uc davis eve161 lecture 13 by @phylogenomics
TRANSCRIPT
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Lecture 13:
EVE 161:Microbial Phylogenomics
!Lecture #13:
Era III: Genome Sequencing and Phylogenomic Analysis
!UC Davis, Winter 2014
Instructor: Jonathan Eisen
!1
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Where we are going and where we have been
• Previous lecture: !12: Guest Lecture
• Current Lecture: !13: Genome Sequencing III
• Next Lecture: !14: Metagenomics
!2
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Phylogenomics I:Major Evolutionary Transitions
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
• Analysis of S. pombe genome by Wood et al 2002
• Compared the genomes of eukaryotes to those of prokaryotes
• “Are there genes found in all eukaryotes with no obvious homologs in any prokaryote?”
Phylogenomics I:Major Evolutionary Transitions
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Evolutionary Model
BacteriaArchaea
Eukaryotes
Giardia
Trichomonas
Naegleria
Trypanosoma
Euglena
Plasmodium
Tetrahymena
Phytophthora
Arabidopsis
Chlamydomonas
Dictyostelium
HumansFly
Worm
Encephalatozoon
S. cerevisiaeS. pombe
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Eukaryotic Specific Genes
• >200 genes found including: – Cytoskeleton components: tubulin,
ankyrin, myosin – Protein degradation: ubiquitin, proteases – Chromatin and DNA packaging
• Of the 200 many had no known function: could encode novel eukaryotic wide processes
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Multi- vs. Single-Cellular Eukaryotes
• Further analysis of S. pombe genome • Compared multi-cellular vs. single-cellular eukaryotes
(animals and plants vs. yeast) • “Are there genes in all multi-cellular and not in any single-
cellular?” • Found only 3 • Concluded that the genetic basis of multi-cellularity was
likely to be gene regulation and not invention of new genes
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Multiple Origins of Multicellularity
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Phylogenomics II:Endosymbiont Evolution
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Endosymbiont Evolution
• Compared to free-living relatives – Smaller genomes – Lower GC content – Higher pIs – Higher rates of sequence evolution
• Baumannia shows ALL of these
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Uses of Whole Genome Trees
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Wolbachia Evolution
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Variation Between Endosymbionts and Free Living
• Repair hypothesis !
• Population genetics hypothesis !
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Variation Between Endosymbionts and Free Living
• Repair hypothesis !
• Population genetics hypothesis !
• PopGen explanations favored
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Variation Among Endosymbionts
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Variation Among Endosymbionts
MutS MutL
+ +
+ +
+ +
+ +
_ _
_ _
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
• Repair hypothesis !
• Population genetics hypothesis !
Variation Among Endosymbionts
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
• Repair hypothesis !
• Population genetics hypothesis !
• Repair explanations favored
Variation Among Endosymbionts
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Phylogenomics III:Lateral Gene Transfer
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Vertical Evolution
From C. Darwin, origin of species, via W. F. Doolittle
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Vertical Inheritance - Binary Bission
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Lateral inheritance I: Competence
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Lateral inheritance II: Conjugation
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Agrobacterium conjugation
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Figure 7.19 - Ab transfer
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Lateral inheritance III: Transduction
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Pathogenicity Island
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Steps in Lateral Gene Transfer (LGT)A B C D
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Steps in Lateral Gene Transfer (LGT)A B C D
1 Gene acquires host features
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Steps in Lateral Gene Transfer (LGT)A B C D
1 Gene acquires host features
2
Transfer
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Steps in Lateral Gene Transfer (LGT)A B C D
1 Gene acquires host features
2
Transfer
3-5 Integration, selection, spread
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Steps in Lateral Gene Transfer (LGT)A B C D
1 Gene acquires host features
2
Transfer
6 Amelioration3-5 Integration, selection, spread
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
How to Infer Gene Transfers
• Unusual distribution patterns !
• Unusual nucleotide composition !
• High sequence similarity to supposedly distantly related species !
• Unusual gene trees !
