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Update

Operating as a User Facility Science GEBA / Bergey Pilot Project (part 1). Update. Focus of the Sequencing Centers After the Human Genome. Biomed / Bioenergy / Environ + Biomed + Biomed + Biomed + DOE Mission USER FACILITY. Venter Wash U Baylor Broad (MIT) . G5. JGI.

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Update

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  1. Operating as a User Facility Science GEBA / Bergey Pilot Project (part 1) Update

  2. Focus of the Sequencing Centers After the Human Genome Biomed / Bioenergy / Environ + Biomed + Biomed + Biomed + DOE Mission USER FACILITY Venter Wash U Baylor Broad (MIT) G5 JGI

  3. Primary JGI User Distribution KEY: RED=Academic; Blue=National Laboratory; Black=Industry

  4. 2007 JGI User Meeting

  5. The Future of SequencingOn the brink of dramatic changes

  6. 60 Million bp/run ABI 3730 ~600Million bp/run Sanger Capillary Based Seq 70,000 bp/run ?bp/run

  7. Scientific DirectionsBioenergy, Bioremediation, C cyclingPlant Genomics Metagenomics Microbes

  8. Role of Biology Sun Cellulose Sugar Alcohol Biomass converting organisms Feedstocks Fermenters Poplar Termite Pichia stipitis • Tamar wallaby forestomach • Poplar biomass degraders • Asian Longhorned Beetle gut • Elephant Grass decomposers Soybean, Maize, Switch Grass, Miscanthus, Sorghum, Cotton, Cassava,Brachypodium, Citrus • White Rot Fungus • Clostridium thermocellum • Saccharophagus degradans • Acidothermus cellulolyticus • Thermoanaerobacter • Ethanolicus • Pichia stipitis

  9. Sugars from Cellulose and Hemicellulose FermentationAlcohol Glucose Xylose

  10. Pichia stipitis A well-studied, xylose-fermenting yeast. Xylose >20% of biomass is comprised of this “wood sugar” Tom Jeffries U of Wis

  11. Selection for High EtOH Producers Pichia stipitis CBS 6054 EtOH Production 0.41 g etoh/g xylose Tom Jeffries U of Wis One Selexa Sequencing Run: Identified 35 Nucleotide Mutagenesis Selection for rapid growth on L-xylose EtOH Production 0.46 g etoh/g xylose FPL Shi21 (cyc1::URA3)

  12. JGI metagenomics projects (>30 Projects) 2005 Gutless worm (MPI) planktonic archaea (MIT) EBPR sludge (UW/UQ) groundwater (ORNL) 2006 AMD nanoarchaea (UCB) Alaskan soil (UW) termite hindgut (CalTech) TA-degrading bioreactor (NUS) Antarctic bacterioplankton (DRI) hypersaline mats (UCol) soil archaea (UW) Korarchaeota enrichment (Diversa) 2007 8 new metagenomic projects

  13. Problem with Analysis of Metagenomic DataWe don’t have completed genomes for the vast majority of Archaea and Bacteria

  14. Archaea + Bacteria Genome Projects1473 http://www.genomesonline.org/

  15. At least 40 phyla of bacteria Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides Chlorobi Fibrobacteres Marine GroupA WS3 Gemmimonas Firmicutes Fusobacteria Actinobacteria OP9 Cyanobacteria Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 OP11

  16. Proteobacteria TM6 OS-K Termite Group OP8 Nitrospira Chlorobi Marine GroupA WS3 Firmicutes Fusobacteria Actinobacteria OP9 Cyanobacteria Synergistes Deferribacteres Chrysiogenetes NKB19 Chlamydia OP3 Spriochaetes Coprothmermobacter OP10 Thermomicrobia TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Well sampled phyla

  17. Proteobacteria TM6 OS-K Termite Group OP8 Nitrospira Chlorobi Marine GroupA WS3 Firmicutes Fusobacteria Actinobacteria OP9 Cyanobacteria Synergistes Deferribacteres Chrysiogenetes NKB19 Chlamydia OP3 Spriochaetes Coprothmermobacter OP10 Thermomicrobia TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Solution: Deep sampling across phyla Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Well sampled phyla No cultured taxa

  18. Goal Create a reference microbial genome set that broadly covers the diversity of bacteria and archaea particularly those with phenotypic information and research community A Genomic Encyclopedia of Bacteria and Archaea (GEBA)/ Bergey Project

  19. Recommended by: DOE Life Sciences Division of Visitors Report, Amer Acad of Micro Report “Reconciling Microbial Systemics and Genomics” NRC Metagenomic report Why Increase Coverage? • Annotation • Functional Prediction • Gene discovery • Species phylogeny and classification

  20. Goal To finish ~100 bacterial and archaeal genomes Selected based on phylogeny, availability of phenotype information and community interest Appoach Select 200 organisms Order DNA from culture collections (DSMZ and ATCC) Sequence 100 for which DNA QC is received GEBA / Bergey Pilot Project at JGI

  21. Project Lead (Jonathan Eisen JGI/UC Davis) Project management (David Bruce JGI/ LANL) Methods for sequencing in changing technology landscape (Paul Richardson JGI) Linking to educational project (Cheryl Kerfeld JGI) GEBA Pilot Project : Components Input / Interactions with: Community Advisory Group , ASM, Academy of Microbiology, Etc…

  22. Miscanthus, Soybean, Maize, Switch Grass, Sorghum, Cotton, Cassava, Brachypodium, Citrus etc…,

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