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    TEM image of O. tauri strain RCC4221. Credit: Herve Moreau
    Tiny Green Algae Reveal Large Genomic Variation
    A decade after the complete representative genomes of three Ostreococcus picoplankton groups were sequenced, researchers have sequenced and analyzed the genomes of 13 members of a natural Ostreococcus population.

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    Genome-wide distribution of fast neutron-induced mutations in the Kitaake rice mutant population. (Guotian Li and Rashmi Jain)
    Mutant Rice Database for Bioenergy Research
    Boosting yields of bioenergy feedstock crops such as grasses requires a functional genomics resource for grass models involved in plant cell wall biosynthesis studies. Using fast-neutron irradiation, rice researchers were able to create the first major, large-scale collection of mutations for grass models.

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    The oil slick in the Gulf of Mexico from the Deepwater Horizon oil spill as seen on April 29, 2010. (NASA Earth Observatory image created by Jesse Allen, using data provided courtesy of the University of Wisconsin’s Space Science and Engineering Center MODIS Direct Broadcast system)
    Lessons from Simulating A Deep Ocean Oil Spill
    Researchers present the first complete picture of how successive waves of microbial populations degraded the released oil. They were also able to recover high-quality genomes of the key microbial players, and determine the metabolic factors driving the shifts between microbial communities.

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  • Our Projects
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    Developing an Ice Plant Gene Atlas
    The ice plant was the first reported halophytic, facultative crassulacean acid metabolism (CAM) species, meaning that the plant can be induced to switch from C3 photosynthesis to CAM following water-deficit or salinity stress treatment.

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    Mark Dopson of Sweden’s Linnaeus University has a project that deploys DOE JGI’s single cell genomics resources on samples sourced from the deep subsurface, including the Pyhäsalmi mine. (Courtesy of Mark Dopson)
    Exploring Deep Biosphere Microbial Communities
    The data from one of the least understood habitats on Earth will have implications for our understanding of global energy and nutrient cycles, the potential for deep terrestrial disposal of nuclear waste and geo-engineering for CO2 storage, while also providing insights about how life could be sustained on other planets.

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    Suillus ampliporus, shown here, is part of the genus-wide molecular phylogeny of Suillus project from Nhu Nguyen of the University of California, Berkeley. Suillus fungi tolerate heavy metals, but the protection varies among hosts. (Image by Nhu Nguyen)
    A Suillus Genus Genome Atlas
    As symbiotic ectomycorrhizal fungi (EMF), Suillus spp. play critical roles in the function of forest ecosystems by providing their plant hosts with mineral resources in exchange for photosynthetically fixed carbon.

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  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
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    • GOLD
    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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    Better Microbial Genome Binning with MetaBAT
    An automated tool called MetaBAT that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes.

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  • User Program Info
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    JGI-NERSC Microbiome Data Science Call
    The Microbiome Data Science call will enable users to perform state-of-the-art computational genomics and metagenomics research and help them translate sequence information, generated by the DOE JGI or elsewhere, into biological discovery.

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    Large-scale CSP Call
    The CSP Annual Call is focused on large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in sustainable biofuel production, global carbon cycling, and biogeochemistry.

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    JGI-EMSL Collaborative Science Call
    The FICUS call between DOE JGI and Environmental Molecular Science Laboratory (EMSL) represents a unique opportunity for researchers to combine the power of genomics and molecular characterization in one proposed research project.

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  • News & Publications
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    The release of 1,003 phylogenetically diverse bacterial and archaeal reference genomes, the single largest release to date, is part of the DOE JGI’s Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative. (Zosia Rostomian, Berkeley Lab Creative Services.)
    Uncovered: 1000 New Microbial Genomes
    DOE JGI scientists have taken a decisive step forward in uncovering the planet’s microbial diversity, reporting the release of 1,003 phylogenetically diverse bacterial and archaeal reference genomes—the single largest release to date—in Nature Biotechnology.

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    Scanning electron micrograph (SEM) of Neocallimastix californiae, a representative of the Neocallimastigomycetes, a clade of the early-diverging fungal lineages that are not well-studied. It's one of three Neocallimastigomycetes sequenced and annotated by the DOE JGI for this study. (Chuck Smallwood, PNNL)
    Fungal Enzymes Team Up to More Efficiently Break Down Cellulose
    In Nature Microbiology, a team led by researchers at UC Santa Barbara has found for the first time that early lineages of fungi can form complexes of enzymes capable of degrading plant biomass. The work was enabled by harnessing the capabilities of two U.S. Department of Energy (DOE) Office of Science User Facilities: the DOE JGI and EMSL.

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    Linderina pennispora ZyGoLife Research Consortium Flickr CC BY-SA 2.0
    Finding A New Major Gene Expression Regulator in Fungi
    DOE JGI scientists report the prevalence of a particular DNA base modification (6mA) in the earliest branches of the fungal kingdom.

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User Advisory Committees

  • Scientific User Advisory Committee (SAC)

    The Scientific Advisory Committee is a board convened by the DOE JGI Director to provide a scientific and technical overview of the DOE JGI. Members include M. Adams, C. Bult, S. Briggs, J. Dangl, C. Fraser, N.L. Glass, G. Kubiak, MA Moran, J. Parkhill, T. McMahon, D. Meldrum, J. Meza.

  • Informatics User Advisory Committee

    Members include A. Arkin, J. Blake, D. Dooling, P. Flicek, S. Kravitz, J. Mesirov, G. Sutton, C. Wu, and K. Yelick.

  • Fungal Program User Advisory Committee

    Members include S. Baker, R. Berka, R. de Vries, A. Gasch, N. L . Glass, S. Goodwin, D. Hibbett, F. Martin, M. O’Malley, J. Spatafora, K. Treseder, A. Tsang.

  • Prokaryotic Super Program User Advisory Committee

    Members include J. Banfield, C. Currie, E. DeLong, J. Eisen, G. Garrity, S. Hallam, P. Hugenholtz, J. Jansson, K. McMahon, M. A. Moran, N. Moran, V. Orphan, R. Roberts, M. Sullivan, R. Stepanauskas.

  • Plant Program User Advisory Committee

    Members include S. Brady, G. Coruzzi, J. Dangl, J. Ecker, S. Hazen, T. Juenger, T. Kellogg, J. Leach, S. Merchant, S. Moose, S. Rhee, B. Schmitz, G. Stacey.

  • Synthetic Biology User Advisory Committee

    Members include R. Bailey, D. Cameron, S. Chandran, J. Flatt, J. Keasling, M. Palmer, E. Sattely, E. Shank, and D. Weller.

  • Scientific User Advisory Committee (SAC)
  • Informatics User Advisory Committee
  • Fungal Program User Advisory Committee
  • Prokaryotic Super Program User Advisory Committee
  • Plant Program User Advisory Committee
  • Synthetic Biology User Advisory Committee
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