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Community Sequencing Program FY2012

Proposer Affiliation Project Description
Acinas, Silvia ICM-CSIC, Spain Microbial metagenomics and transcriptomics from a global deep-ocean expedition
Andresson, Olafur University of Iceland Sequencing of the three cultured partners of the lichen Lobaria pulmonaria and the sequencing of the transcriptomes from the natural tripartite lichen under selected and controlled conditions.
Banfield, Jill University of California, Berkeley Terabase sequencing for comprehensive genome reconstruction to assess metabolic potential for environmental bioremediation
Brodie, Eoin DOE JGI Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.
Brutnell, Thomas Boyce Thompson Institute for Plant Research Development of sequence-based community tools for Setaria viridis-a model genetic system for C4 grasses
Bucking, Heike South Dakota State University Exploring the transcriptome of perennial grasses in association with beneficial microorganisms to increase biomass production and environmental sustainability of bioenergy production
Cary, Stephen University of Delaware Understanding terrestrial microbial biocomplexity in an Antarctic desert landscape: resolving universal drivers of community structure and function in a trophically simple system
Crouch, Jo Anne USDA-ARS Genomic signatures of pathogenicity and endophytism in five species of grass-associated Colletotrichum impacting the health and production of bioenergy feedstocks, agriculture and the environment
Dangl, Jeff University of North Carolina at Chapel Hill Plant associated metagenomes--Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems.
DeAngelis, Kristen University of Massachusetts Microbial ecology and genomics of carbon-storing bacteria in rhizosphere soils
Dubilier, Nicole Max Planck Institute for Marine Microbiology, Germany Understanding novel pathways for energy and carbon use in bacterial symbionts of gutless marine worms
Emerson, David Bigelow Laboratory for Ocean Sciences Single cell genome sequencing of biomineralizing bacteria
Fierer, Noah University of Colorado Cross-site metagenomic analyses to assess the impacts of experimental nitrogen additions on belowground carbon dynamics
 Fredrickson, Jim Pacific Northwest National Laboratory Microbial Interactions in Extremophilic Mat Communities
Gilbert, Jack Argonne National Laboratory Creating a successional model for carbon remediation in the Gulf of Mexico
Gross, Stephen DOE JGI The Agave Microbiome: Exploring the role of microbial communities in plant adaptations to desert environments
Hazen, Samuel University of Massachusetts Creating a multi-functional library of grass transcription factors for the energy crop model system Brachypodium distachyon
Hess, Matthias Washington State University Expression profile of biomass-degrading fungi inhabiting the cow rumen
Kelly, William AgResearch, New Zealand The Hungate 1000. A catalogue of reference genomes from the rumen microbiome.
Kerfeld, Cheryl DOE JGI Enhancing Bacterial Carbon Capture and Sequestration: Synthesis of Building Blocks for the Carboxysome, A Metabolic Module for CO2 Fixation
Kyrpides, Nikos DOE JGI Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project
Laplaze, Laurent Institut de Recherche pour le Developpement (IRD), France Transcriptome Analysis of Salt Tolerance in Casuarina trees
Martin, Francis INRA, France Metatranscriptomics of Soil Forest Ecosystems
McKay, Robert Bowling Green State University Metagenomics and metatranscriptomics of the Lake Erie ‘dead zone’: a seasonal source of greenhouse gases
McMahon, Katherine University of Wisconsin, Madison Dynamics of microbial carbon processing pathways across a decade in a freshwater eutrophic lake revealed through metagenomic sequencing
Mock, Thomas University of East Anglia, UK Sea of Change: Eukaryotic Phytoplankton Communities in the Arctic Ocean
Mohn, William University of British Columbia, Canada Metagenomic and metatranscriptomic analysis of forest soil communities across North America
Moran, Mary Ann University of Georgia The Genetic Basis for Heterotrophic Carbon Processing in the Sea
Murray, Alison Desert Research Institute Lake Vida brine microbial community (LVBMCo) genomics and transcriptomics - a window into diversity, adaptation and processes in extreme cold
Gerard Muyzer Delft University of Technology Genome sequencing of 100 strains of the haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacterium Thioalkalivibrio
Nealson, Kenneth University of Southern California Life at the edge: community cooperation and success in a very extreme (ultrabasic and ultra-reducing) environment
Ohm, Robin DOE JGI Towards functional genomics: development of Schizophyllum commune as a model system to study lignocellulose degradation
Pester, Michael University of Vienna, Austria Targeted metagenomics and metatranscriptomics of a sulfate-reducing rare biosphere member and potentially novel sulfate reducers that impact methane emission from peatlands
Powell, Amy Sandia National Laboratories A Phylogenomic Framework to Investigate Fungal Thermophily
Pukkila, Patricia University of North Carolina at Chapel Hill Functional genomics in the model mushroom Coprinopsis cinerea
Rodrigues, Jorge University of Texas at Arlington Profiling metagenomic consequences of Amazon deforestation at different spatial scales
Schadt, Christopher Oak Ridge National Laboratory Defining the Populus Microbiome: Role of Genotype by Environment Interactions in Shaping the Rhizosphere Microbiome of Populus trichocarpa
Schrenk, Matthew East Carolina University Metagenome-enabled Investigations of Carbon and Hydrogen Fluxes within the Serpentinite-hosted Subsurface Biosphere
Spatafora, Joseph Oregon State University 1000 Fungal Genomes
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Dark ocean microbial single cell genomics
Wing, Rod University of Arizona Empowering functional plant genomics with genomes and transcriptomes of the top 20 Brassicales

 

Community Sequencing Program FY2011

Proposer Affiliation Project Description
Algae
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
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
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
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
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”

 

