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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 FY06

Approved Proposals FY06

Following are the approved user proposals for fiscal year 2006.

Community Science Program (CSP) Plans

Large Eukaryotes

Organism Proposer Affiliation
Arabidopsis lyrata and Capsella rubella (pink shepherd’s-purse) Weigel Max Planck Inst. for Developmental Biology
Mimulus guttatus (monkey flower) Willis Duke Univ.
Sorghum bicolor Paterson Univ. of Georgia

Small Eukaryotes

Organism Proposer Affiliation
Batrachochytrium dendrobatidis (frog-infecting chytrid fungus ) Taylor UC Berkeley
Bicyclus anynana (a butterfly) Long UC Irvine
Campanulales (Grammathotheca bergiana, Isotoma petraea, Lobelia anceps, L. angolenis, L. baumannii, L. cardinalis, L. erinus, L. galpinii, L. gregoriana, L. inflata, L. jasionoides, L. malowensis, L. laxa, L. linearis chloroplast, L. patula, L. siphilitica, L. spicata, L. thermalis, L. boninensis, L. morogoroensis chloroplast
L. holstii chloroplast, Monopsis alba, M. debilis, M. flava, M. stellaroides, Pratia angulata, P. nummularia, Wimmerella hederacea chloroplast, Carpodetus serratus Chloroplast, Cyphia volubilis chloroplast, Cyphia dentariifolia chloroplast, Cyphia angustiloba, Cyphia crenata Chloroplast, Cyphia digitata chloroplast, Cyphia tortilis chloroplast, Cyphia phyteuma chloroplast, Cyphia belfastica chloroplast, Brighamia insignis chloroplast, Porterella carnosula, Cyanea fissa chloroplast)
Knox Indiana Univ.
Ciona intestinalis (sea squirt) Lemaire CNRS, France
Crassostrea gigas (oyster) Hedgecock Univ. of Sourthern California
Hydractinia symbiolongicarpus Buss Yale Univ
Ictalurus punctatus and I. Furcatus (catfish) Liu-J Auburn Univ.
Melampsora larici-populina (poplar rust) Martin Institut National de la Recherche Agronomique
Lake Malawi cichlid fish (Metriaclima zebra, Labeotropheus fuelleborni, Melanochromis auratus, Copadichromis conophorus, Rhamphochromis esox) Kocher Univ. of New Hampshire
Mycosphaerella fijiensis (cause of black Sigatoka ) Goodwin USDA-ARS, Purdue Univ
Mytilus californianus (California mussel) Gracey Stanford Univ.
Ostreococcus (green unicellular alga, low-light strain) Palenik UC San Diego
Parhyale hawaiensis and Jassa slatteryi (amphipod crustaceans) Patel UC Berkeley
Petrolisthes cinctipes (porcelain crab) Stillman San Francisco State Univ.
Phycomyces blakesleeanus Corrochano Univ. of Seville
Phytophthora capsici (root and crown rot) Kingsmore Natl. Ctr. for Genome Resources
Piromyces sp. E2 (a chytrid fungus) Baker, S Pacific Northwest Natl. Lab.
Trichoderma virens Ebbole Texas A&M Univ.
Triphysaria versicolor (a parasitic wildflower) Yoder UC Davis
Xanthoria parietina (a lichen fungus) Crittendon Univ. of Nottingham

Bacteria and Archaea

Organism Proposer Affiliation
Acidovorax avenae subsp. Citrulli AAC00-1, Acidovorax JS42, Thermotoga RQ2, and Acidovorax symbiont (Verminephrobacter eiseniae EF01-2) Stahl Univ. of Washington
Verrucomicrobia (Akkermansia muciniphila, Chthoniobacter flavus Ellin428, bacterium Ellin 514, Opitutus terrae, and Victivallis vadensis ATCC BAA-548) Smidt Wageningen Univ.
Alaskan soil microbial community Handelsman Univ. of Wisconsin- Madison
Antarctic marine bacterioplankton Murray Desert Research Inst.
Bacillus coagulans 36D1 Shanmugam Univ. of Florida
Two caulobacter (Caulobacter sp. K31 and Maricaulis maris MCS10) Stephens Santa Clara Univ.
Crenarchaeote community (phylotype C1b.A1) Simon Oregon Health & Science Univ.
Euryarchaeota community Baker, B UC Berkeley
Six archaea (Halorubrum lacusprofundi ATCC 49239, Methanocorpusculum labreanum Z, Methanoculleus marisnigri JR1, Staphylothermus marinus F1, and Thermofilum pendens Woese/ Anderson Univ. of Illinois at Urbana- Champaign
Thermotogales (hyperthermophiles including Fervidobacterium nodosum Rt17-B1, Petrotoga mobilis SJ95, Thermosipho melanesiensis BI429, Thermotoga lettingae TMO, Thermotoga naphthophila, and Thermotoga petrophila RKU-1) Noll Univ. of Connecticut
Hypersaline microbial mats Pace Univ. of Colorado
Korarchaeota community (Candidatus Korarchaeum cryptofilum OPF8, two others) Stetter/ Elkins Univ. Regensberg, Diversa Corp.
Nitrosomonas (isolate IS-79 and oligotropha Nm45) Norton Utah State Univ.
Polynucleobacter necessarius STIR1 and Polynucleobacter sp. QWL-P1DMWA-1 pol_q Hahn Instit. for Limnology, Austria
Salinispora tropica CNB-440 and S. arenicola CNS205 (marine actinomycetes) Jensen Scripps Inst., UC San Diego
Sinorhizobium medicae WSM 419 Reeve Murdoch Univ.
Termite gut microbial community Leadbetter Caltech
Terephthalate (TA) degrading community Liu/ Hugenholtz Natl. Univ. of Singapore
Hyperthermophilic Archaeal Species (Thermoproteus neutrophilus V24Sta , Pyrobaculum aresenaticum DSM 13514, P. calidifontis, P. islandicum, Caldivirga maquilingensis IC-167) Lowe UC Santa Cruz
Opitutaceae bacterium TAV2 (ex. Verrucomicrobium sp. TAV2) Schmidt/ Rodrigues Michigan State Univ.
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