1. Production Genomics Facility
DOE JGI
Production Genomics Facility
Opened in 1999
~240 UC Employees
~$66M Annual Budget
~47 Tb for 2012
>37 Human genomes / day
Mission:
“User facility providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative energy, carbon cycling & bioremediation.”

2. { { { Evolution of JGI Sequencing Platforms Output (Tb) Staff (#)
FY2009
49 Units
24 FTEs
$11M
1Tb
FY2010
22 Units
15 FTEs
$11M
6Tb
FY2011
15 Units
9 FTEs
$8M
29Tb { { {
Staff (#)
Output (Tb)
3730
Budget ($M)
GAii
454
GAii
Hiseq
454
GAii
Hiseq
454

3. JGI Science Programs

4. Community Sequencing Program
DOE JGI
Community Sequencing Program
>700 Users

5. SCIENCE GOALS CSP 1 CSP 2 CSP 3 CSP 4 FOCUS AREA CSP 1 CSP 2 CSP 3

6. Program Science 2012 - Focus Areas
PLANT-MICROBE
INTERACTIONS
Dangl
Arabidopsis
Boechera
Miscanthus
Tuscan
Poplar
Agave
Gross
Andersson
Lichen
CARBON CYCLING
SOIL
Fierer
Grassland
soil carbon cycling
Brodie
Mediterranean
grassland
Mohn
American
forest soils
Rodrigues
Amazon deforestation
AQUATIC
CARBON CYCLING
McMahon
Crystal Bog Lake
McKay
Lake Erie
Gilbert
Gulf of Mexico
Moran
Ocean
heterotrophs
Dangl: profiling of arabidopsis genotypes and hybrids for gene mapping; profiling of Boechera stricta and Miscanthus as well as prairie site subjected to climate change manipulations.
Poplar: profiling of genotyped trees in Oregon; metagenome sequencing of 24 samples (4 genotypes X 2 locations X 3 replicates)
Lichen: sequencing of all three primary players as well as metagenome sequencing to characterize others; metatranscriptome sequencing to characterize eukaryotic stress responses.
Agave: rhizosphere and phyllosphere of cultivated and wild species, including single cell characterization of endophytes
Fierer: Shallow sequencing of 60 soil samples from different treatments (Co-Is Gilbert, Knight, Earth Microbiome Project)
Brodie: Deep sequencing of 2 soils (different seasons) and 30 isolates
McMahon: 100 community DNA samples for comparative metagenomics (Co-Is Malmstrom, Gilbert, Earth Microbiome Project)
McKay: 4 metagenomes + 4 metatranscriptomes
Moran: Mostly mutant screening but also some metatranscriptomics of environmental samples
Gilbert: 100 samples from oil spill time series (Earth Microbiome Project)

7. Microbial Genomics Nikos Kyrpides
Microbial Genomics and Metagenomics Programs
DOE Joint Genome institute 7

8. Historical perspective Do we need more sequencing?
Overview of the talk
Historical perspective
Do we need more sequencing?
Major Transitions in Genomics

10. The Quest for Darwin’s Grail [unlike understanding an electron]
"To understand life
[unlike understanding an electron]
you must understand its history"
Carl R. Woese

11. Darwin's Dream
"The time will come I believe, though I shall not live to see it, when we shall have fairly true genealogical trees of each great kingdom of nature"
[in a letter to T.H. Huxley]
Charles Darwin, 1857

12. Quotes from “The Microbial World”
“It is a waste of time to attempt a natural system of classification for bacteria”
1st Edition –1957
“The only possible conclusion is, accordingly that the ultimate scientific goal of biological classification cannot be achieved in the case of bacteria”
2nd Edition –1963
“For bacteria, the general course of evolution will probably never be known, and there is simply not enough objective evidence to base their classification on phylogenetic grounds”
3rd Edition – 1970
4th Edition – 1977
Verbatim repeat of the 3rd edition

13. 1978 – 1st Universal Tree of Life

14. History of Genomics

15. Carl Woese 1998 Microbial Genomics
“Genome sequencing has come of age, and genomics will become central to microbiology’s future. It may appear at the moment that the human genome is the main focus and primary goal of genome sequencing, but do not be deceived. The real justification in the long run, is microbial genomics.”
Carl Woese
1998

