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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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    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 FY07

Approved Proposals FY07

Following are the approved user proposals for fiscal year 2007.

Community Science Program (CSP) Plans

Large Eukaryotes

Organism Proposer Affiliation
Aquilegia formosa Hodges UC Santa Barbara
Brachypodium distachyon (Poaceae) Vogel USDA-ARS
Gossypium (cotton) Paterson Univ. of Georgia
Manihot esculenta (cassava) Fauquet Danforth Plant Science Ctr.

Small Eukaryotes

Organism Proposer Affiliation
Cryphonectria parasitica (chestnut blight fungus) Nuss Univ. of Maryland Biotech. Inst.
Reef-building corals and dinoflagellate symbionts (ESTs from Acropora palmata, Montastraea faveolata, and Symbiodinium clade A and clade B) Medina Univ. of California, Merced
Fragilariopsis cylindrus (a diatom) Mock Univ. of Washington
Guillardia theta and Bigelowiella natans Archibald Dalhousie Univ.
Heterobasidion annosum
Stenlid Swedish Univ. of Agricultural Sciences
Three species of Neurospora (N. discreta, N. tetrasperma FGSC2508, N. tetrasperma FGSC2509)
Taylor Univ. of California, Berkeley
Peronosporomycete mtDNAs (26) Hudspeth Northern Illinois Univ.
Pleurotus ostreatus (oyster mushroom) Pisabarro Public Univ. of Navarre
Riftia pachyptila (deep-sea tubeworm) Girguis Harvard Univ.
Switchgrass Tobias USDA-ARS
Tetranychus urticae (two-spotted spider mite) Grbic Univ. of Western Ontario
Thellungiella halophila
Schumaker Univ. of Arizona
Mating loci from Volvox carteri and Chlamydomonas reinhardtii Umen Salk Inst.

Bacteria and Archaea

Organism Proposer Affiliation
Candidatus Amoebophilus asiaticus 5a2 and Encarsia symbiont Cand. Cardinium hertigii
Horn Univ. of Vienna
Actinobacteria (Arthrobacter chlorophenolicus A6 and Micrococcus luteus) Jansson Swedish Univ. of Agricultural Sciences
Beggiatoa alba Mueller Morgan State Univ.
Burkholderia (B. ambifaria IOP40-10, B. ambifaria MEX-5, B. graminis C4D1M, B. sp. SEMIA 6167, B. sp. strain H160, B. sp. strain 144F, B. sp. strain CCGE1001, B. sp. strain CCGE1003, B. cepacia ATCC 25416) Tiedje Michigan State Univ.
Anaerobic benzene-degrading methanogenic consortium (Chloroflexi, Desulfobacterium sp., Desulfosporosinus sp., Methanomicrobiales-like sp., Methanosaeta sp., Methanosarcinales-like spp) Edwards Univ. of Toronto
Crenothrix polyspora enrichment Wagner Univ. of Vienna
Cyanothece strains Pakrasi Washington Univ.
Dechlorinating community (KB-1) (Dehalococcoides, Geobacter, Methanosarcina, Spirochete, Sporomusa) Edwards Univ. of Toronto
Lithifying mat communities of marine stromatolites (Desulfovibrio sp. H0407_12.1Lac, Schizothrix gebeleni sp.A and sp. B, Solentia sp., Sulfate Reducing Bacterium sp. B, and sulfur-oxidizing bacteria) Decho Univ. of South Carolina
Candidatus Endomicrobium trichonymphae, Elusimicrobium minutum Pei191 Brune Max Planck Institute for Terrestrial Microbiology
Symbiont from the basal clade of the Frankiaceae Benson Univ. of Connecticut
Six freshwater iron-oxidizing bacteria (Gallionella ferruginea capsiferriformans ES-2, Leptothrix cholodnii SP-6, Rhodobacter sp. str. SW2, Rhodopseudomonas palustris TIE-1, and Sideroxydans lithotrophicus, Acidovorax delafieldii 2AN) Emerson Amer. Type Culture Collection
Microbiome resident in the foregut of the tammar wallaby (Macropus eugenii) McSweeney CSIRO
Methanomicrococcus blatticola Hackstein Radboud Univ. Nijmegen
Methylocella silvestris BL2, Methylocapsa acidiphila B2, and Beijerinckia indica subsp. indica Dunfield Inst. of Geological and Nuclear Sciences, New Zealand
Pedomicrobium manganicum Mackenzie, Univ. of Texas, Houston
Microbial community (plasmid mobilome) in wastewater treatment plant van der Meer Univ. of Lausanne
Rhizobium leguminosarum bv trifolii (strains WSM1325 and WSM2304) Reeve Murdoch Univ.
Near-shore anoxic basin: Saanich Inlet Hallam Univ. of British Columbia
Thauera sp. MZ1T Sayler Univ. of Tennessee
Thermolithobacter ferrireducens Wiegel Univ. of Georgia
Haloalkaliphilic sulfur-oxidizing bacteria (Thioalkalivibrio sp. HL-EbGR7, and T. sp. K90 mix) Muyzer Delft Univ. of Technology
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