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    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

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    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

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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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    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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    screencap long reads webinar_ Metagenome Program
    Utilizing long-read sequencing for metagenomics and DNA modification detection webinar
    Watch the webinar on how the JGI employs single-molecule, long-read DNA sequences to aid with genome assembly and transcriptome analysis of microbial, fungal, and plant research projects.

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    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

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    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

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    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

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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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Our Science
Home › Our Science › Science Programs › Fungal & Algal Program › Genomic Encyclopedia of Fungi

Genomic Encyclopedia of Fungi

The Genomic Encyclopedia of Fungi is the key project of the JGI Fungal Genomics Program to focus fungal genome sequencing in the areas of:

  • Plant Feedstock Health
    • Mycorrhizal Symbiosis
    • Plant Pathogenicity
    • Biocontrol
  • Biorefinery
    • Lignocellulose Degradation
    • Sugar Fermentation
    • Industrial Organisms
  • Fungal Diversity

Plant health maintenance is critical for sustainable growth of biofuel feedstock and fungi, as symbionts, pathogens, and biocontrol agents, dramatically affect plant health.

Symbionts such as mycorrhizae can increase productivity of bioenergy feedstock plants. Mycorrhizae enter symbiotic relationships with plants and effectively extend the host root system towards regions of decaying organic matter to provide nutrients such as nitrogen and phosphorus. Optimizing feedstock plant growth therefore is dependent on understanding molecular mechanisms of interactions between plants and mycorrhizae.

Pathogens can have dramatic negative effects on bioenergy crops as witnessed with the 1970 epidemic of corn leaf blight. Understanding mechanisms of virulence and pathogenicity, host specificity and the life cycle of pathogenic fungi hold keys to developing methods to control growth of pathogenic fungi and protecting plants. Feedstock protection can also be achieved by biocontrol fungi, which kill fungi, nematodes, and insects pathogenic to plants and are attractive alternatives to the chemical treatments used now.

Comparing genomes of pathogenic and symbiotic fungi to closely related fungi that lack these features will help find specific traits from each group of fungi and will help to understand the mechanisms of their interaction with plants. Reference genomes of mycorrhiza and other soil-inhabiting fungi will also facilitate comprehensive metagenomics studies of the rhizosphere, studies which until now have been mostly limited to bacterial communities.

Biorefinery methods convert biopolymers such as cellulose into simple sugars (eg, glucose and xylose) and then into biofuels employing fungal hosts optimized for large scale industrial processes. Knowing the enzymes and processes employed by diverse fungi in lignocellulose degradation and sugar fermentation as well as understanding the molecular biology of strains adopted by industry are essential for development robust platforms for biomass-to-biofuel production on an industrial scale. Genome sequencing in this area will provide a comprehensive catalog of enzymes, metabolic processes, and regulatory and secretory mechanisms. Resequencing of industrial strains should help to map desirable properties such as morphology, hyperproductivity, thermostability to genomic blueprints.

Fungal diversity. Over a million species in the Kingdom Fungi have evolved over millions of years to occupy diverse ecological niches and have accumulated an enormous but yet undiscovered natural arsenal of potentially useful innovations. While the number of fungal genome sequencing projects continues to increase, the phylogenetic breadth of current sequencing targets is extremely limited. Exploration of phylogenetic and ecological diversity of fungi by genome sequencing is therefore a potentially rich source of valuable metabolic pathways and enzyme activities that will remain undiscovered and unexploited until a systematic survey of phylogenetically diverse genome sequences is undertaken.

  • Plant Program
  • Fungal & Algal Program
    • MycoCosm Fungal Portal
    • PhycoCosm Algal Portal
    • Genomic Encyclopedia of Fungi
    • 1000 fungal genomes
    • Benchmarks
    • Fungal & Algal Publications
  • Metagenome Program
  • Microbial Program
  • DNA Synthesis Science Program
  • Metabolomics Program
MycoCosm, the fungal genomics resource.

MycoCosm, the fungal genomics resource.

PhycoCosm, the algal genomics resource

PhycoCosm, the algal genomics resource.

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