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