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

• 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 +

Biomed +

Biomed +

DOE Mission

USER FACILITY

Primary JGI User Distribution Primary JGI User Distribution

KEY: RED=Academic; Blue=National Laboratory; Black=Industry KEY: RED=Academic; Blue=National Laboratory; Black=Industry

2007 JGI User Meeting2007 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

FermentersBiomass 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 WisXylose

>20% of biomass is comprised of this “wood sugar”

A well-studied, xylose-fermenting yeast.

Pichia stipitis CBS 6054

Selection for High EtOH Producers

MutagenesisSelection for rapid growth on L-xylose

EtOHProduction0.46 g etoh/g xylose

FPL Shi21 (cyc1::URA3)

EtOHProduction0.41 g etoh/g xylose

Tom Jeffries U of WisOne Selexa

Sequencing Run: Identified 35 Nucleotide

JGI metagenomics projects (>30 Projects)

2005

2006

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)

2007 8 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 Projects1473

December, 2006: 1473 Projects (A+B)

WORLD48%

JCVI11%

TIGR17%

JGI24%

http://www.genomesonline.org/

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 40 phyla of bacteria

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

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

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

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

AnnotationFunctional PredictionGene 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…,