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

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

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

2007 JGI User Meeting

The Future of Sequencing On the brink of dramatic changes

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

Scientific Directions Bioenergy, Bioremediation, C cycling Plant Genomics Metagenomics Microbes

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

Fermentation Alcohol Glucose Xylose Sugars from Cellulose and Hemicellulose

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

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

JGI metagenomics projects (>30 Projects) Gutless worm (MPI) planktonic archaea (MIT) EBPR sludge (UW/UQ) groundwater (ORNL) 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) new metagenomic projects

Problem with Analysis of Metagenomic Data We don’t have completed genomes for the vast majority of Archaea and Bacteria

Archaea + Bacteria Genome Projects

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

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

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

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

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

GEBA / Bergey Pilot Project at JGI 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 Pilot Project : Components 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) Input / Interactions with: Community Advisory Group, ASM, Academy of Microbiology, Etc…

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