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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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Our Projects
Home › CSP Plans
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October 3, 2018

Finishing Genomes to Leverage Additional Information

Genomes of important model and many industrially important fungi are still incomplete. The goals of this project are: (a) to finish and annotate the genomes of ~25 strains; and, (b) to carry out functional analyses by novel CRISPR/Cas9 approaches. The next quantum leap in biology will come by integrating all levels of genome, transcriptome, proteome,… [Read More]

October 3, 2018

Insights into Functional Diversity in Neurospora

Morphological diversity of Sordariales growing in the lab. Pierre Gladieux's proposal explores functional diversity in Neurospora and its relatives. (Pierre Gladieux, INRA Montpellier)This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi. The proposal fits into the DOE mission because it focuses on biological processes of industrial interest, it explores the functional diversity… [Read More]

October 3, 2018

Marine Angiosperm Genome Initiative

Seagrasses are the only flowering plants that live in the sea. Understanding the genomic basis for their many unique adaptations is fundamental to successful management, as seagrasses are being lost globally. Seagrasses are among the world’s largest carbon sinks and thus relevant to the DOE missions carbon cycling, biogeochemistry and JGI plant flagship genomics. Translational… [Read More]

October 3, 2018

Sphagnum Microbiome Genetic Interactions

The importance of plant-microbiome systems on carbon and nitrogen processes is perhaps most pronounced in Sphagnum moss dominated ecosystems, which occupy 3% of the Earth’s land surface yet store approximately 25% of terrestrial carbon. Much of the nitrogen needed to support Sphagnum comes from a symbiosis with microbes, yet we don’t know how the symbiosis… [Read More]

October 3, 2018

Microbial Methane Production in Freshwater Wetlands

Increasing atmospheric concentrations of greenhouse gasses like methane are altering the global climate, causing catastrophic wildfires, storm events, and drought. This proposal targets microbial methane production in freshwater wetland soils, as this production is the largest natural source of methane. Results from this proposal can improve greenhouse gas predictions across the globe. Additionally, this research… [Read More]

October 3, 2018

Genome Level Diversity in Brassica rapa

To avoid competing with land use for food crops, biofuel crops are often grown on marginal land. Understanding how to improve soil health and provide enhance stress tolerance traits is essential for improving biofuel production. This study aims to explore the genome level diversity that exists in the important crop model Brassica rapa, a relative… [Read More]

October 3, 2018

Roles of Microbial Communities in the Atacama Desert

At the Heradura Playa in Atacama Desert of Chile. Alessandro Airo's team is interested in the Atacama's microbial communities. (Courtesy of A. Airo)The hyperarid core of the Atacama Desert (Chile) is one of the driest deserts on Earth. Its soils represent one of the few environment types that yet have barely been investigated at the level of metagenomics. Due to the extremely low content of biomass these Atacama Desert sediments have been claimed to be Mars-like. We… [Read More]

October 3, 2018

Exploring Seaweed Genome Diversity

Exploring algal biodiversity for biotechnological applications is the focus of Bradley Moore's accepted proposal. (Courtesy of Bradley Moore)Seaweed represent a 6 billion dollar industry across the world, and are a source of many materials spanning the chemical and food sectors. Understanding how seaweeds construct these molecules will allow us to harness their biosynthetic machinery in the biomanufacturing of fuels, lubricants, polymers, and other commodity and specialty chemicals. To help us understand the… [Read More]

October 3, 2018

Infections and Host-Pathogen Interactions of Chlorella

Vampirovibrio chlorellavorus in yellow on green host. (Courtesy of Judith Brown)The non-photosynthetic, predatory cyanobacterium Vampirovibrio chlorellavorus (Melainabacteria) is a globally important obligate pathogen of Chlorella species/strains of interest as biofuel feedstocks. This project proposes two sequencing approaches to generate information for querying: (i) pathogen and host genomics; and, (ii) the mode of infection and host reaction to infection via transcriptomics); and, (iii) explore evolution and… [Read More]

October 3, 2018

Nitrate in Coastal Waters

The proposal calls for metagenomic and metatranscriptomics sequencing, and metabolomics analysis from salt marsh sediments exposed to a decade of chronic anthropogenic nitrate enrichment. These sediments are part of a multi-PI research project at the Plum Island LTER where the team has been fertilizing two whole salt marsh creeks since 2004, while maintaining two additional… [Read More]
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