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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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    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 3, 2018

Regulatory Genomics of Brachypodium

This is a proposal to develop the most advanced systems-level understanding of transcriptional regulation of grass growth. Brachypodium distachyon is a model system for the study of energy crops such as sorghum, miscanthus, and switchgrass, and the team’s approach depends on a unique combination of reagents that were developed in collaboration with JGI. The identification… [Read More]

October 3, 2018

Fungal Comparative ENCODE Project

The FUNCODE project aims to generate a genome-wide library of the rules that govern gene expression in five important model fungi. The resources generated during the project will support a wide range of basic and applied research and biotechnological and industrial applications of fungi, including an understanding of gene regulatory circuits behind plant waste decomposition… [Read More]

October 3, 2018

Genome Encyclopedia of Bacteria and Archaea VI

The proposed study will advance the sequencing of the type strains of prokaryotes and initiate the functional genomics of understudied groups. The goal of these studies is to improve our understanding of gene function for a wide variety of prokaryotes. Ultimately, a predictive model of prokaryotic life on earth will be developed to unite gene… [Read More]

October 3, 2018

Short-Term Temperature Shift at Harvard Forest

Barre Woods Experimental Warming Site, the location for Jeffrey Blanchard's approved proposal involving a long-term soil warming experiment. (Courtesy of J. Blanchard)Long-term warming results in significant changes in respiration, community structure and microbial processes. The primary goal of this project is to separate molecular changes resulting from long-term warming from temperature effects of gene expression using samples just prior to the power returning and the week afterwards when the soil temperature is again 5°C higher than… [Read More]

September 25, 2017

From Genome to Watershed Scales

East River, CO, USA (Courtesy of Jill Banfield)The quality of water that leaves the watershed is impacted by soil microbial communities that will be studied here. The research will target regions along the East River, a tributary of the Colorado River, focusing on three subsystems: the river corridor and hillslopes and consider effects of time of year, depth below the surface and… [Read More]

September 22, 2017

Microbial Functions at Soil-Aquatic Interfaces

47-55 percent of the terrestrial carbon is transported and processed in rivers. Terrestrial carbon is generally considered to be resistant to aquatic microbial metabolism. However, recent evidence suggests that at soil-aquatic interfaces terrestrial carbon can be respired by aquatic microorganism at the cost of low carbon use efficiency thus contributing to CO2-fluxes to the atmosphere…. [Read More]

September 22, 2017

DNA Methylation Role in Basal Fungi

Mucor circinelloides sporangiophore. (S. Torres-Martínez. University of Murcia, Spain.)DNA methylation is a fundamental epigenetic modification that plays a critical role in genome function in eukaryotes. This proposal will study the function of N6-methyladenine (6mA) in early divergent fungi because it is more abundant than in other eukaryotes and seems to regulate gene expression. The function will be studied in the context of responses… [Read More]

September 22, 2017

Fungal Gene Expression for Biomass Conversion

The filamentous fungus Neurospora crassa is an important model organism for fungal conversion of biomass. It is unknown how DNA structure is altered in response to stimuli to change expression levels of genes involved in biomass conversion. The goal is to define the global regulatory network of DNA structures in N. crassa and its impact… [Read More]

September 22, 2017

Comparative Genomics of Acutodesmus

Green algae are important contributors to global carbon cycling and hold great promise as feedstocks for biomass and biotechnology applications. To date, breeding and natural variation of green algae have not been exploited for strain improvement due to lack of foundational knowledge about strain diversity and sexual cycles. This project will investigate natural strain diversity,… [Read More]

September 22, 2017

Reference Genomes for 50 Rust Fungi

Illustration of disease symptoms caused by rust fungi on different host plants (photos by M. Catherine Aime)Rust fungi are the largest group of plant pathogens. Different species cause disease on important food, timber and bioenergy crops. However, there are comparatively few genetic resources available for this group. The goal of the rust pangenomics project is to provide reference genomes for 50 rust species, including pathogens of JGI plant flagship species (e.g.,… [Read More]
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