Community Sequencing Program FY2010

Proposer Affiliation Project Description
Eukaryotes
Collier, Jackie Stony Brook University Four Labyrinthulomycete species
Cullen, Daniel US Forest Service, Forest Products Laboratory Homkaryotic derivative of Postia placenta
Cullen, Daniel US Forest Service, Forest Products Laboratory Lignin-degrading fungus Phlebiopsis gigantea
Goodwin, Stephen USDA-ARS and Purdue University Dothideomycetes plant pathogens
Grossniklaus, Ueli University of Zurich Apomictic plant Boechera holboellii
Koppisch, Andy Los Alamos National Laboratory Colony forming microalga Botryococcus braunii var Showa
Kubisiak, Thomas US Forest Service, Southern Research Station Fusiform rust fungus Cronartium quercuum f.sp. fusiforme
Martin, Francis Institut National de la Recherche Agronomique Pan-global basidiomycetes Pisolithus tinctorius and Pisolithus microcarpus
Moreau, Herve CNRS and UPMC Resequencing Ostreococcus tauri
Paterson, Andrew University of Georgia Resequencing sorghum
Phister, Trevor North Carolina State University Completion of the Dekkera (Brettanomyces) bruxellensis genome sequence
Pringle, Anne Harvard University Cellulose degrading fungus Amanita thiersii
Quatrano, Ralph Washington University in St. Louis Ceratodon purpureus(moss)
Reeve, Wayne Murdoch University Phytopathogenic oomycete Phytophthora cinnamomi
Roossinck, Marilyn Samuel Roberts Noble Foundation Alteration of Curvularia protuberata transcripts due to presence of Curvularia thermal tolerance virus
Vyverman, Wim Ghent University Diatom transcriptome and genome
Weeks, Donald University of Nebraska-Lincoln Transcriptome analyses of Chlamydomonas and Chlorella
Zhong, Shaobin North Dakota State University Fungal pathogen Cochliobolus sativus
Bacteria and Archaea
Auchtung, Jennifer Michigan State University Role of population microdiversity in adaptation to environmental redox gradients
Anderson, Iain DOE Joint Genome Institute Xylan degraders
Anderson, Iain DOE Joint Genome Institute Genomic survey of haloarchaeal genomes
Bayer, Travis University of California, San Francisco Actinotalea fermentans
Bollmann, Annette Miami University Five isolates from the contaminated subsurface sediment of Oak Ridge’s FRC area
Brown, Igor  NASA Johnson Space Center Two strains of Cyanobacteria for biological remediation
Bryant, Donald Penn State University Representative photosynthetic purple sulfur bacteria
Cavicchioli, Rick University of New South Wales Novel haloarchaea from Deep Lake
Coleman, Nicholas University of Sydney Ethene and vinyl chloride-oxidizing Mycobacterium strains
Cooper, Vaughn University of New Hampshire Adaptive mechanisms in Burkholderia biofilms
Copley, Shelley University of Colorado at Boulder Sphingobium chlorophenolicum
Daly, Michael Uniformed Services University of the Health Sciences Radiation-resistant bacterium Deinococcus grandis
Dopson, Mark Umeå University Psychrotolerant Acidithiobacillus species
Dvornyk, Volodymyr University of Hong Kong Nostoc linckia from “Evolution Canyon”
Edwards, Elizabeth University of Toronto Novel acetogenic bacterial isolates from dechlorinating microbial mixed cultures
Emerson, David Bigelow Laboratory for Ocean Sciences Two novel 'Zetaproteobacteria' from the ocean
Green, Stefan Florida State University Denitrifying bacterial isolates
Grzymski, Joseph Desert Research Institute Microbes integral to the cycling of sulfate and iron
Haggblom, Max Rutgers University Acidobacterium species from Arctic tundra soils
Hedlund, Brian University of Nevada Las Vegas Thermophiles in Great Basin hot springs
Kappler, Ulrike The University of Queensland Alkaliphilic sulfur oxidizing bacteria for sulfur pollution remediation
Lewis, Gillian University of Auckland Freshwater manganese depositing β-proteobacterium (Siderocapsaceae)
Liao, James University of California, Los Angeles Reverse metabolic engineering of Escherichia coli
Liu, Wen-Tso University of Illinois at Urbana-Champaign Comparison of novel methanogens from peatlands and bioreactors
Liu, Wen-Tso University of Illinois at Urbana-Champaign Obligate syntrophic bacteria capable of phthalate isomer compound degradation in methanogenic conditions
Martinez, Robert University of Alabama ORFRC Rahnella sp. Y9602
Mavrommatis, Konstantinos DOE Joint Genome Institute Cyanobacteria (Synechocystis) transcriptome
Mayali, Xavier Lawrence Livermore National Laboratory Marine Roseobacter RCA cluster bacterial strain LE17
Mills, David University of California, Davis Acetobacter aceti ATCC 23746
Muyzer, Gerard Delft University of Technology Haloalkaliphilic chemolithoautotrophic Thioalkalivibrio bacteria
Nesbø, Camilla University of Oslo Thermotogales strain mesG1.Ag.4.1
Norton, Jeanette M. Utah State University Nitrosomonas cryotolerans and Nitrosospira briensis for comparative phylogenomics of ammonia-oxidizing bacteria
Pappas, Katherine University of Athens Zymomonas mobilis transcriptomes and resequencing Z. mobilis industrial strain ZM4
Reeve, Wayne Murdoch University Rhizobia of clover, pea/bean and
lupin microsymbionts
Robb, Frank Center of Marine Biotechnology Carbon monoxide oxidizing thermophiles
Rodrigues, Jorge University of Texas at Arlington Genome closure of lignocellulosic degrader Verrucomicrobium sp. strain TAV2.
Sanchez Amat, Antonio University of Murcia Marine bacterial genus Marinomonas
Sello, Jason Brown University Biomass-degrading bacteria Streptomyces viridosporus ATCC 39115 and Streptomyces setonii ATCC 39116
Smidt, Hauke Wageningen University Halorespiring Firmicutes
Stabb, Eric The University of Georgia Research Foundation Mutations in Vibrio fischeri
Stein, Lisa University of Alberta Methanotrophic Bacteria from diverse environments
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Single cell genome sequencing of mesopelagic bacterioplankton
Tisa, Louis University of New Hampshire An atypical Frankia isolate and Non-Frankia Actinobacteria from Actinorhizal Plants
Vieille, Claire Michigan State University Resequencing of Actinobacillus succinogene
Ward, David Montana State University Synechococcus cyanobacterial isolates
Metagenomes
Breitbart, Mya University of South Florida Modern freshwater microbialites
Chistoserdova, Ludmila University of Washington Functional metagenomics of methane and nitrogen cycles in freshwater lakes
Davidson, Seana University of Washington Metagenome function of the Earthworm egg capsule bacterial community
Deng, Li University of Arizona Viruses that infect freshwater cyanobacteria
Edwards, Elizabeth University of Toronto Dehalobacter-containing dechlorinating community
Hedlund, Brian University of Nevada, Las Vegas Great Boiling Spring sediment and water microbial communities
Kirchman, David University of Delaware Metagenomic analysis of methane degradation in Arctic coastal waters and sediments
Madsen, Eugene Cornell University Naphthalene biodegrading microbial community
Mincer, Tracy Woods Hole Oceanographic Institute Natural microbial community associated with the cyanobacteria Trichodesmium
Moon, Christina AgResearch Limited Lignocellulolytic enzyme discovery from the rumen
Powell, Amy Sandia National Laboratories Eukaryotic microbial metatranscriptome of blue grama grass rhizosphere soils
Sullivan, Matthew University of Arizona Viral community in the Subarctic Pacific Ocean
Sullivan, Matthew University of Arizona Viral community in the Mediterranean Sea
Taylor, Mike University of Auckland Microbial symbionts of New Zealand's endemic wood-degrading insects
Waldrop, Mark US Geological Services Permafrost Soil Microbiota
Ward, Naomi University of Wyoming Metatranscriptomic analysis of bacterial-algal interactions
Warnecke, Falk Friedrich Schiller University of Jena Desert locust (Schistocerca gregaria)
Worden, Alexandra Monterey Bay Aquarium Research Institute Metagenomics of uncultured marine eukaryotes

 