16. UNDERSTANDING vs INFORMATION
GREAT CHALLENGES
P. Chain et al. Science, 2009
UNDERSTANDING vs INFORMATION
Finished
1000
3000
Draft
10000
Genes
8 Million
52 Million
3,000
20,000
92 Million 16

17. Why we need more sequencing
Ribokinase family
Fructokinase family
2-dehydro-3-deoxy glucokinase family

18. We need to change this … Genome projects 2000 Genome projects 2010 11%
71 bacterial genomes
Genome projects 2000
5500 bacterial genomes
Genome projects 2010
11%

19. Many Phyla – many gaps
Poor sequence coverage mainly due to lack of isolates, but many gaps have unsequenced representatives
Norman Pace

20. 99% of microorganisms are not culturable with present methods.
What about the Uncultured majority?
Culturable
Unculturable
99% of microorganisms are not culturable with present methods.

21. The road to success in Metagenomics is through Microbial Genomics
Metagenomic Analysis
Acid Mine Drainage
Sargasso Sea
Termite Hindgut
Human Gut
Soil
Reference Genomes
Species complexity s
Binning ?
The road to success in Metagenomics is through Microbial Genomics
Source: Susannah Tringe, JGI 21

22. Availability of Reference Genomes
Acid Mine Drainage
Human gut
Marine
Termite Gut
Soil
Reference Genomes
100% 60% % % % % ? 22

23. Genomes and Metagenomes
Microbial environments
Genome reconstruction
Single cells
Cultured microbes
Number of Organisms
Coverage of Cultured Microbes with Genome Projects
16S rRNA Distance
Known diversity of cultured vs uncultured organisms
Number of Organisms
16S rRNA Distance

24. GEBA
Goal:
Filling in the gaps in sequencing along the bacterial and archaeal branches of the
Tree of Life
Status:
>120 Complete
>100 Draft
>100 In progress
Wu et al. Nature 2009

25. Improved Gene annotation and characterization of hypothetical gene families based on
novel gene fusions: 7.7 times more fusion events than any other randomly selected 56 genomes
novel gene neighbourhoods: 4.3 times more novel gene neighbourhoods than any other randomly selected 56 genomes
novel connections of protein families: 47 times more novel connections of protein families than any other randomly selected 56 genomes
Mavromatis
Amrita Pati
Wu et al. Nature 2009

26. Rob Knight
25K OTUs from cultured (70%), 10K from uncultured (30%). If the density of OTUs is the same between cultuted and unclutured
We would expect around 140K OTUs from the uncultured
15% 25K
85%
~ 35,000 OTUs
Wu et al. Nature 2009

27. The Microbial Earth Project
STEERING COMMITTEE
Nikos Kyrpides, DOE-JGI
George Garrity, Names4Life
Hans-Peter Klenk, DSMZ
Phil Hugenholtz, JGI
The Microbial Earth Project
Victor Kunin, JGI
Dino Liolios, GOLD

28. Microbial Earth Project

30. Pangenomes 10 Prochlorococcus marinus Pangenome 17
Listeria monocytogenes Pangenome 17 15
Staphylococcus aureus Pangenome

31. Strain / species diversity

32. 14765
2733
= 5.4
10434
5820
= 1.8

33. Metagenome Analysis with Pangenomes
Reference Genome
Best Blast Hit
Pangenome
Synteny blocks

34. HOW REPRESENTATIVE OF THE SPECIES IS THE PANGENOME?
PANGENOMES
HOW REPRESENTATIVE OF THE SPECIES IS THE PANGENOME?
1. How representative is the pangenome phylogenetically?
PANGENOME ☺
16S DIVERSITY
2. How representative is it geographically?
3. How representative is the habitat coverage? ☺

35. PARADIGM SHIFT 1960-1990 1990-2010 16S RNA 2010-2020 Genomes
Pangenomes 35

36. Microbial Genomics Program
Cell isolation
Amplification
16S Screening
Sequencing