DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    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.

    More

    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

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

    More

    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    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.”

    More

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    screencap from Amundson and Wilkins subsurface microbiome video
    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.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

News & Publications
Home › News Releases › How Scavenging Fungi Became a Plant’s Best Friend

November 25, 2013

How Scavenging Fungi Became a Plant’s Best Friend

Glomeromycota is an ancient lineage of fungi that has a symbiotic relationship with roots that goes back nearly 420 million years to the earliest plants. More than two thirds of the world’s plants depend on this soil-dwelling symbiotic fungus to survive, including critical agricultural crops such as wheat, cassava, and rice. The analysis of the Rhizophagus irregularis genome has revealed that this asexual fungus doesn’t shuffle its genes the way researchers expected. Moreover, rather than having lost much of its metabolic genes, as observed in many mutualistic organisms, it has expanded its range of cell-to-cell communication genes and phosphorus-capturing genes.

Image: Spores and hyphae (root-like extensions) of an AMF, R. irregularis, grown among carrot hairy roots. Photo by Guillaume Bécard (University of Toulouse).

Image: Spores and hyphae (root-like extensions) of an AMF, R. irregularis, grown among carrot hairy roots. Photo by Guillaume Bécard (University of Toulouse).

A team led by the French National Institute for Agricultural Research (INRA) and including researchers from the Department of Energy Joint Genome Institute (DOE JGI) reported the complete genome of R. irregularis (formerly Glomus intraradices) in a paper published online November 25 in the journal Proceedings of the National Academy of Sciences (PNAS http://bit.ly/PNAS-Glomus). The fungus is a member of the Glomeromycota family and frequently colonizes many plants important to agriculture and forestry. Glomeromycota, also called arbuscular mycorrhizal fungi (AMF), play a vital role in how phosphorus and carbon cycles through the atmosphere and land-based ecosystems, but exactly how it does this vital job is poorly understood.

“This is the first sequenced genome of arbuscular mycorrhizae, the type that is dominant on the planet,” said Igor Grigoriev, one of the senior authors on the paper and lead for the Fungal Genomics Program at the DOE JGI.

It was a long hard road to a sequenced arbuscular mycorrhizal fungus. In 2006, shortly after the DOE JGI sequenced the first tree genome, Populus trichocarpa, it became apparent that it takes a village (of other organisms) to raise a poplar tree. Researchers Jerry Tuskan of Oak Ridge National Laboratory and Francis Martin of INRA recommended that the assembly of Populus-associated fungi and bacteria be sequenced to inform research on perennial plant growth, ecosystem function and plant microbe interactions. This long passage is outlined in an earlier publication in New Phytologist. Rhizophagus irregularis, is the next in this linage to be released by the DOE JGI, it follows the ectomycorrhizal fungal symbiont Laccaria, the poplar rust pathogen Melampsora, and dozens of bacterial genomes.

A relic of fungal evolution, AMF diverged early on from other forms of fungus. They form dense clusters of branched structures — called arbuscules — in root cells, much like a tight, many-fingered handhold. The arbuscules are the main route of nutrient exchange between plants and fungi.  Unable to live on their own, AMF are entirely dependent on their plant hosts for the sugars they need for food. They have carefully established their relationship with host plants, keeping them alive while sapping nutrients from them.

But AMF are also adept at capturing phosphorus from the soil and making it available for their hosts. Phosphorus, a critical element for cellular function, is otherwise difficult to extract from the soil and is often the limiting factor for how quickly a plant grows.

Scientists theorize that the benefits these fungi provided enabled ancient plants to evolve during the Paleozoic era, about 250 to 500 million years ago. Over time, plants adapted their essentially rootless primordial form and developed deeper and stronger roots to take advantage of the nutrients that underground AMF fed them. In exchange, plants provided nutrients the fungi couldn’t obtain themselves.

Analysis of the R. irregularis genome also revealed several surprising details. The research team found that the genome is among the largest fungal genomes sequenced, weighing in at 153 million base pairs (Mb). For comparison, the button mushroom (Agaricus bisporus), also sequenced and published by the DOE JGI, has a genome of about 30 Mb. Through several generations, portions of R. irregularis’s genome were duplicated, invaded by repeated transposable elements, famously known as ‘jumping genes’. Unlike many other fungi, R. irregularis seems to lack mechanisms that can keep these transposable elements from running amok.

“Among the expanded portions of its genome, R. irregularis had several genes for phosphorus metabolism, which are probably responsible for its large appetite for phosphorus,” said Francis Martin, one of the senior authors on the paper and lead for the Cluster of Excellence, Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE) at the INRA (http://mycor.nancy.inra.fr/ARBRE/). “They also have an abundance of genes for communication between cells via signaling proteins, including small secreted effectors highly expressed during symbiosis. Plant roots send out a plethora of chemical signals and these genes probably help AMF interact with plants, picking up the signals plants pump out.”

Another surprise for the research team was in the genes that govern metabolism. “Obligate parasites often have broken metabolism, missing some genes in critical metabolic pathway which make them dependent on their host,” Grigoriev said. “We did not find such genes here.” R. irregularis has retained much of its metabolic machinery, unlike many other obligate parasitic organisms. It leads a double-life, extracting minerals from the soil while still living in harmony with its host plant.

Though it has nearly 30,000 protein-encoding genes, R. irregularis has also lost hundreds of genes as a result of its close association with plants. For example, it can’t make most of the toxins other plant-interacting fungi release, probably, the researchers speculate, to avoid setting off the host plant’s immune system. It has also cast off most of its genes for breaking down plant cell walls, a critical ability for free-living fungi that feed off dead organic matter in soils.

Teasing apart the complex relationship between soil fungi and plants is likely to have an impact on improving biofuel production from plant biomass. “Through analysis of this and other mycorrhizal genomes, we can help to better understand interactions and conditions critical for a sustainable growth of bioenergy plants, but also staple crops, a prerequisite to help feeding the world,” said Martin.

Learn more from researchers Grigoriev, Martin and other collaborators on the importance of fungal genomics in this video: http://bit.ly/JGI-Fungal-vid.

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.

Tracing the Evolution of Shiitake Mushrooms

A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.

JGI announces final round of 2022 Functional Genomics awardees

Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI at 25: Mapping Switchgrass Traits with Common Gardens

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • 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

© 1997-2023 The Regents of the University of California