This year, the JGI helped a collaborative team produce a pangenome for Sorghum bicolor — a collection of many, many sorghum genome sequences. Lined up and analyzed consistently, these data let researchers compare and learn from a range of different versions of this plant. This opens the door to growing sorghum — and other crops — to more effectively produce biofuels and bioproducts.

In the episode, Nadia Shakoor (Donald Danforth Plant Science Center) walks us through growing sorghum from around the world, and the automated phenotyping that made this project possible. John Lovell (HudsonAlpha) and Jeremy Schmutz (JGI, HudsonAlpha) fill in more details of why we’ve long needed a pangenome, and what allowed this project to happen. And keep an eye out for the next episode, which will focus on the analysis behind this project.

Nature: A sorghum pangenome reference improves global crop trait discovery

Phytozome: SorghumPan, the Sorghum bicolor Pan-Genome Reference

Episode chapters:

0:00 The remarkable range of Sorghum bicolor

3:36 Why study sorghum

5:06 Getting from the BTX623 reference to a pangenome

9:50 How this pangenome became possible

12:19 Nadia Shakoor’s JGI-supported CSP New Investigator projects

15:31 Sourcing sorghum lines from all over the world

19:20 Automated phenotyping with drone flyovers

21:40 Next questions

Another episode on sorghum: Back to the Future! A Sorghum Story

A piece on the sorghum pangenome: A Sorghum Pangenome Opens More Doors to Discovery

Submit your own proposal to work with the JGI: http://jointgeno.me/proposals

Episode Transcript: https://jgi.doe.gov/user-science/podcasts/spectrum-sorghum

Our contact info: jgi-comms at lbl dot gov

Sound effects credit: Outdoor Suburb Summer.aif by timgormly -- -- License: Attribution 4.0

For years, researchers have known that many datasets miss a key part of microbial genomes: the mobile genetic elements, or MGEs, that can move between organisms. But now, deep sequencing and new analysis methods are bringing this mobilome into light, and opening up new options for engineering these microbes in the future. Join Sarah Bagby (Case Western Reserve University) and Simon Roux (JGI) as they talk about their recent work on a time series from Sweden’s Stordalen Mire.

Nature Microbiology: Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Episode chapters:

0:00 Intro

4:10 Meet our researchers, and MGEs

6:34 The galaxy of possibilities that MGEs open

8:15 Why MGEs have escaped analysis before

11:06 How a long time series gives a clearer look at MGEs

14:10 Stordalen Mire, a dynamic sample site

17:37 What they did, and what they saw

25:47 Pieces — like the JGI’s sequencing support — that enabled this

28:55 How this work fits in with JGI’s upcoming projects

31:39 Next questions they’d like to answer

Another episode on a time series: The Megadata of Lake Mendota — Part 3: Boating Out to David Buoy

Submit your own proposal to work with the JGI: http://jointgeno.me/proposals

Episode Transcript: https://jgi.doe.gov//user-science/podcasts/mobilome-mire

Our contact info: jgi-comms at lbl dot gov

Stable Isotope Probing (SIP) is a powerful technique for studying microbial communities. These experiments can show which microbes are handling specific nutrients, or what they're doing with those nutrients, and even how quickly. But there's a catch: SIP labwork and analysis can be very demanding.

The JGI offers SIP analysis to make these experiments accessible to more researchers. Ultimately, the goal is to generate SIP data that can be useful to multiple teams and analyses.

This episode, Rex Malmstrom (JGI), and Roli Wilhelm (Purdue University), share a few different ways they're working to make this technique, SIP, more standardized -- more reproducible, more reusable, and more insightful, for the future of studying microbial communities.

Links from this episode:

• Submit your own proposal to work with the JGI
• Find all episode transcripts on our website

• JGI’s Micro-Scale Applications Group
• MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment
• HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

• Webinar: Metagenome quantitative SIP at the JGI: https://www.youtube.com/watch?v=5OgLDTw7eYA

• Genome Insider: Party in the Rhizosphere
• Genome Insider: A Powerful Technique to Study Microbes, Now Easier

• Simulating metagenomic stable isotope probing datasets with MetaSIPSim

• Microbes Persist: Systems Biology of the Soil Microbiome Science Focus Area (SFA), led by Dr. Jennifer Pett-Ridge at Lawrence Livermore National Laboratory (LLNL)
  • Our contact info:
• X: @JGI
• Email: jgi-comms at lbl dot gov