Community Sequencing Program FY2009

Organism Proposer Affiliation
Eukaryotes
Resequencing Trichoderma reesei
Why?		 Scott Baker Pacific Northwest National Lab
Rhizopogon salebrosus (ectomycorrhizal fungus)
Why?		 Thomas Bruns University of California, Berkeley
Ceriporiopsis subvermispora (lignin-degrading fungus)
Why?		 Daniel Cullen USDA Forest Products Laboratory
Gene expression in Chlamydomonas reinhardtii
Why?		 Maria Ghirardi Natl. Renewable Energy Lab.
Paralvinella sulfincola (polychaete worm)
Why?		 Peter Girguis Harvard Univ.
Thalassiosira rotula (diatom)
Why?		 Bethany Jenkins Univ. of Rhode Island
Dendroctonus frontalis (southern pine beetle) ESTs
Why?		 Scott Kelley San Diego State Univ.
Botryococcus braunii (Oil-Producing Green Microalga) cDNA
Why?		 Andrew Koppisch Los Alamos Natl. Lab.
Chlamydomonas and Volvox transcriptomes
Why?		 Sabeeha Merchant Univ. of California, Los Angeles
Spirodela polyrhiza (duckweed)
Why?		 Todd Michael Rutgers
Zostera marina (seagrass)
Why?		 Jeanine Olsen University of Groningen
Gossypium (cotton)
Why?		 Andrew Paterson Univ. of Georgia
Pine BAC Sequencing
Why?		 Daniel Peterson Mississippi State Univ.
Hansenula polymorpha strain NCYC 495 leu1.1 (ATCC MYA-335)
Why?		 Andriy Sibirny Institute of Cell Biology, Ukraine
Resequencing of Brachypodium distachyon
Why?		 John Vogel USDA-ARS Western Regional Research Center
Nanoflagellates: Paraphysomonas, Ochromonas, and Spumella
Why?		 Alexandra Worden Monterey Bay Aquarium Research Institute
Bacteria and Archaea
Four diverse cellulose degrading microbes
Why?		 Iain Anderson DOE JGI
Escherichia coli MG1655
Why?		 John Battista Lousiana State Univ.
Sinorhizobium meliloti strains AK83 and BL225C
Why?		 Emanuele Biondi Universita' di Firenze
Methylotenera species
Why?		 Ludmila Chistoserdova Univ. of Washington
SAR11 Genome Evolution
Why?		 Stephen Giovannoni Oregon State Univ.
Rhodopseudomonas palustris strain DX-1
Why?		 Caroline Harwood Univ. of Washington
Cycloclasticus pugetii (a PAH-Degrading Bacterium)
Why?		 Russell Herwig Univ. of Washington
Burkholderia sp. Ch1-1 and Burkholderia sp. Cs1-4
Why?		 William Hickey Univ. of Wisconsin
Sphaerochaeta pleomorpha and Sphaerochaeta globus
Why?		 Frank Loeffler Georgia Inst. of Technology
Archaeal transcriptomes
Why?		 Todd Lowe Univ. of California Santa Cruz
Dehalogenimonas lykanthroporepellens
Why?		 William Moe Louisiana State Univ.
Desulfurococcus (hyperthermophilic archaeon)
Why?		 Biswarup Mukhopadhyay Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.
Mesorhizobium ciceri bv biserrulae (strains WSM1271, WSM2073 and WSM2075) (legume symbionts)
Why?		 Kemanthi Nandasena Murdoch Univ.
Thermoacidophiles of deep-sea hydrothermal vents
Why?		 Anna-Louise Reysenbach Portland State Univ.
Alicycliphilus denitrificans strain BC
Why?		 Alfons Stams Wageningen Univ.
Desulfotomaculum species
Why?		 Alfons Stams Wageningen Univ.
Freshwater Actinobacteria belonging to the acI lineage
Why?		 Falk Warnecke DOE JGI
Metagenomes
Novel subsurface microbial phylotypes
Why?		 Jennifer Biddle Univ. of North Carolina, Chapel Hill
Highly efficient, highly stable, reductive dechlorinating bioreactor
Why?		 Eoin Brodie Lawrence Berkeley National Lab
Bankia setacea (shipworm) metagenome.
Why?		 Daniel Distel Ocean Genome Legacy
Hoatzin crop microbiome
Why?		 Maria Dominguez-Bello Univ. of Puerto Rico
Ammonia-oxidizing archaeal enrichment culture
Why?		 Christopher Francis Stanford Univ.
Subarctic Pacific Ocean
Why?		 Steven Hallam Univ. of British Columbia
Lake Vostok accretion ice
Why?		 Philip Hugenholtz DOE JGI
Microbial communities at the Hanford 300A IFC Site.
Why?		 Allan Konopka Pacific Northwest Natl. Lab.
PCE-dechlorinating mixed communities
Why?		 Ruth Richardson Cornell Univ.
Uncultivated marine viruses
Why?		 Grieg Steward Univ. of Hawaii
Great Salt Lake
Why?		 Bart Weimer Utah State Univ.

 

Community Sequencing Program FY2008

Organism Proposer Affiliation
Large Eukaryotes
Eucalyptus tree
Why?		 Myburg Univ. of Pretoria
Foxtail millet (Setaria italica)
Why? 		Bennetzen Univ. of Georgia
Porphyra purpurea (a marine red alga)
Why?		 Brawley Univ. of Maine
Small Eukaryotes
Agaricus bisporus (a leaf-litter degrading homobasidiomycete )
Why?		 Challen Univ. of Warwick
Heterodera glycines (Soybean Cyst Nematode)
Why?		 Lambert Univ. of illinois at Urbana-Champaign
Marchantia polymorpha
Why? 		Bowman Monash Univ. and Univ. of California Davis
Paxillus involutus (an ectomycorrhizal fungus)
Why?
Tunlid Lund Univ.
Phaeocystis antarctica: A dominant phytoplankter and ice alga in the Southern Ocean
Why?		 Berg Stanford Univ.
Phaeocystis globosa
Why?		 Allen The Inst. for Genomic Research
ESTs for Pines and Other Conifers
Why?		 Dean Univ. of Georgia
Tetrahymena thermophila strain SB210
Why?		 Collins Univ. of California Berkeley
Metagenomes
Type I Accumulibacter
Why? 		McMahon Univ. of Wisconsin-Madison
Anammox bacteria (Scalindua marina, Brocadia fulgida, and Anammoxglobus propionicus)
Why?		 Jetten Radboud Univ.
A biogas-producing microbial community
Why?		 Wu Univ. of California Davis
Extreme microbial habitats across the Yellowstone geothermal ecosystem
Why?		 Inskeep Montana State Univ.
Isolates
Allochromatium vinosum DSM 180(T)
Why?		 Dahl Univ. of Bonn
Uncultivated methane-oxidizing archaeon ANME-1
Why?		 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)
Why?		 Brun Indiana Univ.
Diaphorobacter sp. strain TPSY, Ferrutens nitratireducens strain 2002, and Azospira suillum strain PS
Why? 		Coates Univ. of California Berkeley
Frankia strains (EuI1c, BCU110501, R43, BMG5.12, and AmMr)
Why?		 Tisa Univ. of New Hampshire
Haloalkaliphilic sulfate-, thiosulfate- and sulfur-reducing bacteria (Desulfonatronovirga dismutans ASO3-1, Desulfovibrio alkaliphilus AHT2, and Dethiobacter alkaliphilus AHT1)
Why?		 Muyzer Delft Univ. of Technology
Halothiobacillus neapolitanus and Thiomonas intermedia
Why?		 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)
Why?		 Whitman Univ. of Georgia
Type I and Type II methanotrophic bacteria (Methylomicrobium album BG8 and Methylosinus trichosporium OB3b)
Why?		 Stein Univ. of California Riverside
Two Micromonosporas (aurantiaca and L5)
Why?		 Hirsch Univ. of California Los Angeles
Natrialba magadii ATCC 43099
Why?		 Maupin-Furlow Univ. of Florida
Pseudonocardia dioxanivorans CB1190
Why?		 Mahendra Univ. of California Berkeley
Selenospirillum indicus
Why? 		Bini Rutgers Univ.
Starkeya novella
Why? 		Kappler Univ. of Queensland
Thermovibrio ammonificans DSM 15698
Why?		 Vetriani Rutgers Univ.
Variovorax paradoxus strains (S110 and EPS)
Why?		 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
Why?		 Pappas Univ. of Athens

