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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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News & Publications
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November 6, 2023

Researching and Solving Real-World Problems with the 2023 JGI-UC Merced Interns

2023 JGI-UC Merced interns (Zhong Wang/Berkeley Lab)Reflections from this year’s JGI-UC Merced summer cohort about their onsite internships and enrichment activities. [Read More]

October 27, 2023

RECAP: Multi-Omic Journeys with 2023 JGI Annual Meeting Keynotes

Bruce Hungate stands at a podium and gesticulates as he discusses microbes.The 2023 JGI Annual Meeting keynote speakers shared the journeys of their research careers, and showcasing the broad applications of their genomics and multi-omics work. [Read More]

October 27, 2023

Tracking & Subduing the Plague of California’s Oak Woodlands

Left to right: Lea Green, Matteo Garbelotto, Douglas Schmidt and Natalie Chapman. At UC Berkeley, Garbelotto and Schmidt launched a concerted SOD defensive campaign. Green and Chapman are a couple of the community college students who conduct DNA analyses of samples collected on SOD Blitz expeditions. (Thor Swift/Berkeley Lab)From genome to community science: a UC team oversees engagement activities to control the spread of sudden oak death. [Read More]

October 26, 2023

Celebrating a Decade of Science through the JGI-UC Merced Genomics Internship Program

A decade on, the JGI-UC Merced genomics internship has led to groundbreaking science and opportunities to speak on a national level. [Read More]

October 19, 2023

Webinar: Metagenome quantitative SIP at JGI

slide from Matthew Kellom's qSIP webinarThe JGI offers metagenome quantitative stable isotope probing (Metagenome – qSIP) capabilities to investigate metabolic activity of metagenome-assembled genomes (MAGs). [Read More]

October 19, 2023

JGIota: A Surprise for Chloroflexota — The First Flagella!

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. [Read More]

September 7, 2023

Natural Prodcast Episode 21 – Elizabeth Parkinson

Natural Prodcast podcast logoNatural Prodcast guest Betsy Parkinson from Purdue on bacterial signaling molecules and regulation of biosynthetic pathways, student mental health, and getting kids interested in microbiology. [Read More]

September 1, 2023

A Collaboration to Improve Plant Genome Annotations Across Species

A tiled collage of square photos of different plants - soybeans, and sorghum, for example.Described in Nucleic Acids, the JGI Plant Gene Atlas is a huge updateable transcriptome resource spanning diverse plant species. [Read More]

July 12, 2023

From Berkeley to Binghamton: Tracking Strawberry Evolution

In Nature Communications, a method to correctly identify polyploid subgenomes without needing to know the genomes of their ancestors. [Read More]

May 19, 2023

Request for Information: BERAC Unified Data Framework

Image of network data cables courtesy of Berkeley LabThe US Department of Energy’s Office of Science is seeking input on the need and the structure of a unified data framework that links or integrates existing data activities within the Biological and Environmental Research Program (BER).  The aim is to gather current and future science questions that require a more integrated data infrastructure for… [Read More]
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