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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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April 28, 2021

Gut Fungi: Unexpected Source of Novel Chemicals

The anaerobic fungus Anaeroromyces robustus growing on reed canary grass. (Vaithiyalingam Shutthanandan, PNNL/EMSL)Combing through the genomes of four anaerobic fungal species has revealed, for the first time, that this group is unexpectedly powerful: they can whip up dozens of complex natural products, including new ones. [Read More]

December 21, 2020

An Automated Tool for Assessing Virus Data Quality

Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)The CheckV tool helps researchers to assess the completeness of virus genome sequences and complements a community effort to develop guidelines and best practices for defining virus data quality. [Read More]

December 21, 2020

A One-Stop Shop for Analyzing Algal Genomes

Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)By bringing together publicly available algal genomes into one place, PhycoCosm allows users to easily compile data that answers what genes are present in which organisms, when are they expressed, and what they do. [Read More]

December 8, 2020

How Maize Makes An Antibiotic Cocktail

Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)Maize produces a family of compounds that protects it against infections — using surprisingly few enzymes. The Science Maize (Zea mays) produces a plethora of antibiotics called zealexins. Even though scientists have identified at least 15 zealexins, they suspect there are even more to find. Zealexins are produced in every corn variety and protect maize… [Read More]

November 13, 2020

From Competition to Cooperation

The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)Comparing 135 fungal genome sequences, researchers looked at how multiple forest fungi have independently evolved to establish symbiotic relationships with plants, and particularly how fungi that feed on decaying plant matter have transitioned to the symbiotic lifestyle. [Read More]

November 11, 2020

A Grass Model to Help Improve Giant Miscanthus

Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)The reference genome for Miscanthus sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum. [Read More]

September 8, 2020

In Hot Spring Microbial Mat, Viruses Ride “Piggyback”

Microbial mat under the microscope. Visible layers contain different microbial communities and minerals. The team characterized viruses in a subset of the mat layers. (John Spear)Scientists have used sequencing methods to comprehensively characterize viral-host interactions in a microbial mat for the first time. [Read More]

August 20, 2020

Effects of Polar Light Cycle on Microbial Food Web

Effects of Polar Light Cycle on Microbial Food WebLight-harvesting bacteria (phototrophs) in Antarctica’s Ace Lake defy the norm when it comes to nutrient cycling in polar regions. [Read More]

August 6, 2020

Gene Expression: From On-Off Switch to Dial

Gradient of the betaxanthins production in yeast across various different cultures. (Courtesy of Matthew Deaner)Scientists have developed a more nuanced library approach for fine-tuning gene expression in metabolic pathways in metabolic pathways. [Read More]

July 21, 2020

Computationally Classifying Fungal Lifestyles

As a proof of concept, researchers developed an algorithm that “taught” a computer how to classify 101 representative genomes of Dothideomycetes, the largest class of fungi, by lifestyles. [Read More]
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