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    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.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    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.

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    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    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.

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    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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    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.

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    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.

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    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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    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.

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    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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    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.

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    image from gif that shows where in the globe JGI fungal collaborators are located.
    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.

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    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.

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July 19, 2019

Improving the Cacao Genome and Phytozome

According to the International Cocoa Organization (ICCO), global cocoa bean production in 2017-2018 was 4.6 million metric tons. The global chocolate brands couldn’t exist without cocoa.  But today the plant is under threat due to climate change and devastating fungal infections. That’s why Mars, Inc., a maker of chocolate for more than 100 years and…

July 15, 2019

Better Genome Editing for Bioenergy

The lipid producing yeast, Yarrowia lipolytica, examined with light microscopy (left) and fluorescence microscopy (right), after being stained with Nile Red to visualize the lipid droplets inside (shown here in white). (Courtesy of Hal Alper)

A team has optimized a crucial part of CRISPR-Cas9 technology to enable improvements in microbial oil production. The Science CRISPR-Cas9 is a powerful, high-throughput gene-editing tool that can help scientists engineer organisms for bioenergy applications. Cas9 needs guide RNA to lead it to the correct sequence to snip — but not all guides are effective….

July 10, 2019

Cultivating Symbiotic Antarctic Microbes

FISH of Nha-C enrichment with Hrr. lacusprofundi ACAM34-hmgA. Fluorescence micrograph shows individual Nha-C cells amongst Hrr. lacusprofundi cells. Nha-C cells labelled with a Cy5 (red fluorescence) conjugated probe; Hrr. lacusprofundi cells labelled with a Cy3 (yellow fluorescence, recolored to green to improve contrast) probe; all nucleic-acid containing cells stained with DAPI (blue fluorescence). Composite image of all three filters. Scale bars represent 2 µm. (Josh Hamm, UNSW)

Nanohaloarchaeota cultures reveal they are symbionts and not free-living organisms. The Science Researchers employed multiple microbiology and ‘omics techniques to experimentally determine that Nanohaloarchaeota are symbionts, rather than free-living organisms as had been originally thought. The Impact The Antarctic lakes are a “treasure trove” of unknown microbes that play critical roles in environmental processes (related…

June 11, 2019

Developing Switchgrass for Biomass Production

Left to Right: Jerry Jenkins, JGI Plant Program head Jeremy Schmutz, Adam Healey and study senior author Tom Juenger of UT-Austin.

Switchgrass community gardens help distinguish genetic bases of fitness traits from climactic influence. The Science To better understand the genetic basis of local adaptation, researchers established community gardens of switchgrass plants in 10 different field sites on a north-south gradient across the United States. Hundreds of the switchgrass plants in these gardens are clonally propagated…

June 10, 2019

Tracking Permafrost Thaw

Virginia Rich, Ohio State, at the JGI 2019 User Meeting

Notes from the JGI 2019 User Meeting The Arctic peatlands are among the northern ecosystems that collectively store up to half of the planet’s soil carbon. With the frozen peatlands thawing, said Virginia Rich of The Ohio State University, “if we project this out, permafrost is virtually eliminated by the end of the century.” Just…

June 7, 2019

Engaging the Workforce through Tiny Earth

Amanda Hurley of the University of Wisconsin–Madison at the JGI 2019 User Meeting

Notes from the JGI 2019 User Meeting Amanda Hurley, a postdoctoral fellow in Jo Handelsman’s lab at the University of Wisconsin–Madison, began her talk with a reminder that pathogens damage 16% of the global crop yield. That number is expected to rise due to climate change. “We need something that tips the scales back in…

May 14, 2019

JGI Early Career Researchers Featured in mSystems Special Issue

Left to Right: Rex Malmstrom, Emiley Eloe-Fadrosh, and Simon Roux.

In a special issue of mSystems, out May 14, 2019, JGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like. In one article, Micro-Scale Applications head Rex Malmstrom and Metagenome Program head Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental…

April 29, 2019

Graduate Students Get Thesis Research Opportunity at the JGI

Kaze and Rambo SCGSR recipients 2018 solicitation 2 cycle

Twice a year, the DOE Office of Science Graduate Student Research (SCGSR) program awards graduate students the opportunity to pursue part of their thesis research at one of the DOE national laboratories or national user facilities. As a result of the latest call, a total of 70 graduate students from 52 universities were selected to…

April 17, 2019

Notes on the Microbial Diversity of Puerto Nuevo’s Coastline

w Sabah-Zhong_posters_UM13

Puerto Nuevo is a small town along the Baja California coastline in Mexico. While conducting early field studies related to her thesis on cone snails, UC Merced graduate student Sabah Ul-Hasan and alumnus of the JGI-UC Merced Genomics Internship Program, first sampled the area in summer 2016.  She described the microbial diversity patterns of Puerto…

March 29, 2019

Year in Review: JGI’s 2018 Progress Report Available Now

2018 JGI Progress Report cover

The latest edition of the JGI Progress Report highlights notable research and scientific collaborations in 2018. The cover is an image of Mono Lake, a saline soda lake east of California’s Yosemite National Park, taken by JGI’s own Jon Bertsch. Microbes isolated from Mono Lake were sequenced by the JGI (isolates here, here and here),…

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