 

Community Sequencing Program FY2007

Organism Proposer Affiliation
Large Eukaryotes
Aquilegia formosa
Why? 		Hodges UC Santa Barbara
Brachypodium distachyon (Poaceae)
Why? 		Vogel USDA-ARS
Gossypium (cotton)
Why? 		Paterson Univ. of Georgia
Manihot esculenta (cassava)
Why? 		Fauquet Danforth Plant Science Ctr.
Small Eukaryotes
Cryphonectria parasitica (chestnut blight fungus)
Why? 		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)
Why?		 Medina Univ. of California, Merced
Fragilariopsis cylindrus (a diatom)
Why? 		Mock Univ. of Washington
Guillardia theta and Bigelowiella natans
Why? 		Archibald Dalhousie Univ.
Heterobasidion annosum
Why? 		Stenlid Swedish Univ. of Agricultural Sciences
Three species of Neurospora (N. discreta, N. tetrasperma FGSC2508, N. tetrasperma FGSC2509)
Why? 		Taylor Univ. of California, Berkeley
Peronosporomycete mtDNAs (26)
Why? 		Hudspeth Northern Illinois Univ.
Pleurotus ostreatus (oyster mushroom)
Why?		 Pisabarro Public Univ. of Navarre
Riftia pachyptila (deep-sea tubeworm)
Why?		 Girguis Harvard Univ.
Switchgrass
Why? 		Tobias USDA-ARS
Tetranychus urticae (two-spotted spider mite)
Why? 		Grbic Univ. of Western Ontario
Thellungiella halophila
Why? 		Schumaker Univ. of Arizona
Mating loci from Volvox carteri and Chlamydomonas reinhardtii
Why? 		Umen Salk Inst.
Bacteria and Archaea
Candidatus Amoebophilus asiaticus 5a2 and Encarsia symbiont Cand. Cardinium hertigii
Why? 		Horn Univ. of Vienna
Actinobacteria (Arthrobacter chlorophenolicus A6 and Micrococcus luteus)
Why? 		Jansson Swedish Univ. of Agricultural Sciences
Beggiatoa alba
Why? 		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)
Why? 		Tiedje Michigan State Univ.
Anaerobic benzene-degrading methanogenic consortium (Chloroflexi, Desulfobacterium sp., Desulfosporosinus sp., Methanomicrobiales-like sp., Methanosaeta sp., Methanosarcinales-like spp)
Why? 		Edwards Univ. of Toronto
Crenothrix polyspora enrichment
Why?		 Wagner Univ. of Vienna
Cyanothece strains
Why? 		Pakrasi Washington Univ.
Dechlorinating community (KB-1) (Dehalococcoides, Geobacter, Methanosarcina, Spirochete, Sporomusa)
Why? 		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)
Why? 		Decho Univ. of South Carolina
Candidatus Endomicrobium trichonymphae, Elusimicrobium minutum Pei191
Why? 		Brune Max Planck Institute for Terrestrial Microbiology
Symbiont from the basal clade of the Frankiaceae
Why? 		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)
Why? 		Emerson Amer. Type Culture Collection
Microbiome resident in the foregut of the tammar wallaby (Macropus eugenii)
Why?		 McSweeney CSIRO
Methanomicrococcus blatticola
Why? 		Hackstein Radboud Univ. Nijmegen
Methylocella silvestris BL2, Methylocapsa acidiphila B2, and Beijerinckia indica subsp. indica
Why? 		Dunfield Inst. of Geological and Nuclear Sciences, New Zealand
Pedomicrobium manganicum
Why? 		Mackenzie, Univ. of Texas, Houston
Microbial community (plasmid mobilome) in wastewater treatment plant
Why? 		van der Meer Univ. of Lausanne
Rhizobium leguminosarum bv trifolii (strains WSM1325 and WSM2304)
Why? 		Reeve Murdoch Univ.
Near-shore anoxic basin: Saanich Inlet
Why?		 Hallam Univ. of British Columbia
Thauera sp. MZ1T
Why? 		Sayler Univ. of Tennessee
Thermolithobacter ferrireducens
Why? 		Wiegel Univ. of Georgia
Haloalkaliphilic sulfur-oxidizing bacteria (Thioalkalivibrio sp. HL-EbGR7, and T. sp. K90 mix)
Why? 		Muyzer Delft Univ. of Technology

 

