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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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    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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    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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August 12, 2014

High quality reference Brassicales genomes

The Brassicaceae constitute not only one of the most diverse plant families, but also one rich in agronomically-important vegetable and oilseed crops. Several species have been domesticated and include different cabbages, broccoli, turnip, rapeseed, horseradish, and several mustards. Brassicaceae include a number of species that are current and emerging biodiesel crops. Researchers plan to generate… [Read More]

August 12, 2014

Reducing methane emission from peatlands

Peatlands harbor up to one third of the world pool of soil carbon and are estimated to be responsible for as much as 20 percent of the global emission of the greenhouse gas methane.  Sequencing the metagenome and metatranscriptome of peat soil, and in particular, the rare peatland Desulfosporosinus species, as well as potentially novel… [Read More]

August 12, 2014

Metagenomic consequences of Amazon deforestation

The Amazon rainforest plays an essential role in global ecological processes. It is the largest terrestrial carbonsequestering ecosystem in the world, controlling global temperature and precipitation, and balancing the flux of atmospheric gases. It is also the largest repository of plant and animal species on Earth. Despite its importance, it is one of the least… [Read More]

August 12, 2014

Developing a thermophilic fungal model group

Thermophilic fungi have been an important source of industrial enzymes for decades but research and development efforts have historically focused on the identification and characterization of cellulolytic genes from just a few strains. This approach has produced advanced enzymes over time, but recent genomics-based investigation has almost instantaneously yielded a diverse palette of novel, thermostable,… [Read More]

August 12, 2014

1000 Fungal Genomes

More than any other group of eukaryotic microbes, fungi are essential biological components of the global carbon cycle. Collectively, fungi are capable of degrading almost any naturally occurring biopolymer and numerous human-made ones. The use of fungi for the continued benefit of humankind, however, requires an accurate understanding of how they interact in naturally and… [Read More]

August 12, 2014

Investigating the Serpentinite-hosted Subsurface Biosphere

Serpentinization is the aqueous alteration of ultramafic rocks, characteristic of the Earth’s mantle, and results in the generation of highly-reducing, hydrogen- and methane- rich fluids with extremely high pH’s (commonly greater than 11). Microbial communities hosted within serpentinites may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere…. [Read More]

August 12, 2014

Functional genomics in Coprinopsis cinerea

While most basidiomycetes are difficult to cultivate in the laboratory, Coprinopsis cinerea is a notable exception in that it can complete its life cycle on artificial media in just two weeks. The C. cinerea genome is well-characterized, and both forward and reverse genetic approaches are now standard, allowing enormous scope for experimental manipulation in this… [Read More]

August 12, 2014

Defining the Populus Microbiome

Populus is considered the model organism for the study of woody perennials, and represents the first tree genome to be fully sequenced. Populus is also one of only a few species that are capable of establishing associations with both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi, as well as various specific endophytic and rhizosphere associated… [Read More]

August 12, 2014

Dark ocean microbial single cell genomics

Considered one of the largest biomes on Earth, the dark ocean is comprised of the water column below the epipelagic, including meso-, bathy- and abyssopelagic and the hadal zones. It contains an active and metabolically diverse microbial assemblage that is responsible for about half of marine organic carbon mineralization. A large-scale single cell genomics study… [Read More]

August 12, 2014

Developing Schizophyllum commune as a model system

The study of wood breakdown into simple sugars is an important field of research due to its possible application in biofuel production. Developing S. commune as a model system to study the processes of wood degradation would allow researchers to study roles of enzymes in a fungus for which exist many protocols for studying genes… [Read More]
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