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    Serpula lacrymans var. lacrymans, an aggressive decomposer of the built environment, attacking this dresser. (Inger Skrede)
    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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    Sexual reproduction in Rhizopus microspores: (a) Successful mating between fungi harboring bacteria; (b) Lack of sex between mates cured of endobacteria. (Stephen Mondo)
    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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    In Nature Communications, researchers sequenced and analyzed the genome of Kalanchoe fedtschenkoi (lavender scallops) to better understand how this plant transitioned from C3 to CAM photosynthesis. (Forest and Kim Starr, Flickr CC BY 2.0)
    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
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    Morphological diversity of Xylariaceous endophytes. (J.M. U'Ren)
    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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    Virus-infected Brachypodium (Courtesy of Kranthi Mandadi)
    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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    Yellowstone National Park, Octopus hot spring biofilms (Courtesy of Devaki Bhaya)
    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
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    • GOLD
    DOE JGI BOOST logo
    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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    This graphic depicts the geographic distribution of GOLD biosamples and organisms. Organism location of isolation is marked in pink while Biosample location of collection is denoted with blue dots. Updates to the Genomes OnLine Database (GOLD) are reported in the upcoming Database issue of Nucleic Acids Research. (Image from Supratim Mukherjee et al. Nucl. Acids Res. 2016;nar.gkw992)
    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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    Sakinaw Lake UBC
    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
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    Tobias Erb, MPI Marburg (Courtesy of Tobias Erb)
    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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    Colleen Hansel, WHOI
    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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    J. Chris Pires, University of Missouri
    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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    Depiction of rumen microbiome. (Ella Maru studio, www.scientific-illustrations.com)
    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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    https://jgi.doe.gov/tracking-microbial-diversity-through-terrestrial-subsurface/
    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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Our Projects
Home › Our Projects › Legacy Projects

Legacy Projects

Past JGI projects and their associated programs.

  • Laboratory Science Program Small-Scale Sequencing Plans

    These past projects include Five Archaea (Methanohalobium evestigatum, Methanobacterium formicicum, Halococcoides, Ferroglobus placid us, and Acidianus sp. JP7) from LBNL, Aspergillus terries EST from PNNL, and Avena Barbata ESTs from BNL.

  • DOE Microbial Genome Program

    Past DOE Microbial Genome Program projects were from 2001 – 2007.

  • Sequencing for the DOE Genomics: GTL Program

    GTL projects include Desulfitobacterium hafniense DCB-2 DSM 10664, South African Gold Mine Metagenome (Candidatus Desulforudis audaxviator MP104C), and Desulfovibrio desulfuricans 27774

  • DOE Sequencing Projects

    Past DOE sequencing projects include Branchiostoma floridae (Florida lancelet), Chlamydomonas reinhardtii (a green alga), Ciona (sea squirt) fosmids, Daphnia pulex (water flea), and Fugu rubripres (puffer fish)

  • Laboratory Science Program Small-Scale Sequencing Plans
  • DOE Microbial Genome Program
  • Sequencing for the DOE Genomics: GTL Program
  • DOE Sequencing Projects

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