Community Sequencing Program FY2006

Organism Proposer Affiliation
Large Eukaryotes
Arabidopsis lyrata and Capsella rubella (pink shepherd's-purse)
Why? 		Weigel Max Planck Inst. for Developmental Biology
Mimulus guttatus (monkey flower)
Why? 		Willis Duke Univ.
Sorghum bicolor
Why? 		Paterson Univ. of Georgia
Small Eukaryotes
Batrachochytrium dendrobatidis (frog-infecting chytrid fungus )
Why?		 Taylor UC Berkeley
Bicyclus anynana (a butterfly)
Why?		 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)
Why?		 Knox Indiana Univ.
Ciona intestinalis (sea squirt)
Why?		 Lemaire CNRS, France
Crassostrea gigas (oyster) Hedgecock Univ. of Sourthern California
Hydractinia symbiolongicarpus
Why?		 Buss Yale Univ
Ictalurus punctatus and I. Furcatus (catfish)
Why?		 Liu-J Auburn Univ.
Melampsora larici-populina (poplar rust)
Why?		 Martin Institut National de la Recherche Agronomique
Lake Malawi cichlid fish (Metriaclima zebra, Labeotropheus fuelleborni, Melanochromis auratus, Copadichromis conophorus, Rhamphochromis esox)
Why?		 Kocher Univ. of New Hampshire
Mycosphaerella fijiensis (cause of black Sigatoka )
Why?		 Goodwin USDA-ARS, Purdue Univ
Mytilus californianus (California mussel)
Why?		 Gracey Stanford Univ.
Ostreococcus (green unicellular alga, low-light strain)
Why?		 Palenik UC San Diego
Parhyale hawaiensis and Jassa slatteryi (amphipod crustaceans)
Why?		 Patel UC Berkeley
Petrolisthes cinctipes (porcelain crab)
Why?		 Stillman San Francisco State Univ.
Phycomyces blakesleeanus
Why?		 Corrochano Univ. of Seville
Phytophthora capsici (root and crown rot)
Why?		 Kingsmore Natl. Ctr. for Genome Resources
Piromyces sp. E2 (a chytrid fungus)
Why?		 Baker, S Pacific Northwest Natl. Lab.
Trichoderma virens
Why?		 Ebbole Texas A&M Univ.
Triphysaria versicolor (a parasitic wildflower)
Why?		 Yoder UC Davis
Xanthoria parietina (a lichen fungus)
Why?		 Crittendon Univ. of Nottingham
Bacteria and Archaea
Acidovorax avenae subsp. Citrulli AAC00-1, Acidovorax JS42, Thermotoga RQ2, and Acidovorax symbiont (Verminephrobacter eiseniae EF01-2)
Why? 		Stahl Univ. of Washington
Verrucomicrobia (Akkermansia muciniphila, Chthoniobacter flavus Ellin428, bacterium Ellin 514, Opitutus terrae, and Victivallis vadensis ATCC BAA-548)
Why?		 Smidt Wageningen Univ.
Alaskan soil microbial community
Why?		 Handelsman Univ. of Wisconsin- Madison
Antarctic marine bacterioplankton
Why?		 Murray Desert Research Inst.
Bacillus coagulans 36D1
Why? 		Shanmugam Univ. of Florida
Two caulobacter (Caulobacter sp. K31 and Maricaulis maris MCS10)
Why?		 Stephens Santa Clara Univ.
Crenarchaeote community (phylotype C1b.A1)
Why?		 Simon Oregon Health & Science Univ.
Euryarchaeota community
Why?		 Baker, B UC Berkeley
Six archaea (Halorubrum lacusprofundi ATCC 49239, Methanocorpusculum labreanum Z, Methanoculleus marisnigri JR1, Staphylothermus marinus F1, and Thermofilum pendens
Why?		 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)
Why?		 Noll Univ. of Connecticut
Hypersaline microbial mats
Why?		 Pace Univ. of Colorado
Korarchaeota community (Candidatus Korarchaeum cryptofilum OPF8, two others)
Why?		 Stetter/ Elkins Univ. Regensberg, Diversa Corp.
Nitrosomonas (isolate IS-79 and oligotropha Nm45)
Why?		 Norton Utah State Univ.
Polynucleobacter necessarius STIR1 and Polynucleobacter sp. QWL-P1DMWA-1 pol_q
Why?		 Hahn Instit. for Limnology, Austria
Salinispora tropica CNB-440 and S. arenicola CNS205 (marine actinomycetes)
Why?		 Jensen Scripps Inst., UC San Diego
Sinorhizobium medicae WSM 419
Why? 		Reeve Murdoch Univ.
Termite gut microbial community
Why?		 Leadbetter Caltech
Terephthalate (TA) degrading community
Why?		 Liu/ Hugenholtz Natl. Univ. of Singapore
Hyperthermophilic Archaeal Species (Thermoproteus neutrophilus V24Sta , Pyrobaculum aresenaticum DSM 13514, P. calidifontis, P. islandicum, Caldivirga maquilingensis IC-167)
Why?		 Lowe UC Santa Cruz
Opitutaceae bacterium TAV2 (ex. Verrucomicrobium sp. TAV2)
Why? 		Schmidt/ Rodrigues Michigan State Univ.

 

Community Sequencing Program FY2005

Organism Proposer Affiliation
Microbes
Olavius algarvensis symbionts
Why?		 Dubilier Max Planck Institute of Marine Microbiology
Crenarchaeota
Why? 		Delong MIT
Marinobacter aquaeolei VT8
Why?		 Edwards Woods Hole Oceanographic Institution
Staphylococcus aureus subsp. aureus JH1 and JH9
Why? 		Tomasz Rockefeller University
Prochlorococcus ACM A12II
Why?		 Chisholm MIT
Rhodocyclus-like polyphosphate accum.
Why?		 Hugenholtz JGI
Rhodobacter sphaeroides ATCC17025 and ATCC17029
Why?		 Kaplan University of Texas, Houston
Contaminated groundwater
Why?		 Zhou ORNL
Lactobacillus reuteri strains 100-23 and F275
Why? 		Tannock University of Otago, Dunedin, NZ
Ignicoccus hospitalis KIN4/I Podar Diversa
Bacillus cereus subsp. cytotoxis NVH 391-98 and
Bacillus weihenstephanensis KBAB4
Why? 		Sorokin INRA, France
Basal Organisms
Selaginella moellendorffii
Why?		 Banks Purdue University
Trichoplax
Why?		 DellaPorta Yale University
Sporobolomyces roseus
Why?		 Wolfe Trinity College, Dublin
Reniera
Why?		 Degnan University of Queensland, Australia
Mycosphaerella graminicola
Why?		 Goodwin Purdue University
Spironucleus vortens and Naegleria gruberi
Why?		 Cande UC Berkeley
Higher Animals and Plants
Physcomitrella patens
Why? 		Mishler UC Berkeley
Lottia gigantea (limpet)
Why?		 Edsinger-Gonzalez, Rokhsar, Lindberg UC Berkeley, JGI
Helobdella robusta (leech)
Why?		 Weisblat UC Berkeley
Capitella sp. I
Why?		 Seaver University of Hawaii
ESTs and Targeted Sequencing
Alvinella pompejana
Why?		 Tainer Scripps Research Institute
Seed plant mitochondria (Amborella trichopoda, Citrullus lanatus watermelon, Cucumis melo (melon), Cucumis melo Iroquois, C. sativus, Cucurbita pepo zucchini, Digitalis purpurea, Liriodendron tulipifera, Plantago lanceolata, Pelargonium hortorum, Plantago media, Cucumis metulliferus, Vigna radiata)
Why?		 Palmer Indiana University, Bloomington
Karenia brevis
Why?		 Bhattacharya University of Iowa
Dipteran fosmids
Why?		 Eisen LBNL

 

Laboratory Science Program Small-Scale Sequencing

Organism Proposer Affiliation
Five Archaea (Methanohalobium evestigatum, Methanobacterium formicicum, Halococcoides, Ferroglobus placidus, and Acidianus sp. JP7) Kyrpides LBNL
Aspergillus terreus EST Baker PNNL
Avena Barbata ESTs Anderson BNL
Burkholderia cepacia Bu72 van der Lelie BNL
ChIP-enriched binding sequences Stubbs LLNL
CRISPR loci of Leptospirillum Banfield  
Cochliobolus heterostrophus Turgeon Cornell University
Columbia River Microbiota Magnuson PNNL
Dehalococcoides Brodie LBNL
Etolico Lagoon in Greece Kyrpides LBNL
Fungal comparative genomics (Orpinomyces) Baker PNNL
Hypersaline microbial mat Raymond LLNL
Leonotis nepetifolia Shanklin BNL
Low Dose DiTags Anderson BNL
Medaka Fish Glenn SRNL
Microbial community actively decaying poplar biomass van der Lelie BNL
Microbial diversity in tropical and temperate forests Pett-Ridge LLNL
Microcoleus vaginatus FGP-2 Kuske LANL
New Orleans Floodwaters Andersen LBNL
Nuclear matrix attachment regions (MARs) Doggett LANL
Peromyscus Glenn SRNL
Phycomyces blakesleeanus Baker PNNL
Poplar in Response to Dehydration Yang ORNL
Prunus persica Rokhsar LBNL
Soluble protein domains Terwilliger LANL
Tallgrass Prairie soil Bailey PNNL
Grass-feeding termite hindgut communities Hugenholtz LBNL
Thielavia terrestris Berka Novozymes
Tremella mesenterica Heitman Duke University
Viruses in nasopharyngeal swab samples from healthy subjects Mariella LLNL
454 Sequencing of Viruses Han LANL
Yellowstone Archaeal Virus Community (Nymph Lake and Crater Hills) Roberto INL

