Genome Insider

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

In this episode, undergraduates adopt genomes that the JGI sequenced, but never published in the literature. These students analyze the genomes, write reports, and publish first-author papers, making the data available for future research. 

Hear from Rekha Seshadri (JGI) and Matt Escobar (California State San Marcos) about how the Adopt-A-Genome project got started. Plus, Kalyani Maitra (California State Fresno) and two students, Angela and Mark Soghomonian share what it was like to take on one of these genomes.

Links from this episode:

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

• For more information about Adopt-A-Genome:
  • Rekha Seshadri: [email protected] 
  • Matt Escobar: [email protected] 

• Adopt-A-Genome Papers: 
  • Draft genome sequence of Nitrobacter vulgaris DSM 10236T
  • Draft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615T) and Butyrivibrio fibrisolvens DSM 3071 (D1T)
  • Genome sequences of key bacterial symbionts of entomopathogenic nematodes: Xenorhabdus cabanillasii DSM17905, Xenorhabdus ehlersii DSM16337, Xenorhabdus japonica DSM16522, Xenorhabdus koppenhoeferii DSM18168, and Xenorhabdus mauleonii DSM17908

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

Kasey Markel and Patrick Shih (UC Berkeley and the Joint BioEnergy Institute) are looking for new ways to engineer plants. So they’ve looked into wasps that program oak trees to grow structures called galls.

In this episode, hear from Kasey and Patrick about how this project unfolded, and how they worked with the JGI's metabolomics program to find out more about these weird little pods.

Links from this episode:

• Submit your own proposal to work with the JGI
• Join us at the 2024 JGI User Meeting

• Find all episode transcripts on our website
• Paper: Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls

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

• Sound effects credits: 
  • oars.wav by hazure
  • Parma Park Bird Song with Stream.WAV by muneio

To engineer yeast to do more, and understand genomes in general, Jef Boeke, Weimin Zhang (NYU Langone Health) and Leslie Mitchell (Neochromosome) have worked to replace yeast’s native chromosomes with synthetic versions. This project has turned out to be an international collaboration, with some artistic endeavors along the way. Eventually, the goal is to create an entirely human-generated yeast genome.

Links from this episode:

• Submit your own proposal to work with the JGI
• Join us at the 2024 JGI User Meeting

• Find all episode transcripts on our website
• Paper: Manipulating the 3D organization of the largest synthetic yeast chromosome
• NYU Release: Researchers Assemble Nine Synthetic Yeast Chromosomes

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

Three stories of JGI-supported research, connected to nutrient cycles. Francis Martin and Lucas Auer discuss their work on communities of forest floor fungi. Allison Joy looks into seagrass meadows' carbon sequestration with insights from Adam Healey and Xiao Ma. And Karen Serrano and Benjamin Cole explain their research on the symbiotic relationship between mycorrhizal fungi and plant roots. 

Links from this episode:

• Submit your own proposal to work with the JGI
• Join us at the 2024 JGI User Meeting
• Find all episode transcripts on our website

• Feature: Getting to the Bottom of Fungal Functions Across Earth’s Forests
• Paper: Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

• Feature: Eelgrass proves to be much younger than we thought
• Paper: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)
• Paper: Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

• Paper: Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

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

Rainforests store a big fraction of all the carbon on Earth, and soil microbes play a key role in pulling that carbon out of the atmosphere. This episode, researchers take a look at what happens to that storage when a rainforest hits a drought. Tag along with their experiments in a fully enclosed, human-made ecosystem: Biosphere 2. 

Links from this episode:

• Submit your own proposal to work with the JGI
• Join us at the 2024 JGI User Meeting
• FICUS program

• Find all episode transcripts on our website
• Paper: Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest  https://doi.org/10.1038/s41564-023-01507-7

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

This is the third and final episode of our series on a giant metagenome assembly from Wisconsin’s Lake Mendota. In the last two episodes, we’ve covered the specialized software and supercomputers behind this project. But every part of this project depends on lakewater samples — so this episode is a look at how researchers get these specialized snapshots of a freshwater ecosystem.

Links from this episode:

• Submit your own proposal to work with the JGI
• Find all episode transcripts on our website
• Related papers: 
  • Species invasions shift microbial phenology in a two-decade freshwater time series
  • Terabase-Scale Coassembly of a Tropical Soil Microbiome
• Our contact info:
  • Twitter: @JGI
  • Email: jgi-comms at lbl dot gov

This series is the story of a giant metagenome assembly from Wisconsin’s Lake Mendota. In this episode: a look at the supercomputing that stitches together large datasets with the assembler program MetaHipMer2.

Oak Ridge National Lab is home to two supercomputers — Summit and Frontier — that process terabytes of data with MetaHipMer2. And the National Energy Research Scientific Computing (NERSC) has another supercomputer, Perlmutter that works at large scale. But nearby the JGI, a cluster called Dori is also capable of running smaller assemblies — so we head there for a sense of what this supercomputing looks like.

Links from this episode:

• Submit your own proposal to work with the JGI
• Find all episode transcripts on our website
• Robert Riley at the 2016 DOE JGI Genomics of Energy & Environment Meeting
• MetaHipMer
• The ExaBiome Project
• Our contact info:
  • Twitter: @JGI
  • Email: jgi-comms at lbl dot gov