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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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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
  • Secondary Metabolites
MycoCosm, the fungal genomics resource.

MycoCosm, the fungal genomics resource.

PhycoCosm, the algal genomics resource

PhycoCosm, the algal genomics resource.

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