 

DOE Microbial Genome Program FY2007

Organism(s) Est. Genome Size
Acremonium alcalophilum ATCC90507
40 MB
Azolla Cyanobacterium, Arthrospira maxima, and Cyanobacterium JSC-1 NA
bacterioplankton pool cDNA day, night, night + DOC1, night + DOC2
NA
Clostridum carboxidivorans, Clostridium sp. strains, Clostridium straminisolvens, Clostridum thermocellum LQR1 DSM2360 , Clostridium thermocellum JW20 DSM 4150
Thermoanaerobacter italicus Ab9 DSM9252, T. ethanolicus X513, T. ethanoloicus X561, T. mathrani, Thermoanaerobacterium thermosaccharaolyticum, Thermoanaerobacterium xylanolyticum LX11 DSM7097 		3.5-4.0 MB
Cyanobiont in Azolla NA
Elephant Grass Decomposer Community
NA
Exiguobacterium sp. AT1b, Exiguobacterium sibiricum 255-15 NA
Flavobacteria sp. MS024-2A, Flavobacteria sp. MS0243-3C, Flavobacteria sp. MS311-3, Flavobacteria sp. MS190-1F, Lynne Flavobacteria sp. MS220-5C NA
Geobacillus sp. G11MC16, sp. WCH70, sp. Y412MC10 6.4 MB
Gluconacetobacter diazotrophicus 448, G.d. PAI 5 NA
Gut consortium of Anoplophora glabripennis
NA
Kosmotoga olearia TB 19.5.1 NA
Lactobacillus buchneri B-30929 and NRRL B30929 NA
Lost City Methanosarcinales
3 MB
Methanosphaerula palustris E1-9c NA
Mucor circinelloides CBS277.49
36.05 MB
Paenibacillus sp. JDR-2
NA
Pelotomaculum schinkii strain HH
3 MB
Phanerochaete carnosa
35 MB
Rhodosporidium babjevae WP1
20 MB
Serpula lacrymans
25 MB
Sporotrichum thermophile ATCC42464
43 MB
Thermoacetogenium phaeum  
Tipula abdominalis gut
NA
Tropical picophytoeukaryotes site 1, site 2, site 3
NA

 

DOE Microbial Genome Program FY2006

Organism(s) Est. Genome Size
Anaeromyxobacter dehalogenans strain 2CP-1 5 MB
Acidithiobacillus ferrooxidans ATCC 53993  
Anaeromyxobacter sp. Fw109-5 5 MB
Anaeromyxobacter sp. K 5 MB
Bison Pool, hydrothermal ecosystem NA
Burkholderia ambifaria MC40-6 7.4 MB
Burkholderia cenocepacia MC0-3 7.9 MB
Burkholderia multivorans ATCC 17616 6.8 MB
Burkholderia phymatum STM815 8.9 MB
Burkholderia phytofirmans PsJN 8 MB
Chlorella sp. NC64A 40 MB
Chlorella vulgaris C-169 40 MB
Clostridium cellulolyticum H10 5 MB
Comamonas testosteroni KF-1 6 MB
Dehalococcoides sp. Strain GT 1.5 MB
Delftia acidovorans SPH-1 6 MB
Desulfatibacillum alkenivorans AK-01 6 MB
Desulfococcus oleovorans Hxd3 6 MB
Dictyostelium purpureum 34 MB
Dinoroseobacter shibae DFL-12 6 MB
Dunaliella salina UTEX 130 MB
Enterobacter sp. 638 , 5 MB
Escherichia coli C str. ATCC 8739 4 MB
Geobacter Lovleyi SZ 4 MB
Leptospirillum ferroxidans Markosian 2.5 MB
Marinomonas sp. strain MWYL1 5 MB
Metallosphaera sedula DSM 5348 1.89 MB
Methanococcus aeolicus Nankai-3 2 MB
Methanococcus maripaludis C5 2 MB
Methanococcus maripaludis C6 2 MB
Methanococcus maripaludis C7 2 MB
Methanococcus vannielii SB 2 MB
Methanococcus voltae A3 2 MB
Methanoregula boonei 6A8 3 MB
Methylobacterium chloromethanicum CM4 7 MB
Methylobacterium extorquens PA1 7 MB
Methylobacterium nodulans ORS 2060 7 MB
Methylobacterium populi BJ001 7 MB
Methylobacterium radiotolerans JCM 2831 7 MB
Methylobacterium sp. 4-46 7 MB
Methylotroph strain L1N13 10 MB
Nitrosopumilus maritimus SCM1 3 MB
Parvibaculum lavamentivorans DS-1 6 MB
Plasmids in prokaryotes 7 MB
Poplar endophytic bacteria (Pseudomonas putida strain W619, Serratia proteamaculans 568, Stenotrophomonas maltophilia R551-3) 37.3 MB
Prochlorococcus, its phages, and the surrounding microbial community at the Hawaii Ocean Times Series Station (HOT) 2 GB
Pseudomonas mendocina strain ymp 4.6 MB
Pseudomonas putida strain GB-1 6 MB
Pseudo-nitzschia (diatom) 250 MB
Ralstonia pickettii 12D 3 MB
Ralstonia pickettii 12J 3.5 MB
Rice endophyte metagenome 100 MB
Schizophyllum commune 38 MB
Shewanella halifaxensis HAW-EB4 5 MB
Shewanella pealeana ATCC 700345 5 MB
Shewanella sediminis HAW-EB3 5 MB
Shewanella woodyi ATCC 51908 5 MB
Sphingomonas wittichii Strain RW1 5 MB
Sulfolobus islandicus strains (eight) 24 MB
Thermosinus carboxydivorans Nor1 3 MB
Trichoderma actroviride 40 MB

 

DOE Microbial Genome Program FY2005

Strains of Shewanella

Organism Est. Genome Size
Shewanella baltica OS195 5 Mb
Shewanella sp. ANA-3 5 Mb
Shewanella sp. MR-4 5 Mb
Shewanella sp. MR-7 5 Mb
Shewanella sp. W3-18-1 5 Mb
Shewanella baltica OS223 5 Mb

Strains of Chloroflexi

Organism Est. Genome Size
Chloroflexus aggregans DSM 9485 5 Mb
Chloroflexus sp. Y-396-1 5 Mb
Chlorothrix halophila (Candidatus) 5 Mb
Herpetosiphon aurantiacus DSM 785 5 Mb
Roseiflexus castenholzii HLO8 5 Mb
Roseiflexus sp. strain RS-1 5 Mb
Chloroflexus sp. Y-400-fl  

Strains of Rhodopseudomonas palustris

Organism Est. Genome Size
R. palustris BisA53 5.5 Mb
R. palustris BisB5 4.9 Mb
R. palustris BisB18 5.5 Mb
R. palustris HaA2 5.5 Mb

