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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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    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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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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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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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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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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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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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 FY08

Approved Proposals FY08

Following are the approved user proposals for fiscal year 2008.

Community Science Program (CSP) Plans

Large Eukaryotes

Organism Proposer Affiliation
Eucalyptus tree Myburg Univ. of Pretoria
Foxtail millet (Setaria italica) Bennetzen Univ. of Georgia
Porphyra purpurea (a marine red alga) Brawley Univ. of Maine

Small Eukaryotes

Organism Proposer Affiliation
Agaricus bisporus (a leaf-litter degrading homobasidiomycete ) Challen Univ. of Warwick
Heterodera glycines (Soybean Cyst Nematode) Lambert Univ. of illinois at Urbana-Champaign
Marchantia polymorpha Bowman Monash Univ. and Univ. of California Davis
Paxillus involutus (an ectomycorrhizal fungus) Tunlid Lund Univ.
Phaeocystis antarctica: A dominant phytoplankter and ice alga in the Southern Ocean Berg Stanford Univ.
Phaeocystis globosa Allen The Inst. for Genomic Research
ESTs for Pines and Other Conifers Dean Univ. of Georgia
Tetrahymena thermophila strain SB210 Collins Univ. of California Berkeley

Metagenomes

Organism Proposer Affiliation
Type I Accumulibacter McMahon Univ. of Wisconsin-Madison
Anammox bacteria (Scalindua marina, Brocadia fulgida, and Anammoxglobus propionicus) Jetten Radboud Univ.
A biogas-producing microbial community Wu Univ. of California Davis
Extreme microbial habitats across the Yellowstone geothermal ecosystem Inskeep Montana State Univ.

Isolates

Organism Proposer Affiliation
Allochromatium vinosum DSM 180(T) Dahl Univ. of Bonn
Uncultivated methane-oxidizing archaeon ANME-1 Hallam Univ. of British Columbia
Budding and non-budding stalked bacteria from aquatic environments (Asticcacaulis biprosthecum, Asticcacaulis excentricus, Brevundimonas subvibrioides, Herschia baltica, Hyphomicrobium denitrificans, and Rhodomicrobium vannielii) Brun Indiana Univ.
Diaphorobacter sp. strain TPSY, Ferrutens nitratireducens strain 2002, and Azospira suillum strain PS Coates Univ. of California Berkeley
Frankia strains (EuI1c, BCU110501, R43, BMG5.12, and AmMr)
Tisa Univ. of New Hampshire
Haloalkaliphilic sulfate-, thiosulfate- and sulfur-reducing bacteria (Desulfonatronovirga dismutans ASO3-1, Desulfovibrio alkaliphilus AHT2, and Dethiobacter alkaliphilus AHT1)
Muyzer Delft Univ. of Technology
Halothiobacillus neapolitanus and Thiomonas intermedia Heinhorst Univ. of Southern Mississippi
Thermophilic or hyperthermophilic methanoarchaea within the Methanococcales (Methanothermococcus okinawensis IH1, Methanotorris igneus Kol 5, Methanotorris formicicus Mc-S-70, Methanocaldococcus fervens AG86, Methanocaldococcus infernus ME, Methanocaldococcus vulcanius M7, and Methanocaldococcus strain FS406-22)
Whitman Univ. of Georgia
Type I and Type II methanotrophic bacteria (Methylomicrobium album BG8 and Methylosinus trichosporium OB3b)
Stein Univ. of California Riverside
Two Micromonosporas (aurantiaca and L5)
Hirsch Univ. of California Los Angeles
Natrialba magadii ATCC 43099
Maupin-Furlow Univ. of Florida
Pseudonocardia dioxanivorans CB1190
Mahendra Univ. of California Berkeley
Selenospirillum indicus Bini Rutgers Univ.
Starkeya novella Kappler Univ. of Queensland
Thermovibrio ammonificans DSM 15698
Vetriani Rutgers Univ.
Variovorax paradoxus strains (S110 and EPS)
Han Rensselaer Polytechnic Inst.
Zymomonas mobilis strains: Zymomonas mobilis strains: subsp. mobilis ATCC 10988, ATCC 29191, ATCC 31821 (ZM4), CP4; subsp. pomaceae ATCC 29192; sp. NCIB 11163
Pappas Univ. of Athens
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