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
    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

    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.

    More

    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

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

    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

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

    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.

    More

    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

  • 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

    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 › Podcasts › JGIota: Looking Back at Sequencing for Soybeans

September 15, 2022

JGIota: Looking Back at Sequencing for Soybeans

The soybean is a crop that could boost biofuels and fertilize fields. So in 2010, the JGI helped publish the original genome sequence for the soybean, Glycine max. With a full genome sequence, researchers have been able to look into soybean’s strengths – along with a fungus that threatens this important crop. Hear more about that work from researchers Gary Stacey (University of Missouri), Peter van Esse (The Sainsbury Laboratory) and Sebastien Duplessis (INRAE).

Find show notes here

Get the RSS FeedListen on Apple Podcasts

Episode Transcript:

Allison: And now, a JGIota – a snippet about JGI-related research, tools, people, discoveries and more. I’m Allison Joy, your host for this Iota.

Allison: For 25 years, the JGI has been supporting genomics research. In honor of this year’s 25th anniversary celebration, we’re taking a look back at all kinds of species JGI researchers have studied. And today, we’re focusing on soybeans.The soybean plant is a flagship genome of the JGI’s Plant Program, and there’s a major reason researchers study it. 

Gary Stacey: There’s a huge market for soybean oil.

Allison: Gary Stacey is a professor of plant science and technology at the University of Missouri. And he knows about the soybean oil market, because he’s been studying soybeans for decades. Specifically, soybean crops. The kinds of plants that leave fields and become biodiesel.  

Gary Stacey: Since it’s renewable, then it’s a green fuel. And, and of course in transportation now we’re moving to electric cars, and so on and so forth. There’s still a lot of thinking that truck fuel and airplane fuel and things like that are not going to be replaced by electricity anytime soon. And so there’s going to be a need for these biofuels. And that’s a good niche market for soybean oil.

Allison: Right now, about a third of the soybeans grown in the US become biodiesel. But with federal mandates pushing growers toward more biofuel production, that share is set to grow. And there are other environmental and energy reasons for growers to fill fields with soybeans. 

Gary Stacey: Soybean has another impact on the environment from the standpoint of reducing the need for nitrogen fertilizer. About 1% of the global energy use actually goes to produce nitrogen fertilizer.

Allison: Nitrogen is an essential nutrient for all kinds of crops.But nitrogen fertilizers can be hard on the environment — they often make their way out of the field and into our waterways and beyond. We also burn natural gas to create it, using multiple finite resources. Soybean plants, on the other hand, function like a fertilizer in plant form. They pull nitrogen from the air into fields – it’s a process called nitrogen fixation. Basically, the soybean plants leave behind nutrients that other crops can use.  

Gary Stacey: And so soybean then contributes to the sustainability of cropping systems. 

Allison: So Gary and other researchers have been working to understand the soybean plant, to pave the way for stronger soybeans and bigger crop yields. He and collaborators published the original sequence for the soybean genome in the journal Nature in 2010, and Stacey’s work on the legume continues. 

Gary Stacey: We’ve been studying the questions of interest to us, like symbiotic nitrogen fixation, but we’ve been applying the knowledge of the genome sequence to that.

Allison: With the soybean genome sequenced, researchers have also looked at another key part of getting the most out of soybean crops: keeping the plants themselves healthy. Which has brought them not just to soybeans, but to the kinds of diseases they’re prone to. To that end, the JGI has helped researchers study the most devastating soybean pathogen out there: a fungus called Phakopsora pachyrhizi that causes brown rust pustules to form on the leaves of a plant. 

Peter van Esse is a group leader with The Sainsbury Laboratory in the UK. He’s part of a consortium working on this fungus.

Peter van Esse: The disease that I study can cause up to 80-90% yield loss if it’s not properly managed. 

Allison: But it’s not the easiest pathogen to study, for a number of reasons. First, the sheer size of its genome. The genome is 1.25 gigabasepairs, that’s billions of basepairs, in size, compared to other fungi which are usually around 50 megabasepairs, that’s millions of basepairs— which is a significant size difference. It also contains a lot of repetition, meaning, a lot of stuff just looks the same. And so what scientists are looking for, and really interested in, gets hidden. 

Also – it can’t really be grown in a lab. Here’s Sebastien Duplessis. He’s a researcher at the French National Institute for Agricultural Research or INRAE, working in the same consortium as Peter. 

Sebastien Duplessis: Compared to other fungi that we can cultivate on synthetic media, in laboratory conditions, this one has to be cultivated on the host

Allison: So they collected these fungi from soybean plants – the hosts themselves. JGI annotated not one but three separate genomes for the fungus.  

Peter van Esse: Now we have three isolates, annotated in exactly the same way, so there cannot be confusion about which gene is which. This is a very powerful data set and it’s gonna yield results for years to come. And we’re really, truly grateful for the JGI for enabling that to happen, because it’s really a treasure trove for the community.

Allison: And Peter says that work is already afoot with industry partners to develop resistance traits to soybean rust. 

Peter van Esse: One thing I find very powerful about the JGI actually is that they do this for a lot of diseases. People should not underestimate what a key resource that has been created and, and, what a national treasure it is actually.

Allison: Shucks, man – if it were possible to make an institution blush, that would do it. Well, that’s a wrap on this JGIota, but you can learn more about the JGI’s work related to soybean on our website and Youtube channel. We’ve also got a number of highlights on our website about other discoveries the JGI has made in its 25-year tenure. There’s a link in the show notes! 

This episode was written and hosted by me, Allison Joy! I had production help from Menaka Wilhelm, Massie Ballon and Ashleigh Papp.

If you liked this episode, help someone else find it! Tell them about it, send a link over, or leave us a review wherever you’re listening to the show. 

Genome Insider is a production of the Joint Genome Institute, a user facility of the US Department of Energy Office of Science located at Lawrence Berkeley National Lab in Berkeley, California.

Thanks for tuning in – until next time!

Show Notes

  • JGI@25 Stories
  • The original soybean sequence: Nature
  • Gary Stacey presents at the 2010 JGI Annual Meeting
  • Soybean on Phytozome
  • Phakopsora pachyrhizi on MycoCosm

 

  • Our contact info:
    • Twitter: @JGI
    • Email: jgi-comms at lbl dot gov

Genome Insider is a production of the Joint Genome Institute. 

 

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)
Genome Insider is available on Apple Podcasts, Google Play, Spotify, iHeart Radio, and TuneIn Radio - Subscribe today! Natural Prodcast is available on Apple Podcasts, Google Play, and Spotify - Subscribe today!

Filed Under: Podcasts Tagged With: genome insider, jgi25

More topics:

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

Related Content:

Genome Insider S4 Episode 1: Crops as Tough as World Cup Turf – James Schnable and Guangchao Sun

JGIota: A biofuel breakthrough in anaerobic fungi with Michelle O’Malley and Tom Lankiewicz

A Genome Insider Logo Image

JGIota: Sequencing Shiitakes with David Hibbett

A Genome Insider Logo Image

Natural Prodcast Episode 19 – Bill Fenical

Natural Prodcast Episode 18 – A CSP Primer

Natural Prodcast podcast logo

Genome Insider S3 Episode 5: Work With the JGI! Tips for a Winning CSP Proposal

A Genome Insider Logo Image
  • 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