Organisms Involved in Microbial Arsenic Transformation

Organism Est. Genome Size
Bacillus selenitireducens MLS-10 2-4 Mb
Mono Lake Deltaproteobacter MLMS-1 6.06 Mb
Alkaliphilus oremlandii OhILAs 2-4 Mb
Alkalilimnicola ehrlichei MLHE-1 2-4 Mb

Two species of Micromonas pusilla

Organism Est. Genome Size
M. pusilla NOUM17(RCC 299) 15 Mb
M. pusilla CCMP1545 15 Mb

Single microbes

Organism Est. Genome Size
Acidiphilium cryptum JF-5 2.46 Mb
Acidobacteria bacterium Ellin 345 3 Mb
Acidothermus cellulolyticus 11B 6 Mb
Actinobacillus succinogenes 130Z 2 Mb
Aspergillus niger  32 Mb
Aureococcus anophagefferens 32 Mb
Bradyrhizobium sp. BTAi1 9.2 Mb
Burkholderia cepacia AMMD 7.2 Mb
Caldicellulosiruptor saccharolyticus  DSM 8903 4.3 Mb
Candidatus Ruthia magnifica Cm (Proteobacterial symbiont of the clam Calyptogena magnifica) 4 Mb
Dehalococcoides sp. BAV1 2 Mb
Dehalococcoides sp. VS 1.5 Mb
Desulfotomaculum reducens MI-1 4 Mb
Flavobacterium johnsoniae UW101 6.07 Mb
Geobacter sp. FRC-32 5 Mb
Halorhodospira halophila  SL1 4 Mb
Methanosaeta thermophila PT 3 Mb
Mycobacterium gilvum PYR-GCK 5 Mb
Mycobacterium vanbaalenii PYR-1 6.46 Mb
Nectria haematococca MPVI 40 Mb
Polaromonas naphthalenivorans CJ2 6 Mb
Postia Placenta 40 Mb
Pseudoalteromonas atlantica T6c 3.5 Mb
Pseudomonas putida F1 6.2 Mb
Psychromonas ingrahamii 4 Mb
Xanthobacter autotrophicus Py2 5 Mb

Communities

Organism
Microbial Population from The Cedars (California)
Acid mine drainage community (Iron Mountain, California)
Obsidian Hot Spring (Yellowstone: Alicyclobacillus sp., Dictyoglomus turgidum, Geobacillus sp Y412MC61, Geobacillus sp. Y412MC52, Hydrogenobaculum strain Y04AAS1, Mixed Community, Sulfolobus solfataricus 98/2, Sulfurihydrogenibium sp. Y03AOP1, Thermareobacter sp. Y412MC57)
PAH Degrading Mycobacteria (Mycobacterium sp. MCS, JLS, and KMS
Active methylotroph community from Lake Washington

 

DOE Microbial Genome Program FY2004

Chlorobia (avg:~2.4Mb)

Organism Genome Size
Chlorobium ferrooxidans DSM 13031 2.40 Mb
Chlorobium limicola DSMZ 245 2.4 Mb
Chlorobium phaeobacteroides BS1 2.4 Mb
Chlorobium phaeobacteroides DSM 266 2.3 Mb
Pelodictyon luteolum DSMZ 273 2.3 Mb
Pelodictyon phaeoclathratiforme BU-1 (DSM 5477) 2.4 Mb
Prosthecochloris aestuarii DSM 271 2.4 Mb
Prosthecochloris vibrioformis DSM 265 2.4 Mb
Chlorobaculum parvum n/a
Chloroherpeton thalassium n/a

Model Syntrophic Consortium

Organism Genome Size
Syntrophobacter fumaroxidans MPOB 3.3 Mb
Syntrophomonas wolfei Göttingen (DSM 2245B) 3 Mb
Methanospirillum hungatei JF1 3.70 Mb

Facultative Metal-reducing Gamma proteobacteria

Organism Genome Size
Shewanella amazonensis SB2B 4.40 Mb
Shewanella baltica OS155 5.20 Mb
Shewanella baltica OS185  
Shewanella denitrificans OS217 4.70 Mb
Shewanella frigidimarina NCIMB 400 4.90 Mb
Shewanella putrefaciens 200 4.5 Mb
Shewanella putrefaciens CN-32 4.5 Mb
Shewanella loihica PV-4 4.5 Mb

Five bacteria involved in nitrification

Organism Genome Size
Nitrobacter hamburgensis X14 5.011530 Mb
Nitrobacter winogradskyi Nb-255 3.40 Mb
Nitrosococcus oceani ATCC 19707 3.5 Mb
Nitrosomonas eutropha C71 2.70 Mb
Nitrosospira multiformis ATCC 25196 3.20 Mb

Single microbes

Organism Genome Size
Alkaliphilus metalliredigenes QYMF 4.5 Mb
Anaeromyxobacter dehalogenans 2CP-C 5.20 Mb
Arthrobacter sp. FB24 5.20 Mb
Bath hot springs metagenome and thermophages Y4.1MC1, Y4.1MC4, and Y5.1MC23  
Burkholderia cenocepacia AU 1054 7.30 Mb
Burkholderia cenocepacia HI2424 7.70 Mb
Chromohalobacter salexigens DSM 3043 3.90 Mb
Clostridium beijerincki NCIMB 8052 7.80 Mb
Clostridium phytofermentans ISDg 5 Mb
Deinococcus geothermalis DSM 11300 3 Mb
Frankia sp. CcI3 5.43 Mb
Frankia sp. EAN1pec 10 Mb
Jannaschia sp. CCS1 4.5 Mb
Nocardioides sp. JS614 5.5 Mb
Paracoccus denitrificans PD1222 3.70 Mb
Polaromonas sp. JS666 5.20 Mb
Prochlorococcus marinus NATL2A 2 Mb
Psychrobacter cryohalolentis K5 3.20 Mb
Silicibacter sp. TM1040 3.20 Mb
Solibacter usitatus Ellin6076 10.20 Mb
Sphingopyxis alaskensis RB2256 3.20 Mb
Sulfurimonas denitrificans DSM 1251 2.20 Mb
Synechococcus sp. CC9605 (oligotrophic) 2.5 Mb
Synechococcus sp. CC9902 (coastal) 2.5 Mb
Thermoanaerobacter pseudethanolicus 39E 3 Mb
Thermoanaerobacter sp. X514 3 Mb
Thermus aquaticus Y51MC23  
Thiobacillus denitrificans ATCC 25259 3 Mb
Thiomicrospira crunogena XCL-2 2.40 Mb

Eukaryotes

Organism Genome Size
Glomus intraradices 15 Mb
Laccaria bicolor 40 Mb
Pichia stipitis, CBS 6054 12 Mb

Communities

Organism Genome Size
200 BACs from anaerobic bioreactor granules ~100 Mb
acid mine drainage community ~80 Mb
Picoplankton BACS from HOTS site ~150 Mb
Boiling thermal pool ~50 Mb

 

DOE Microbial Genome Program FY2003

Eukaryotes

Organism Genome Size
Emiliania huxleyi 220 Mb
Ostreococcus lucimarinus 9.3 Mb
Monosiga brevicollis  

