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: rseshadri@lbl.gov Matt Escobar: mescobar@csusm.edu 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

Lake Mendota sits right next to the University of Wisconsin, Madison. And Trina McMahon's lab has been sampling the microbes of that lake for over 20 years, to understand how the freshwater ecosystem works. So a few years ago, when they set out to analyze 500 metagenomes, it was the biggest project the JGI had ever put together. The next 3 episodes are the story behind that giant assembly from Lake Mendota. In this episode: the software evolution that made metagenome assemblies like this possible. Links from this episode: Submit your own proposal to work with the JGI Find all episode transcripts on our website The ExaBiome Project Paper: Hofmeyr, S., Egan, R., Georganas, E. et al. Terabase-scale metagenome coassembly with MetaHipMer . Sci Rep 10, 10689 (2020). https://doi.org/10.1038/s41598-020-67416-5 Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov

To set up flexible, repeatable experiments on plants and microbes, Trent Northen’s group at Berkeley Lab created a fabricated ecosystem – an EcoFAB. These small plastic growth chambers let researchers around the world compare their work consistently. And EcoFABs also work well in the classroom. This episode, we visit Los Medanos College to see EcoFABs in action in Jill Bouchard’s BIO 21 lab course. Links from this episode: Submit your own proposal to work with the JGI Find out more about EcoFABs Connect with Ying Wang about her lab at Texas A&M Find all episode transcripts on our website Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov

To understand how organisms adapt to extreme environments, Marike Palmer and Brian Hedlund study organisms living in hot springs. Hear how their recent work revealed more about the history of the Chloroflexota phylum and a new way of moving: a tail-like flagella. Submit your own proposal to work with the JGI Join us at the 2023 JGI User Meeting Links from this episode: Find all episode transcripts on our website Publication: Palmer, M, et al. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past The ISME Journal . (2023). doi: 10.1038/s41396-023-01405-0 Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov

A quick snippet on Antonio Camargo and Simon Roux, a few of the JGI researchers behind software that finds plasmids and viruses within microbial genomes. As mobile genetic elements like viruses spread their DNA, they can affect how microbes cycle nutrients and adapt to climate change. Find all episode transcripts on our website Publication: Camargo, A.P., et al. “ Identification of mobile genetic elements with geNomad ,” Nature Biotechnology . (2023). doi: 10.1038/s41587-023-01953-y Science Highlight: You can move, but you can't hide Learn more about geNomad and download it Submit your own proposal to work with the JGI Explore IMG/VR and IMG/PR Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov

Meet researchers who have hiked, rafted and met local wildlife (a marmot!) as they’ve sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains. These lakes are isolated, but varied. They’re a great way to see how climate change affects freshwater ecosystems, and how those ecosystems work. Links from this episode: Submit your own proposal to work with the JGI http://jointgeno.me/proposals Join us at the 2023 JGI User Meeting http://jointgeno.me/JGI2023 Find all episode transcripts on our website Publication: Perez-Coronel, E., Michael Beman, J. Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis . Nat Commun 13, 6454 (2022). doi: 10.1038/s41467-022-34105-y Learn about the IMG/M system JGI Webinars: http://jointgeno.me/Webinars Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov Sound Effects Credits: Marmot sound courtesy of slunali, freesound.org

Right now, our natural rubber comes from just one tree species: Hevea brasiliensis . It’s great at producing latex that becomes rubber, but it’s vulnerable to disease and climate shifts. So researchers are looking into a desert shrub that’s native to North America: guayule. This episode was made in collaboration with our friends at the HudsonAlpha Institute for Biotechnology. Links from this episode: Submit your own proposal to work with the JGI : http://jointgeno.me/proposals Join us at the 2023 JGI User Meeting : http://jointgeno.me/JGI2023 Find all episode transcripts on our website HudsonAlpha Institute's Tiny Expeditions Podcast Guayule: Can genetics create a natural US rubber source? Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov

The ocean depths are vast and dark. But there are hotspots on the ocean floor — underwater volcanoes and hydrothermal vents — where lively microbial communities thrive, and even support entire ecosystems. Hear from researchers Anna-Louise Reysenbach, Emily St. John, Gilberto Flores, and Peter Girguis about sampling these communities, and understanding how they’ve adapted to this extreme environment. Links from this episode: Submit your own proposal to work with the JGI : http://jointgeno.me/proposals Join us at the 2023 JGI User Meeting : http://jointgeno.me/JGI2023 Find all episode transcripts on our website Paper: Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov

In our warming world, we’ll need corn, sorghum and other crops to grow well in worse conditions: with more heat, less water and less fertilizer. Grasses do better in these conditions, so plant biologists James Schable, Guangchao Sun and Vladimir Torrres have looked into traits that could transfer from grasses into other crops. One grass they studied just happened to be the same species that covered World Cup pitches in 2022. Links from this episode: Submit your own proposal to work with the JGI Join us at the 2023 JGI User Meeting Find all episode transcripts on our website Publication: Sun, G., Wase, N., Shu, S. et al. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass . Nat Commun 13, 7731 (2022). doi: 10.1038/s41467-022-35507-8 Phytozome: Paspalum vaginatum data Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov

On June 8th, Genome Insider is back! We've got a batch of 4 new episodes where researchers discover the expertise encoded in our environment — in the genomes of plants, fungi, bacteria, archaea, algae, and environmental viruses — to power a more sustainable future. Stick around for a snippet of the next episode. Join us at our User Meeting: jointgeno.me/JGI2023 Find out how to become a JGI user here: jointgeno.me/proposals Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov

Michelle O'Malley and Tom Lankiewicz of UC-Santa Barbara discuss the importance of studying anaerobic fungi, as well as a recent discovery that turns scientific presumption on its head and opens up a new avenue to explore for efficient biofuel production. Find all episode transcripts on our website Publication: Lankiewicz, T.S., Choudhary, H., Gao, Y. et al. Lignin deconstruction by anaerobic fungi . Nat Microbiol 8, 596–610 (2023). doi: 10.1038/s41564-023-01336-8