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    John Vogel with Brachypodium plants at the DOE JGI. (Roy Kaltschmidt, Berkeley Lab)
    Grasses: The Secrets behind Their Stomatal Success
    Grasses have two guard cells that swell to create the stomate and two subsidiary cells flanking the guard cells, which may be linked to improved stomatal physiology. The unique subsidiary cells in grasses may allow for enhanced performance when stressors such as drought are placed on the plant.

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    Researchers investigated Tulasnella calospora as both a free-living mycelium and in symbiosis with the photosynthetic orchid long-lipped serapias. (Ziegler175, Wikimedia Commons, CC BY-SA 3.0)
    Nitrogen Uptake Between Fungi and Orchids
    Orchids are an example of an experimentally tractable plant that is highly dependent on its relationship with its mycorrhizal fungal partners for nutrient supply. For the first time, researchers identified some genetic determinants potentially involved in nitrogen uptake and transfer in orchid mycorrhizas.

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    The newly discovered CRISPR-CasY system was found in bacteria from deep underground at Crystal Geyser in California. (Jill Banfield, UC Berkeley)
    Metagenomics Leads to New CRISPR-Cas Systems
    In a study led by longtime DOE JGI collaborator Jill Banfield of UC Berkeley, researchers report discovering for the first time, a CRISPR-Cas9 system in archaea, as well as of simple CRISPR-Cas systems in uncultivable bacteria.

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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
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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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    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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    Giant virus acquiring genes from different eukaryotic host cells. (Ella Maru studio, http://www.scientific-illustrations.com/)
    Discovered: Novel Group of Giant Viruses
    After discovering a novel group of giant viruses with a more complete set of translation machinery genes than any other virus known to date, DOE JGI scientists believe that this group (dubbed “Klosneuviruses”) significantly increases our understanding of viral evolution.

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A DOE Office of Science National User Facility

http://jgi.doe.gov/finding-major-gene-expression-regulator-fungi/
NEWS RELEASE: Finding A New Major Gene Expression Regulator in Fungi
http://jgi.doe.gov/discovered-novel-group-of-giant-viruses/
NEWS RELEASE: Discovered: Novel Group of Giant Viruses
http://jgi.doe.gov/events/2017-microbial-plant-systems-modulated-secondary-metabolites-meeting/
REGISTER for the 2017 Secondary Metabolites Meeting
http://jgi.doe.gov/about-us/progress-report/
YEAR IN REVIEW: Check out the 2016 JGI Progress Report
The Integrative Genomics Building at LBNL: Future Home of JGI
The Integrative Genomics Building at Berkeley Lab
Home of JGI and KBase in 2019 [click to see construction progress]

Latest News

May 26, 2017

Fungal Enzymes Team Up to More Efficiently Break Down Cellulose

May 8, 2017

Finding A New Major Gene Expression Regulator in Fungi

April 6, 2017

Discovered: Novel Group of Giant Viruses

Latest JGI News Releases

Announcements

Register Now: Microbial and Plant Systems Modulated by Secondary Metabolites Meeting is July 24-26, 2017

Register Now: Mining Microbial Genomes and Metagenomes for Biotechnological Applications Workshop is July 30, 2017 at SIMB Meeting

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Featured Video

Science Highlights

April 28, 2017

A Gene that Influences Grain Yields in Grasses

Field of Setaria viridis growing in western Nebraska. In the current issue of Nature Plants Huang and colleagues use Setaria viridis to identify the inflorescence mutant, sparse panicle 1. A mutation in the maize ortholog conditions a very similar panicle defect, demonstrating the utility of S. viridis for gene discovery in the panicoids. (Pu Huang)

Genetic screen identifies mutations that impact green foxtail panicle formation. The Science Through deep sequencing of the model grass green foxtail (Setaria viridis), researchers pinpointed a gene critical for the development of flowers that give rise to the grain. Using this information, a … [Read More]

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