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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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    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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    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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    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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October 24, 2013

The heat is on – microbial mat communities in Hot Lake

Diverse underwater communities of cyanobacteria and other microorganisms are capable of withstanding drastic changes in salinity. The Science The microbial mat communities—multi-layered sheets of bacteria and archaea that grow at the interface between submerged, moist or even desiccated surfaces—in a remote lake near the border with Canada are relatively stable, despite weathering a 10-fold increase… [Read More]

October 21, 2013

Combining profiling and genomics yields novel metabolites

Cyanobacteria’s ability to capture solar energy and fix CO2 holds promise for biotech applications The Science Researchers studied 10 different cyanobacteria to identify their secondary metabolites (compounds produced during normal cellular metabolism not directly involved in cell growth, that may play an important role in interactions outside the cell) and the genes linked to those… [Read More]

October 18, 2013

DOE JGI Science Highlight: The inner workings of cyanobacteria carbon fixation

New research upholds theoretical structure for cyanobacteria carboxysomes. The Science Researchers described the structure of a protein critical to the outer shell of carboxysomes, the organelle-like structure that cyanobacteria use for carbon fixation. The Impact The structure and interaction of the proteins that make up the carboxysome’s outer shell aren’t clearly understood. A detailed study… [Read More]

September 30, 2013

Analyzing the Role of DNA Methylation in a Bioremediation Bacterium

Characterizing functional roles in a microbe with bioremediation applications a first step toward similar studies for other prokaryotes The Science Researchers studied the role of DNA methylation on gene expression and other processes in the heavy-metal reducing bacterium Shewanella oneidensis MR-1 with the help of next-generation Single-Molecule Real Time (SMRT) sequencers from Pacific Biosciences. The… [Read More]

September 13, 2013

Beetle gut microbes bore through woody tissues

Profile of wood-boring beetle’s midgut microbial community identifies candidate genes involved in processes including lignin degradation The Science Metagenomics allowed researchers to conduct a functional analysis of the midgut microbial community in the Asian longhorned beetle (Anoplophora glabripennis), an invasive insect that feeds on lignin in deciduous trees such as poplars and willows. The Impact… [Read More]

September 6, 2013

POPSEQ for Plant Genome Assembly

New approach allows researchers to work on many species regardless of sequence resources The Science Plant genomics researchers evaluated POPSEQ, a method for assembling complex plant genomes using next-generation sequencing. The Impact Using a large, complex and highly-repetitive plant genome, the findings yielded results comparable to the previously assembled sequence. The proof of principle demonstrates… [Read More]

August 30, 2013

Subsurface Sediment Yields Novel Organism

Metagenomic analysis emphasizes the “extraordinary microbial novelty” of poorly-explored subsurface ecosystems The Science Through metagenomics, researchers reconstructed a dominant organism and member of a new phylum-level lineage from an aquifer sediment in Colorado. The Impact Analysis of the complete microbial genome led to a detailed metabolic model with evidence for multiple new enzymes and pathways…. [Read More]

August 23, 2013

Hope for Re-establishing Gulf of Mexico Microbial Populations

Comparative Analysis Shows Petroleum Reduced Species Diversity The Science Researchers used metatranscriptomic analyses to compare the microbial populations in the Gulf of Mexico before and after the Deepwater Horizon oil spill to learn more about the impact of adding petroleum to the waters. The Impact Though the oil spill reduced the diversity of the microbial… [Read More]

August 16, 2013

Solving the Secrets of Sedimentary Microbes

Microbes from Phylum Chloroflexi Provide Clues to Carbon Cycling, Respiration in Sediments The Science Through metagenomics, researchers sequenced 86 organisms from the phylum Chloroflexi that represent 15 distinct lineages in order to discover the secrets of microbial life within terrestrial aquifer sediment deposits. The Impact These Chloroflexi microbes were found to have metabolic processes involved… [Read More]

August 9, 2013

Moss Sequencing “Ennobles” Flagship Genome

Physcomitrella Genome Expected to Provide Help with Global Climate Change The Science An international team of scientists has annotated all 32,275 genes of Physcomitrella patens, a moss sequenced by the DOE Joint Genome Institute that contains about 10,000 more genes than humans. The Impact It is widely believed that the P. patens genome contains information… [Read More]
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