DOE Joint Genome Institute

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

    More

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

    More

    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

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

    Listen

    A light green shrub with spiny leaves, up close.
    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.

    Listen

    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.

    More

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

    More

    Abstract image of gold lights and squares against a black backdrop
    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.

    More

    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.

    More

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

    More

    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.

    More

    croppe image of the JGI helix sculpture
    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.

    Listen

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

    More

    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.

    More

    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.

    More

News & Publications
Home › News Releases › Symbiosis a Driver of Truffle Diversity

November 14, 2018

Symbiosis a Driver of Truffle Diversity

Insights from a comparative analysis of five truffle-forming fungal species.

Truffe noire du Peěrigord (Tuber melanosporum). (Francis Martin)

The Périgord black truffle (Tuber melanosporum), first truffle to have its genome sequenced. (Francis Martin)

While the sight of black or white truffles being shaved over on pasta is generally considered a sign of dining extravagance, they play an important role in soil ecosystem services. Truffles are the fruiting bodies of the ectomycorrhizal (ECM) fungal symbionts residing on host plant roots. In many Ascomycota and Basidiomycota lineages, truffle-forming species have evolved independently in nearly every major group. This suggests that symbiosis drives evolution of truffle diversity and selects for specific traits.

A team led by Francis Martin and his colleagues at the French National Institute for Agricultural Research (INRA), Genoscope, and University of Torino, and including researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, sought insights into the ECM lifestyle of truffle-forming species. As reported in Nature Ecology & Evolution, the team conducted a comparative analysis of eight Pezizomycete fungi, including four species prized as delicacies.

A Decade of ECM Symbiosis Studies

The underground networks that link ECM fungi and their host plant roots shape these ecosystems, impacting the plant’s health and tolerance to stressors such as drought or disease, as well as the global carbon cycle. Studies have suggested that ectomycorrhizal fungi may slow soil carbon cycling down by limiting nitrogen. The fungi absorb mineral nutrients from the soil and exchange them for sugars that plants produce through photosynthesis.

Through the JGI’s Community Science Program, JGI de novo sequenced the genomes of two truffle-forming fungi: the Pig truffle (Choiromyces venosus) and, the Desert truffle (Terfezia boudieri) as well as of two other Pezizomycetes not forming truffles: Ascobolus immersus and Morchella importuna. These four genomes as well as the genome of the Piedmont white truffle (Tuber magnatum) were annotated through the JGI’s pipeline. The genome of the Burgundy Truffle (T. aestivum) was sequenced by Genoscope.

The work builds on earlier fungal symbiosis studies involving the first ECM fungal genome (Laccaria bicolor, sequenced a decade ago by the JGI), and the first truffle genome (T. melanosporum) sequenced by Genoscope, which is part of this analysis. “We have learned from the Laccaria bicolor and Tuber melanosporum genome that the ECM symbiosis evolved by the massive loss of genes involved in plant cell wall degradation (CAZymes) and de novo innovation of communication proteins, such as the mycorrhiza-induced small secreted proteins controlling the host plant immunity,” said study senior author and longtime JGI collaborator Martin. In a 2015 study with the JGI, Martin and his colleagues then showed that ECM species evolved from saprotrophs that feed on decaying organic matter, and that these evolutionary patterns are present in many Basidiomycota groups.

Truffle orchard in Lorraine, France. (Francis Martin)

Truffle orchard in Lorraine, France. (Francis Martin)

“Here,” Martin added, “we showed that the loss of genes involved in lignocellulose/plant cell wall degradation (CAZymes) and a higher evolution rate of symbiosis-related orphan genes have shaped the genomes of pezizomycetes truffles, one of the oldest/basal clade of ectomycorrhizal Ascomycota. This means that similar evolutionary mechanisms have independently driven symbiosis in Ascomycota and Basidiomycota. We also showed that developmental and metabolic pathways expressed in ectomycorrhizal roots and fruiting bodies of the white (T. magnatum) and black (T. melanosporum) truffles are unexpectedly very similar, owing to the fact that they diverged ~100 million years ago.”

Scenting Next Steps

Detecting and disseminating these underground delicacies depends on trained animals scenting the distinctive odors of truffles. Martin and his team suggest the volatile organic compounds that produce these scents may also be altered by the microbial communities flourishing into truffles.

‘In addition to the small secreted proteins critical for fungal interactions with their plant hosts these small molecules encoded in the truffle genomes by clusters of secondary metabolite genes offer another channel of communications between fungi and the environment,” added Igor Grigoriev, the JGI Fungal Program head. He concluded: “Thus, the sequenced genomes open doors for exploration of multi-dimensional fungal plant interactions.”

Researchers from the following institutions also participated in this study: Chinese Academy of Medical Sciences; Hungarian Academy of Sciences (Hungary); National Research Council – Institute for Sustainable Plant Protection (Italy); University of Parma (Italy); Aix-Marseille Université (France); UOS di Perugia (Italy); University of L’Aquila (Italy); Université Paris-Sud (France); Université de Montpellier (France); Ben-Gurion University of The Negev (Israel); Goethe University Frankfurt (Germany); Ruhr-Universität Bochum (Germany); Institute of Microbiology of the CAS (Czech Republic);  University of Bologna (Italy); Oregon State University; Centre National de la Recherche Scientifique (France); University of California, Berkeley; King Abdulaziz University (Saudi Arabia); Beijing Forestry University (China).

 

Publication: Murat C et al. Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle. Nature Ecology & Evolution. 2018 Nov 12. doi: 10.1038/s41559-018-0710-4.

Nature Ecology & Evolution BEHIND THE PAPER: Truffle Hunting, Genome Sequencing & Gastronomic Delicacies

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:

JGI announces 2023 CSP Functional Genomics awardees

Digital index card with JGI logo reads: Community Science Program (FY23) Congratulations to our CSP Functional Genomics recipients! Picture from left to right: (top) Thom Booth, Gabriel Castrillo, Han Li; (bottom) Jorge A. Marchand, Emre Özdemir, Fong Tian Wong

Researching and Solving Real-World Problems with the 2023 JGI-UC Merced Interns

2023 JGI-UC Merced interns (Zhong Wang/Berkeley Lab)

RECAP: Multi-Omic Journeys with 2023 JGI Annual Meeting Keynotes

Bruce Hungate stands at a podium and gesticulates as he discusses microbes.

For the Tiniest Archaea, A Genomic Switch of Friend or Foe

A grey microscopy photo taken at micron-scale. Microbes shown are small, round and slightly spiky in shape.

Doubling Down on Known Protein Families

An illustration of a microscope emitting a beam of light that hits a small, nondescript item.

The JGI announces 2024 awardees for our Community Science Program annual call

A series of headshots: From left to right: [above] Olivia Ahern, Adriana Corales, Hugh Cross, Megan DeMarche, Joanne Emerson, Matthew Hudson, Megan Keller and Julia Kelliher; [below] Vassili Kouvelis, Seppe Kuehn, Tesfaye Mengiste, Egbert Schwartz, Hannah Schulman, Bram Stone and Jana Voriskova
  • 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