the microbial communities in the Arthur R. Marshall Loxahatchee National Wildlife Refuge, a 226-square mile area of the northern Everglades in Palm Beach County, and particularly about the microbes that play roles in the methane cycle.
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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.
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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)

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Submit a Proposal
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Your Partner for Integrative Genome Science brochure
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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.

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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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