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Our Science
The fungus that made itself at home
Due to its aggressive capacity to damage the wood in homes, bioenergy researchers have been interested in harnessing the brown rot Serpula lacrymans towards breaking down plant mass for conversion to sustainable, alternative biofuels and bioproducts. In The ISME Journal, insights on how the fungus has responded to manmade changes in its ecological habitat, adapting to thrive in built environments.
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An Addiction Crucial to a Fungus’ Reproduction
In the absence of the Burkholderia endobacteria, the Rhizopus fungus cannot act as a plant pathogen, and researchers have now discovered that endobacteria also regulate its sexual reproduction. The work sheds light on a poorly understood group of oleaginous or oil-producing fungi, and the impact this mutualistic interaction has on these potential large-scale biodiesel producing fungi.
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Succulent Genes for Water Use Efficiency
To understand how many plant lineages have independently transitioned from C3 to CAM photosynthesis, researchers sequenced and analyzed the genome of Kalanchoë fedtschenkoi (lavender scallops). As the first CAM eudicot to have its genome sequenced, Kalanchoë offers researchers a reference to trace the evolution of CAM photosynthesis in this group.
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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
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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Meet a JGI User: J. Chris Pires
"My mission is to train the next generation of scientists by doing high impact, interdisciplinary science in a collaborative atmosphere. JGI is an important partner in this team science effort in cross-training students and postdoctoral researchers."
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News & Publications
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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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Tracking Microbial Diversity Through the Terrestrial Subsurface
In Nature Microbiology, JGI researchers collaborated with a team led by longtime collaborator Jill Banfield of the University of California, Berkeley and Cathy Ryan of the University of Calgary in Canada, investigating samples collected at Utah's Crystal Geyser over one of the its complex, five-day eruption cycles.
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December 9, 2013

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