DOE Joint Genome Institute

  • COVID-19
  • About
  • Phones
  • Contacts
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    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.

    More

    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.

    More

    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.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    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.

    More:

    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.

    Read more

    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.

    Read more

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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.

    More

    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.

    More

    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.

    Read more

  • User Programs
    • Calls for User Proposals
    • Special Initiatives & Programs
    • User Support
    • Submit a Proposal
    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.

    Read more

    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.

    Read more

    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.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Publications
    • Scientific Posters
    • Newsletter
    • Logos and Templates
    • Photos
    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 .

    More

    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.

    More

    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.

    Read more

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 scale-up 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 Group:
    • 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
MycoCosm, the fungal genomics resource.

MycoCosm, the fungal genomics resource.

PhycoCosm, the algal genomics resource

PhycoCosm, the algal genomics resource.

  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • RSS feed
  • Flickr
  • LinkedIn
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2021 The Regents of the University of California