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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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    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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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    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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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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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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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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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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    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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Our Science
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October 15, 2012

Button Mushroom Marks Niche in Forest Carbon Storage

Many people know the button mushroom (Agaricusbisporus) as a tasty ingredient in their food. In the forest, though, this mushroom helps break down leaf litter in environments rich with humus, a mixture of soil and compost that contributes to the health of the microbial communities in, on and around the plant as well as the… [Read More]

September 28, 2012

Comparing White Rots to Shed Light on Wood-Colonizing Habit

White-rot basidiomycetes can degrade all components of lignocellulosicbiomass, including lignin, cellulose and hemicellulose. Thus, harnessing the metabolic potential of these organisms is key to developing cost-effective technologies for the production of renewable energy and value-added co-products from residual plant biomass. A comparative analysis of the white rot fungus, Phanerochaetecarnosa, isolated from softwoods, andPhanerochaetechrysosporium, isolated from… [Read More]

September 14, 2012

Targeted metagenomics approach pins down role of “wild” alga

Marine microbes play key roles in cycling carbon between the atmosphere and the ocean depths, but little is known about their populations throughout the waters. As global temperatures change, so do these populations, which in turn impacts their contributions to the carbon cycle. Researchers want to learn more about these effects, but one of the… [Read More]

August 31, 2012

Algal Lipid Pathways Linked to Those in Plants and Fungi

Red algae play an important role in carbon and nitrogen cycles in the ocean, and are potential biomass for biofuel production. However, few red algae have been studied at the genomic level to date. An international collaboration of researchers has found that some species of the extremophilic red algae Porphyra have a pathway similar to… [Read More]

August 24, 2012

Methylobacteria Shed Light on the C and N Cycles

Methylobacteriaare vital for processing single-carbon compounds like methanol, methylamine, and the greenhouse gas methane. They play a central role in the carbon and nitrogen cycle. While many researchers are studying the bacteria, their full functionality is still unknown– but it’s becoming more complete, thanks to a recent publication of six genomes of different strains of… [Read More]

August 17, 2012

Drifting Poplar Populations Inform Breeding Strategies

Since the publication of the genome sequence of the first tree, the black cottonwood or poplar Populustrichocarpain 2006 by the DOE Joint Genome Institute, a growing community of researchers have been engaged in advancing the development of poplar as a candidatefeedstockfornext-generationbiofuelsowing to the tree’s compact genome, rapid growth and life cycle. One area of study… [Read More]

August 10, 2012

Rethinking Rhodanobacter

Denitrification, or breaking down nitrates in soil, is important. It removes the chemicals from potentially contaminating groundwater, but it can also release nitrous oxide, a greenhouse gas, into the atmosphere. Scientists discovered that many species of the low-pH dwelling bacteria in the Rhodanobactergenus are capable of denitrification. This is on the heels of the discovery… [Read More]

August 3, 2012

Prototypical genomic study of Plant-Microbe Interaction

Instead of using dangerous and toxic pesticides or expensive fertilizers, farmers may one day use microbes to fully manage diseases in soil. Already the microbial community in and surrounding plant roots fights pests and manages carbon and other soil nutrients, ultimately contributing to plant health and growth. What’s more, they aid plants in sequestering pollutants…. [Read More]

July 27, 2012

Soybeans Annotated, Revisited

[Read More]

July 20, 2012

Understanding a Cereal Disease with DNA Sequencing

An international coalition of researchers, including those from the DOE Joint Genome Institute have now isolated the Barley stripe mosaic virus resistance gene from  Brachypodium distachyon. They found the single dominant gene responsible by analyzing the offspring of intercrossed disease-resistant and disease-susceptible Brachypodium. Their results were published in June in PLoSOne. Brachypodium distachyonis a good… [Read More]
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