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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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Our Projects
Home › CSP Plans
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August 1, 2015

Developing Colletotrichium genomics resources

The genus Colletotrichum contains at least 150 species divided into nine major clades, and one of the largest is the Colletotrichum acutatum species complex (CAs). Species belonging to this complex are associated with diseases that infect a wide diversity of crop plants worldwide, and some insects as well. Despite being one of the largest lineages… [Read More]

August 1, 2015

Gene expression profiling in bioenergy grasses

Sugarcane and Miscanthus are closely related to the DOE JGI Flagship plant Sorghum and comprise the Andropogoneae, a tribe of highly productive grasses prominent in energy production. Miscanthus is a nascent DOE JGI flagship, pending completion of a reference genome draft. Sugarcanes and Miscanthus are both polyploids with complex genomes, which has limited the use of modern,… [Read More]

August 1, 2015

Acquired immunity in poplar

Populus trichocarpa was the first tree species whose whole genome was sequenced, assembled and annotated by the DOE JGI for bioenergy applications. This project has two major aims: 1) document the evolutionary process (i.e., the accumulation of mutations) that a single poplar tree undergoes during its lifetime; and, 2) examine the hypothesis that perennial plants… [Read More]

August 1, 2015

Columbia River estuary systems biology

River and ocean end members are heavily populated areas subjected to powerful physical forces and vulnerable to the impacts of human activity and climate change. Estuaries buffer the ocean from the effects of land loads of reactive nitrogen, but can also enhance microbial production of the greenhouse gases carbon dioxide, methane and nitrogen dioxide. This… [Read More]

August 1, 2015

Dung fungi as a model system

Fungi are the primary decomposers of organic matter in terrestrial ecosystems. In order to understand decomposition, it is critical to know how species interact and why species identities change during the decomposition process. This project aims to improve understanding of the community basis for fungal decomposition by developing a model system for decomposition using coprophilous… [Read More]

August 1, 2015

Insights into Coral-Symbiodinium symbiosis

Coral reefs are threatened tropical marine ecosystems whose fundamental unit is the reef building coral. A coral colony is a complex community comprised of both the coral host and its associated microbiome, the coral holobiont. The coral microbiome is important in shaping host health but its metabolic contribution to the coral holobiont is poorly understood,… [Read More]

August 1, 2015

Genomic diversity of Pseudomonas

Pseudomonas is a large and heterogeneous genus, and these bacteria exhibit varied lifestyles in a wide range of environments, including soil, water, plant surfaces, and animals. Due to their roles in bioremediation, biological control, diseases of plants and animals, and many other environmental processes, the metabolic capacities and ecological functions of these bacteria have been… [Read More]

August 1, 2015

Driving the carbon cycle in the dark ocean

The oceans contain the largest reservoir of rapidly exchangeable carbon yet also effectively sequester carbon from the atmosphere for thousands of years. The drivers of this delicate equilibrium are the abundant marine microbial communities ubiquitously present in the Earth’s oceans. This project will provide insight into the major metabolic pathways and key carbon compounds involved… [Read More]

August 1, 2015

Insights on uncultured microbes in wastewater

Currently, anaerobic wastewater treatment serves as an essential municipal waste remediation strategy due to its low cost and efficient waste removal, and the production of methane as a sustainable energy source. To effectively enhance process operation for bioenergy recovery, however, researchers need to better understand the microbial ecology of wastewater treatment. Three primary ecological groups–fermenters,… [Read More]

August 1, 2015

Exploiting Actinobacteria genomes

Actinobacteria are ubiquitously distributed in both aquatic and terrestrial ecosystems and have developed diverse lifestyles, as well free living as in association with a wide variety of eukaryotes. Next to Proteobacteria and Firmicutes, Actinobacteria constitute the third most populated phylum among the Bacteria. This project calls for sequencing the genomes of 1,000 environmental isolates (type… [Read More]
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