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    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: 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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Home › Our Projects › Approved User Proposals › Approved Proposals FY11

Approved Proposals FY11

Following are the approved user proposals for fiscal year 2011.

Community Science Program (CSP) Plans

Algae

Proposer Affiliation Organism
Kerfeld, Cheryl DOE JGI Genome and Transcriptome Analyses of Two Extremely Acidophilic and One Neutrophilic Eukaryotic Algal Species with Diverse Mechanism for CO2 Acquisition
Lovejoy, Connie Laval University, Canada Small planktonic single celled eukaryotes from the Arctic Ocean

Plants

Proposer Affiliation Organism
Muehlbauer, Gary University of Minnesota Whole genome shotgun sequencing of the barley genome
Vogel, John USDA-ARS Surveying natural diversity of the model grass Brachypodium distachyon

Fungi

Proposer Affiliation Organism
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre, the Netherlands Comparative analysis of Aspergilli to facilitate novel strategies in fungal biotechnology
Goodwin, Stephen Purdue University Sequencing of pathogens and extremophiles in the Dothideomycetes
Hibbett, David S. Clark University Community proposal to sequence a diverse assemblage of saprotrophic Basidiomycota (Agaricomycotina)
Jeffries, Thomas Forest Products Laboratory Yeasts of Biotechnological, Taxonomic and Physiological Interest
Martin, Francis INRA, France Exploring the Genome Diversity of Mycorrhizal Fungi to Understand the Evolution and Functioning of Symbiosis in Woody Shrubs and Trees
Pisabarro, Antonio Public University of Navarre, Spain Comparative transcriptomics pipeline for saprophytic basidiomycota
Pringle, Anne Harvard University Comparative transcriptomics of closely related saprotrophic and ectomycorrhizal Amanita species.
Spatafora, Joseph Oregon State University Phylogenomics and the origin and diversification of Kingdom Fungi
Turgeon, Gillian Cornell University Cochliobolus: expanded and deepened
Turk, Martina University of Ljubljana, Slovenia The varieties of the black yeast-like fungus Aureobasidium pullulans: evolution and use in biotechnology

Bacteria/Archaea

Proposer Affiliation Organism
Bertilsson, Stefan Uppsala University, Sweden Genome wide diversity and population genetics in uncultured aquatic bacteria: single cell genomics of the freshwater SAR11 group and the ubiquitous Actinobacteria ac1 lineage
Chistoserdova, Ludmila University of Washington Genomes of fifty methylotrophs isolated from Lake Washington
Eichorst, Stephanie Los Alamos National Laboratory Populating the branches of the Phylum Acidobacteria with relevant soil strains
Eisen, Jonathan DOE JGI Continuation of the Genomic Encyclopedia of Bacteria and Archaea pilot project
Kalyuzhnaya, Marina University of Washington Coupling function to genomics via single-cell phenotyping and genome sequencing
Liu, Wen-Tso University of Illinois Single cells genomics for uncultured Archaea dominating in a terrestrial subsurface aquifer abundantly containing methane
Sievert, Stefan Woods Hole Oceanographic Institute Shedding Light on the Dark: Single-cell Genomics of Uncultivated Epsilonproteobacteria Inhabiting the Subseafloor Biosphere at Deep-Sea Hydrothermal Vents
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Generating reference genomes for marine ecosystem research: Single cell sequencing of ubiquitous, uncultured bacterioplankton clades
Tsiamis, George University of Ioannina, Greece Unraveling the unique microbial diversity of the Etoliko lagoon in Western Greece through a single cell genomics approach

Metagenomes

Proposer Affiliation Organism
Bryant, Donald Penn State University Metagenomic and metatranscriptomic analysis of anoxygenic, chlorophototrophic microbial mat communities in Yellowstone National Park
Campbell, Barbara University of Delaware Metagenomic and metatranscriptomic analysis of carbon cycling in Delaware coastal waters
Dionisi, Hebe Patagonian National Research Center, Argentina Microbial Community Structure and Metabolic Potential of Chronically Polluted Marine Sediments from Cold Regions of the Northern and Southern Hemispheres
Distel, Dan Ocean Genome Legacy Foundation, Center for Marine Research The complete shipworm microbiome: a comparative genomic and metagenomic analysis of lignocellulose-degrading microbial communities from multiple species of wood-boring bivalves.
Girguis, Peter Harvard University Linking mantle to microbe: a community-wide effort to ally hydrothermal vent microbial identity and ecology to geochemical cycles via metagenomics
Hallam, Steven University of British Columbia, Canada Microbial Systems Ecology of Expanding Oxygen Minimum Zones in the Eastern Subtropical North Pacific Ocean
Kerfeld, Cheryl DOE JGI Metagenomic Sequencing for Understanding Microbial Carbon Cycling by Biological Soil Crusts of Arid Lands
Macalady, Jennifer Penn State University Uncultivated and novel microbial lineages in terrestrial subsurface biofilms from a sulfidic aquifer
McMahon, Katherine University of Wisconsin High-resolution temporal and spatial dynamics of microbially-mediated carbon processing revealed though time-series metagenomics in freshwater lakes
Moran, Mary Ann University of Georgia Transcriptional analysis of a marine bacteria-phytoplankton binary model system
Muyzer, Gerard Delft University of Technology, the Netherlands Metagenomics of microbial communities from soda lakes and soda solonchak soils
Tringe, Susannah DOE JGI Microbial community impact on carbon sequestration in managed wetland “carbon farming”
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