Bacteria

Organism Genome Size
Anabaena variabilis ATCC 29413 7 Mb
Burkholderia sp. 383 8.80 Mb
Burkholderia vietnamiensis G4 8.40 Mb
Chlorobium aggregatum  
Chlorobium chlorochromatii CaD3 2.6 Mb
Chlorochromatium aggregatum Lake Dagow  
Crocosphaera watsonii WH 8501 6.40 Mb
Kineococcus radiotolerans SRS30216 4.90 Mb
Methylibium petroleiphilum PM1 4.60 Mb
Methylobacillus flagellatus KT 2.80 Mb
Moorella thermoacetica ATCC 39073 2.60 Mb
Prochlorococcus marinus str. MIT 9312 2.40 Mb
Rubrobacter xylanophilus DSM 9941 3.20 Mb
Synechococcus elongatus PCC7942 2.70 Mb

Communities

Organism
Acid Mine Drainage community

 

DOE Microbial Genome Program FY2002

Eukaryotes

Organism Genome Size
Thalassiosira pseudonana CCMP 1335 (diatom) 32 Mb

Lactic Acid Bacteria

Organism Genome Size
Bifidobacterium longum DJO10A 2.4 Mb
Brevibacterium linens BL2 4.5 Mb
Lactobacillus brevis ATCC 367 1.8 Mb
Lactobacillus casei ATCC 334 2.8 Mb
Lactobacillus delbrueckii ATCC BAA-365 1.6 Mb
Lactobacillus gasseri ATCC 33323 1.9 Mb
Lactococcus lactis subsp. cremoris SK11 2.6 Mb
Leuconostoc mesenteroides ATCC 8293 2 Mb
Oenococcus oeni PSU-1 1.8 Mb
Pediococcus pentosaceus ATCC 25745 1.8 Mb
Streptococcus thermophilus LMD-9 1.8 Mb

Single Microbes

Organism Genome Size
Azotobacter vinelandii AvOP 5.33 Mb
Clostridium thermocellum ATCC 27405 3.80 Mb
Dechloromonas aromatica RCB 4.5 Mb
Desulfovibrio desulfuricans G20 3.73 Mb
Desulfuromonas acetoxidans DSM 684 4.1 Mb
Ehrlichia canis Jake 1.60 Mb
Ehrlichia chaffeensis Sapulpa 1.80 Mb
Exiguobacterium sibiricum 255-15 3.10 Mb
Geobacter metallireducens GS-15 4.30 Mb
Haemophilus somnus 129PT 2.00 Mb
Haemophilus somnus 2336  
Mesorhizobium sp. BNC1 5 Mb
Methanococcoides burtonii DSM 6242 2.60 Mb
Pseudomonas syringae B728a 6.10 Mb
Psychrobacter arcticus 273-4 2.60 Mb
Ralstonia eutropha JMP-134 7.25 Mb
Rhodospirillum rubrum ATCC 11170 4.40 Mb
Saccharophagus degradans 2-40 5.10 Mb
Streptococcus suis 89/1591 2 Mb
Trichodesmium erythraeum IMS101 7.80 Mb
Yersinia pestis Pestoides F 4.73 Mb

Community

Organism
Anaerobic Methane Oxidizing community

 

DOE Microbial Genome Program FY2001

Organism Genome Size
Burkholderia xenovorans LB400 8 Mb
Chloroflexus aurantiacus J-10-fl 3 Mb
Cupriavidus metallidurans CH34 6.8 Mb
Cytophaga hutchinsonii ATCC 33406 4.4 Mb
Desulfitobacterium halfniense DCB-2 4.7 Mb
Enterococcus faecium DO 2.8 Mb
Ferroplasma acidarmanus fer1 1.8 Mb
Magnetococcus sp. MC-1 4.7 Mb
Methanosarcina barkerii fusaro 4.8 Mb
Nitrosomonas europaea ATCC 19718 2.8 Mb
Nostoc punctiforme PCC 73102 9.2 Mb
Novosphingobium aromaticivorans DSM 12444 4.2 Mb
Prochlorococcus marinus MED4 1.66 Mb
Prochlorococcus marinus MIT9313 2.4 Mb
Pseudomonas fluorescens PfO-1 6.7 Mb
Rhodobacter sphaeroides 2.4.1 4.6 Mb
Rhodopseudomonas palustris CGA009 5.5 Mb
Synechococcus sp. WH8102 2.4 mb
Thermobifida fusca YX 3.6 Mb
Xylella fastidiosa Ann-1 5.1 Mb
Xylella fastidiosa Dixon 2.6 Mb

 

DOE Genomics: GTL Program

Organism Est. Genome Size
Desulfitobacterium hafniense DCB-2 DSM 10664  
South African Gold Mine Metagenome (Candidatus Desulforudis audaxviator MP104C)  
Desulfovibrio desulfuricans 27774  
Desulfovibrio fructosovorans  
Desulfovibrio hanfordii  
Desulfovibrio salexigens  
Desulfovibrio vulgaris Miyazaki F 3.57 Mb
Desulfovibrio vulgaris subsp. vulgaris DP4 3.64 Mb
Geobacter bemidjiensis Bem  
Geobacter sulfurreducens  
Geobacter uraniireducens Rf4 4.9 Mb
Geobacter sp. M18  
Geobacter sp. M21  
Geobacter sp. M22  
Pelobacter carbinolicus 7.2 Mb
Pelobacter propionicus DSM 2379 7.2 Mb
Prochlorococcus marinus HOT_152-C11  
Rhodoferax ferrireducens DSM 15236 4.969788 Mb
Switchgrass ESTs  
Geobacter Uranium Bioremediation Community D07-1  

 

DOE Sequencing Projects

Organism Est. Genome Size
Branchiostoma floridae (Florida lancelet) 600 Mb
Chlamydomonas reinhardtii (a green alga) (improve existing genome)
Why?		 100 Mb
Ciona (sea squirt) fosmids (improve existing genome)
Why?		 180 Mb
Daphnia pulex (water flea) 200 Mb
Fugu rubripres (puffer fish) (fosmid)
Why?		 400 Mb
Glycine Max (soybean)
Why? 		1115 Mb
Homo sapiens chromosome 5
Why?		 180.8 Mb
Homo sapiens chromosome 16
Why?		 88.7Mb
Homo sapiens chromosome 19
Why?		 63.8 Mb
Nematostella vectensis (burrowing anemone) 340 Mb
Phakopsora pachyrhizi (soybean rust pathogen) 50 Mb
Phytophthora sojae (soybean blight pathogen)
Why?		 62 Mb
Phytophthora ramorum (sudden oak death pathogen)
Why?		 60 Mb
Phaeodactylum tricornutum (a diatom) 30 Mb
Phanerochaete chrysosporium (white rot fungus)
Why?		 30 Mb
Populus trichocarpa (black cottonwood)
Why?		 550 Mb
Trichoderma reesei (a filamentous fungus)
Why?		 30 Mb
Xenopus tropicalis (western clawed frog) (improve existing genome to ~7.5x)
Why?		 1.7 Gb
Zea mays (corn) 2.2 Gb