Genome Insider

David Hibbett (Clark University) fills us in on the kind of decay that makes shiitake mushrooms special. This week, he 39 collaborators published a paper tracing how these mushrooms have evolved.

• Find all episode transcripts on our website
• Publication: Sierra-Patev S et al. A global phylogenomic analysis of the shiitake genus Lentinula. Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2214076120. doi: 10.1073/pnas.2214076120.  
• The Lentinula genomes are publicly available on JGI’s MycoCosm data portal

This work was supported by the JGI’s Community Science Program. Find out how to become a JGI User here: https://jgi.doe.gov/user-programs/ 

The JGI’s Community Science Program gives researchers access to all kinds of sequencing, ‘omics and bioinformatics capabilities — and it’s open to scientists at any career stage, anywhere in the world, for free. We accept new projects related to energy and the environment several times a year. A few proposal calls have deadlines coming up – in January, March, and later on in the spring.

In this episode, hear proposal tips from Tanja Woyke, who runs user programs at the JGI, and project manager Miranda Harmon-Smith, who helps shepherd CSP projects along. 

Find more information about proposal calls and capabilities on the JGI website, jgi.doe.gov. 

• Find all episode transcripts on our website

Links from this episode: 

• Community Science Program
• Webinars on JGI Product Offerings
  • Pro Tips for Successful CSP Applications
  • Accessing Functional Genomics Capabilities
• JGI Calls for User Proposals 
• Our contact info:
  • Contact our Project Management Office with any questions about proposals
  • Twitter: @JGI
  • Email: jgi-comms at lbl dot gov

Back in 2011, JGI-supported researchers published a paper in the journal Science. They’d used metagenomics to sift for microbial genes encoding carbohydrate-chomping enzymes in cow rumen — and found 27,000 candidates. The data from that study is now used across California State University campuses for biotechnology education as part of a course-based undergraduate resource experience. Hear from CSU San Marcos Professor Matt Escobar and UC Davis Associate Professor Matthias Hess, also the chair of the JGI User Executive Committee, on how that study went from the lab to the classroom. 

Links from this episode:

• Find all episode transcripts on our website
• JGI@25 Stories
• Paper: Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
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• Our contact info:
  • Twitter: @JGI
  • Email: jgi-comms at lbl dot gov

Genome Insider is a production of the Joint Genome Institute. 

Every year, the JGI sequences around 35,000 samples — from plants, algae, bacteria, archaea, fungi, viruses — to support scientists around the world. Most of those researchers send their samples in from afar, without ever hearing much about the sequencing lab. So today, Chris Daum walks through the JGI’s sequencing pipeline, where there are freezers with names — but not doors — and robots handle a bunch of benchwork.

Links from this episode:

• Find all episode transcripts on our website
• Submit a proposal to work with the JGI
• Webinar: Long-read sequencing for metagenomics and DNA modification detection
• Our contact info:
• Twitter: @JGI
• Email: jgi-comms at lbl dot gov

Genome Insider is a production of the Joint Genome Institute. 

Sound Effects Credits: George Hopkins “Mechanical keyboard typing”

We count on livestock for food and fiber, but raising these animals also produces an atmosphere-warming gas: methane. Those emissions mainly come from gut microbes — the bacteria and archaea breaking down plant matter. So since 2010, the JGI has supported researchers studying those microbial methane-makers. Eventually, that could help us dial back their emissions, while still producing things like meat, milk, and wool. Hear more from JGI collaborators Sinead Leahy (New Zealand Agricultural Greenhouse Gas Research Centre) and Bill Kelly (AgResearch).

Links from this episode:

• Find all episode transcripts on our website
• JGI@25 Stories
• The JGI’s IMG/M data portal 
• Video: More on the AgResearch DNA sequencing of rumen microbes
• Our contact info:
  • Twitter: @JGI
  • Email: jgi-comms at lbl dot gov

Genome Insider is a production of the Joint Genome Institute. 

Black fungi are microscopic and mighty. They survive everywhere from Antarctica to Joshua Tree National Park, despite extremely harsh conditions. And their survival secrets could one day help other organisms survive hotter, drier climates. So University of Tuscia researchers Laura Selbmann and Claudia Coleine are working with scientists from around the world – and the JGI – to understand them better.

Links from this episode:

• Find all episode transcripts on our website
• Integrated Microbial Genomes and Microbiomes
• Submit a proposal to work with the JGI
• Our contact info:
  • Twitter: @JGI
  • Email: jgi-comms at lbl dot gov

Genome Insider is a production of the Joint Genome Institute. 

Some audio in the opening scene comes from an expedition Laura took to Antarctica. Laura.Selbmann©PNRA

All the sampling activities in Antarctica have been performed in the frame of italian expeditions of the Italian National Program for Antarctic Researches (PNRA),  funded by the Italian Ministry of University and Research; all specimens collected and fungi isolated are preserved in the Culture Collection of Fungi from Extreme Environment, the Italian National Antarctic Museum (MNA-CCFEE)

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).

Links from this episode:

• Find all episode transcripts on our website
• The original Glycine max sequence: Nature
• Our contact info:
  • Twitter: @JGI
  • Email: jgi-comms at lbl dot gov

Genome Insider is a production of the Joint Genome Institute. 

In this episode, we peer into plant cells. Researchers are using measurements from single cells to understand which genes help plants grow, get nutrients, weather drought, and more. And eventually, their findings could help us grow better crops, with less impact on our planet.

Links from this episode:

• Find all episode transcripts on our website
• Monet’s Waterloo Bridge at Sunset (1904)
• Serat’s A Sunday on La Grande Jatte (1884)
• Submit a proposal to work with the JGI: https://jointgeno.me/proposals 
• Margot’s 2021 Berkeley Lab SLAM talk 

Genome Insider is a production of the Joint Genome Institute. 

This episode uses two pieces of music from Free Music Archive: 

Sad French Accordion by Dana Boulé (CC BY-NC 4.0)

Sonata No. 20 in G Major, Op. 49 No. 2 - I. Allegro ma non troppo by Daniel Veesey (Public Domain)

This shorter episode is about a tiny, single-celled alga – Chlamydomonas reinhardtii – that’s managed to have a big impact. UC Berkeley plant biologist Sabeeha Merchant explains why she works on this alga, how researchers managed to sequence its genome, and what it has to teach us about other organisms – like plants. 

Links from this episode

• Find all episode transcripts on our website
• Chlamydomonas reinhardtii on Phytozome and PhycoCosm 
• The original sequence: Science

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

Genome Insider is a production of the Joint Genome Institute. 

We know all kinds of things about plastic – except, how to break it down for recycling. But some hungry insects can digest plastic. So researchers are taking a look at how these critters process plastic, to improve plastic recycling by following their lead. 

Links from this episode:

• Find all episode transcripts on our website
• Submit a proposal to work with the JGI!

Genome Insider is a production of the Joint Genome Institute. 

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Sound Effects Credits:

"Splash, Small, A.wav" by InspectorJ (www.jshaw.co.uk) of Freesound.org

“Water movements big splashes and waves” by KyleS of Freesound.org

“Fishing-rod” by KirstenBrooks3232 of Freesound.org

“By a Pond Ambience” by Cueckermann of Freesound.org

“Splash, edited” by MRicken1 of Freesound.org

“Fishing Rod Whip” by TyroneW of Freesound.org