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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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    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    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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    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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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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    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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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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    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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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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    image from gif that shows where in the globe JGI fungal collaborators are located.
    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

Fungal & Algal Program

The Fungal & Algal Program scales up sequencing and analysis of fungal and algal genomes to explore functional the characterization of stains that play a critical role in bioenergy and environmental research.

The Fungal & Algal Program, led by Igor Grigoriev, targets the large-scale sequencing and analysis of fungal and algal genomes to explore the diversity of fungi and algae. Encoded in the genomes of these organisms are biological mechanisms with relevance to the DOE missions in biofuels and bioproducts process development, the characterization of carbon cycling, and biogeochemistry. Combining new sequencing technologies and comparative genomics analysis, JGI works on large and complex sequencing projects such as surveying the broad phylogenetic and ecological diversity of fungi and algae, and capturing genomic variation in natural populations and engineered strains and promoting functional studies on a system level. This approach enables JGI to build a foundation for translating the genomic potential of fungi and algae into practical applications.

Fungal genomics: There are more than 1.5 million fungal species and they play a critical role in shaping the Earth’s ecosystems. A better understanding of pathogens and symbionts is critical for the sustainable growth of plants. Fungi are the most efficient degraders of plant biomass to enable conversion into bioenergy and bioproducts. Many new metabolic processes and enzymes are encoded in fungal genomes. Fungal genomics may offer answers to critical areas of research, including food, medicine, energy, and the environment.  (see examples here)

Diversity of algae and algae-related applications.

Algal genomics: Algae are a phylogenetically diverse group of eukaryotes that are collectively responsible for 50% of photosynthesis on Earth. The enormous phylogenetic and functional diversity of algae require a systematic genomics exploration to better understand their complex evolution, mechanisms of photosynthesis, and potential for bioenergy, bioproducts, and biomanufacturing. (see examples here)

Among the major initiatives of this program are:

  • MycoCosm, the JGI’s web-based fungal genomics resource, which integrates fungal genomics data and analytical tools for fungal biologists. It provides navigation through sequenced genomes, genome analysis in context of comparative genomics and genome-centric view. MycoCosm promotes user community participation in data submission, annotation and analysis.
  • PhycoCosm, the JGI algal genomics resource, which integrates genomics data and analytical tools.
  • Genomic Encyclopedia of Fungi, which focuses on aspects of plant feedstock health (including symbiosis, pathogenicity and biocontrol), biorefinery mechanisms (conversion of biopolymers to sugars for fuel production), and fungal diversity.
  • 1000 Fungal Genomes Project, a five-year international collaboration to sequence 1000 fungal genomes from across the Fungal Tree of Life.
  • Computational systems and methods

    • MycoCosm
    • PhycoCosm
    • Annotation Pipeline
    • Benchmarks
  • More about this program

    • Fungal and Algal Program Lead

 

  • 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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