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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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November 7, 2013

Why sequence metagenomic approach to managed wetland “carbon farming”?

Wetlands store more carbon per unit area than any ecosystem, and wetland restoration is a means by which society can sequester carbon, reduce flood dangers and improve wildlife habitat and water quality, yet the microbial communities inhabiting freshwater wetlands are only minimally characterized. This first-of-a-kind carbon sequestration project will employ metagenomic, metatranscriptomic and single-cell sequencing… [Read More]

November 6, 2013

Why sequence soda lake and soil metagenomics?

Sequencing the metagenomes of microbial communities that inhabit soda lakes and soda solonchak (salt marsh) soils will uncover the microbial diversity of these extreme environments, and provide insight into the molecular mechanisms for adaptation to high pH and high salinity, the CO2-uptake mechanisms, and the pathways that generate energy from sulfur compounds. In addition, the… [Read More]

November 6, 2013

Why sequence marine bacteria-dinoflagellate interactions?

Interactions between marine bacteria and phytoplankton influence the fate of one of the largest active carbon reservoirs on Earth. To explore these associations and understand how they influence they influence the release of climate-relevant gases from the ocean to the atmosphere, this project focuses on a transcriptomic analysis of a bacteria-dinoflagellate model system in which… [Read More]

November 6, 2013

Why sequence metagenomics in freshwater lakes?

Aquatic microbial communities represent one of the largest reservoirs of genetic and biochemical diversity on the planet, and metagenomic studies have led to the discovery of novel gene families and a deeper understanding of how microbial communities mediate the flow of carbon and energy. However, most of these studies have been based on a static… [Read More]

November 6, 2013

Why sequence sulfur cycling in the Frasassi aquifer?

The terrestrial subsurface remains one of the least explored microbial habitats on earth, and is critical for understanding pollutant migration and attenuation, subsurface processes such as limestone dissolution (affecting porosity), and the search for life elsewhere in the solar system and beyond. The deep and sulfidic Frasassi aquifer (of Ancona, Italy) has emerged as a… [Read More]

November 6, 2013

Why sequence topsoil metagenomics in arid lands?

Biological Soil Crusts (BSC) are globally relevant complex topsoil microbial communities and locally important agents of carbon cycling in arid lands. Because arid lands make a sizeable proportion of all continents, the global standing carbon stock in BSCs probably exceeds 1014 g C, making soil crusts arguably the most extensive biosynthetic biofilm on the planet…. [Read More]

November 6, 2013

Why sequence microbial communities in expanding dead zones?

Oxygen minimum zones (OMZs) are widespread oceanographic features expanding due to global warming. There is increasing evidence that ocean warming trends will decrease dissolved oxygen concentrations, causing hypoxic boundary layer expansion that impacts the global carbon cycle, marine nutrient cycles and the climate system. To properly diagnose these transitions, this project launches a systems-level investigation… [Read More]

November 6, 2013

Why sequence a metagenomic survey of hydrothermal vents?

Deep-sea hydrothermal vents are one of the premier locations for discovering a wide diversity of novel non-photosynthetic microorganisms capable of fixing carbon dioxide at the most extreme conditions within our biosphere. This project represents the first comprehensive metagenomic survey of hydrothermal vent microbial communities, in part to develop an extensive metagenomic database to enable the… [Read More]

November 6, 2013

Why conduct the comparative analysis of shipworm microbiome?

Wood-boring bivalves are only marine animals known to sustain normal growth and reproduction feasting solely on wood. The shipworm has two bacterial populations that can break down lignocellulose, one in the gut and the other in a specialized organ in the gills. The DOE JGI sequenced the only shipworm species adapted to cold water as… [Read More]

November 6, 2013

Why sequence marine sediments from high-latitude regions?

High-latitude regions are often seen as being relatively pristine areas due to their remote location and low population densities, but human activities are affecting these regions dramatically at a global and local scale. This project considers microbial communities of cold polluted coastal sediments from four geographically distant regions, in part to potentially identify key environmental… [Read More]
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