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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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  • Data & Tools
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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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  • News & Publications
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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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October 1, 2019

Genomic Variation in Mustard Family Metabolism

Studies of genomic variation are critical to developing a synthetic, systems and quantitative understanding of how to improve crops. However, modern short-read methodologies may actually miss the very genes that are critical to adapting crops to new environments or making them healthier. This project will create high-quality genomes of multiple crops and species from the mustard family to test new methods and technologies to ensure that these genes essential for adaptation and improvement are identified. [Read More]

October 1, 2019

Fungal Root Endophytes of Soybean

This project investigates fungal root endophytes of the oilseed crop soybean for their potential to deter biotic stresses from root pathogen such as the soybean cyst nematode and the sudden death syndrome fungal root-rot pathogen. [Read More]

October 1, 2019

Expanding Metabolic Understanding of C- and S- Cycling Microbes

Is there more biochemistry to be discovered in the microbial world? How universal is biochemistry between distantly related bacteria? A massive amount of microbial genome data exists, yet every new sequence finds genes for which we cannot predict a concrete function. This proposal seeks to combine genomic information with direct detection of metabolites to answer these questions and provide a path for assigning gene functions in two distantly related microbial groups that play key roles in carbon and sulfur cycling in multiple ecosystems across the planet. [Read More]

October 1, 2019

Scaling Microbial Traits From Genomes to Watersheds

Soil core showing redoximorphic features sampled from watershed zone of high vegetation nitrogen uptake. (Courtesy of Eoin Brodie)Using remote sensing, metagenomics and machine learning, we are building new ways to predict of how plant and microbial metabolism interact to influence biogeochemistry across watersheds in the headwaters of the Colorado River. [Read More]

October 1, 2019

Wood Decay by Soft Rot Fungi

This project seeks to ascertain the mechanisms of lignocellulose deconstruction employed by these soft rot fungi. [Read More]

October 1, 2019

How Black Fungi Adapt to Extremes

Black fungi spread in diverse extreme environments playing a crucial role by recycling organic matter, enabling nutrient uptake. They are also involved in biogeochemical processes, including rock transformations, bioweathering, mineral formation. The STRES project aims to dig into the genome diversity and metabolites involved in stress response to: i) gain insights into the evolutionary processes allowing black fungi to successfully adapt to extremes; ii) clarify their role in the functioning and balance in extreme-ecosystems; iii) explore the role of melanin in energy processes. [Read More]

October 1, 2019

Grass Genes Regulating Bioenergy Relevant Traits

Grass species have a tremendous potential to be engineered to generate biofuels that can feed our economy. A major challenge has been accessing the energy stored in plants. Purple false brome (Brachypodium distachyon), a wild grass species from the Mediterranean region, is a perfect model for testing novel ways of changing plants to help produce biofuels. In this study, researchers are accessing variation in this species to identify genes that could transform bioenergy crops. These resources are openly shared with the scientific community in order to speed up research and transform society. [Read More]

October 1, 2019

Mapping Methanogenic Metabolic Networks

Anaerobic digestion (AD) systems produce methane-rich biogas, which can be upgraded and distributed within the existing energy grid. Despite the widespread adoption of AD for waste management and bioenergy generation, the microbial networks driving methane production from organic matter remain poorly constrained, limiting our capacity to predict impacts of process perturbations. Here, we will combine stable isotope and amino acid tracers with genomic sequencing to determine “who is doing what” in AD, with the overall aim of improving biofuel production efficiency from renewable biomass. [Read More]

October 1, 2019

Microbial Roles in Plant Drought Tolerance in the Sahel

The Sahel region in West Africa is highly vulnerable to drought, endangering the livelihood of millions of millet subsistence farmers in the region. However, a solution has been revealed; when farmers grown millet in close proximity with native woody shrub gueira, the millet has greater biomass and yields. We predict that the millet-associated microbial community is influenced by the shrub such that the microbes are able to confer better drought resistance to their host millet in the presence of the shrub. We will characterize the metagenomes of millet to test this hypothesis. [Read More]

October 1, 2019

Plant-Microbe Interactions of a Wood Decay Fungus

This research project focuses on elucidating the plant-microbe interactions of the wood decay fungus Perenniporia fraxinea, a serious pathogen of hardwood trees. Multi-omics analyses will reveal the comprehensive mechanisms and key fungal genes involved in the wood infection and degradation processes will be identified. Furthermore, key fungal proteins involved in the processes will be biochemically characterized and subjected to chemical screening in our efforts to identify specific inhibitors with potential as novel wood-protective agents against P. fraxinea and related wood-decay fungi. [Read More]
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