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Our Science
Innovative Technology Improves Our Understanding of Bacterial Cell Signaling
Cyclic di-GMP (Guanine Monophosphate) is found in nearly all types of bacteria and interacts with cell signaling networks that control many basic cellular functions. It plays an important role in regulating microbial cellulose production and biofilm formation, which affects a number of environments, including plants, soil, and the gut. To better understand the dynamics of this molecule, researchers developed the first chemiluminescent biosensors for measuring cyclic di-GMP in bacteria through work enabled by the JGI’s Community Science Program (CSP).
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Building Sphagnum Genomic Resources
Sphagnum’s impact on global carbon cycling and climate is estimated to be larger than any other single plant genus. Researchers estimate that the peatlands hold about 25 percent of the world’s soil carbon. Enabled by the JGI’s Community Science Program (CSP), researchers are developing a number of resources to build up Sphagnum as a plant model system focused on carbon cycling studies.
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Iron-rich Microbial Mats’ Main Players: Marsarchaeota
Through a combination of sequencing tools and techniques applied to samples collected from acidic iron-oxide microbial mats in Yellowstone National Park over time, researchers have discovered and characterized a novel phylum-level lineage of archaea with at least two major subgroups dubbed Marsarchaeota.
Our Projects
Comparative and Population Genomics of Xylariaceae
A genomic survey of the Xylariaceae, one of the largest and most diverse families of fungi made up of endophytic, pathogenic, and saprotrophic (including wood degrading) species.
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Gene Atlases of Grass-Microbe Interactions
This proposal seeks to build comprehensive gene atlas maps for diverse bioenergy grass-microbe interactions, including pathogenic and beneficial interactions in two grass models, Brachypodium and Setaria.
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Quantifying Cyanobacteria Interactions
The long term objective is to quantify dynamic interactions between phototrophs and their virus predators. This will help to build quantitative, dynamic and predictive models of host-viral interactions and the effect on carbon and nutrient cycling.
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Data & Tools
- IMG
- Genome Portal
- MycoCosm
- Phytozome
- GOLD
New Software Tools Streamline DNA Sequence Design-and-Build Process
Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows.
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DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform
In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers.
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Benchmark Study for Improving Microbial Community Profiling
Researchers used synthetic and natural microbial lake communities to compare the microbial community profiles generated from high throughput short-read sequencing and high throughput long-read sequencing approaches.
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User Program Info
DAS Tool for Genome Reconstruction from Metagenomes
Through the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published in Nature Microbiology.
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Meet a JGI User: Tobias Erb
"The JGI has been crucial for our research because it has provided the scientific community with a tremendous amount of gene sequences over the last couple of years. These gene sequences have become a true treasure grove for synthetic biologists like us."
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Meet a JGI User: Colleen Hansel
"We have been working on genomic and transcriptome studies of a unique group of manganese (Mn) oxidizing Ascomycete fungi that were isolated from coal mine drainage treatment systems and metal-laden freshwater ponds. The staff and facilities at the JGI were critical for conducting this research. "
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News & Publications
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Reproducibility Matters in Large-Scale Maize Study
In PNAS, an international team of researchers reported on the results of a large-scale field study that partially replicates earlier trials to identify soil microbes that colonize plants and which can be associated with particular traits.
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Freedom and Flexibility: Thinking Outside the Cell for Functional Genomics
The latest proposal approved through the JGI’s Emerging Technologies Opportunity Program (ETOP) aims to develop an optimized cell-free platform that will enable researchers to speed up the “build” and “test” portion of the design-build-test-analyze cycle in synthetic biology.
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A Reference Catalog for the Rumen Microbiome
In Nature Biotechnology, an international team presents one of the largest targeted cultivation and sequencing projects to date: a reference catalog of rumen microbial genomes and isolates cultivated and sequenced from the Hungate1000 collection produced through the coordinated efforts of rumen microbiology researchers worldwide.
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December 9, 2013

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