• Observe transfer events
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Case Study I: Aphids
Fig. 1 Coloration and carotenoids in the pea aphid. Typical green (A) and red (B) aphid clones, (C) 5AY, a green mutant clone arising from the red clone 5A. (D) Profiles of carotenoids in red (5A, LSR1), mutant redgreen (5AY, two samples), and green (8-10-1, 7-2-1) pea aphid clones. Torulene and a related red compound are restricted to red clones; the mutant 5AY clone lacks these and displays an elevation in their predicted precursor, -carotene.
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Table 1 Genes in the A. pisum genome with closest homology to carotenoid biosynthetic enzymes, including scaffold of origin and matching EST sequences. Similar color indicates that the gene is on the same scaffold. The 3' end of scaffold NW_001925130 overlaps with the 5' end of NW_001923501 for 5400 base pairs, and PCR demonstrated continuity of these scaffolds. Pink row is the gene corresponding to torR and conferring red color (see text). Protein length, amino acids; ESTs are those present in GenBank, mostly from clone LSR1.
Case Study I: Aphids
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Fig. 2 Phylogenetic relations of inferred carotenoid biosynthetic enzymes from the pea aphid genome. (A) Carotenoid desaturases and (B) carotenoid cyclase–carotenoid synthases. Sequences are from aphids, bacteria, plants, and fungi; no homologs were detectable in other sequenced animal genomes. Bootstrap support greater than 50% is indicated on branches.
!
Case Study I: Aphids
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Case Study II: GEBA
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Tree of Life
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Genomes Poorly Sampled
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
TIGR Tree of Life Project
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !41
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Genomes Still Poorly Sampled
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Genomic Encyclopedia of Bacteria & Archaea
Wu et al. 2009 Nature 462, 1056-1060
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Genomic Encyclopedia of Bacteria & Archaea
Wu et al. 2009 Nature 462, 1056-1060
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
GEBA Lesson 1: rRNA utility in IDing novel genomes
From Wu et al. 2009 Nature 462, 1056-1060!45
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
GEBA Lesson 2: rRNA Tree is not perfect
Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.
16s WGT, 23S
!46
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
GEBA Lesson 3: Phylogenetic sampling improves annotation
• Took 56 GEBA genomes and compared results vs. 56 randomly sampled new genomes
• Better definition of protein family sequence “patterns” • Greatly improves “comparative” and “evolutionary”
based predictions • Conversion of hypothetical into conserved hypotheticals • Linking distantly related members of protein families • Improved non-homology prediction
!47
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
GEBA Lesson 4 : Metadata Important
!48
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
GEBA Lesson 5:Improves discovering new genetic diversity
!49
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Protein Family Rarefaction Curves
• Take data set of multiple complete genomes
• Identify all protein families using MCL
• Plot # of genomes vs. # of protein families
!50
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014Wu et al. 2009 Nature 462, 1056-1060
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Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014Wu et al. 2009 Nature 462, 1056-1060
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Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014Wu et al. 2009 Nature 462, 1056-1060
!51
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014Wu et al. 2009 Nature 462, 1056-1060
!51
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014Wu et al. 2009 Nature 462, 1056-1060
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Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Synapomorphies exist
Wu et al. 2009 Nature 462, 1056-1060!52
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Phylogenetic Distribution Novelty: Bacterial Actin Related Protein
Haliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla, Victor Kunin
A. cliftonii gi14269497U. pertusa gi50355609
C. boidinii gi57157304S. cerevisiae gi14318479L. starkeyi gi166080363 S. japonicus gi213407080
H. sapiens gi4501889M. cerebralis gi46326807
C. cinerea gi169844021N. crassa gi85101929I. scapularis gi215507378 H. sapiens gi5031569
S. japonicus gi213404844S. cerevisiae gi6320175D. melanogaster gi24642545G. gallus gi45382569C. neoformans gi58266690S. cerevisiae gi6322525D. melanogaster gi17737543H. sapiens gi5031573 H. ochraceum gi227395998
P. patens gi168051992 A. thaliana gi18394608
S. cerevisiae gi1008244
D. melanogaster gi17737347
D. hansenii gi218511921S. cerevisiae gi6323114
S. japonicus gi213408393 S. cerevisiae gi1301932
D. discoideum gi66802418
O. sativa gi182657420 A. thaliana gi1841 1737
D. melanogater gi19920358M. musculus gi226246593
99
67
100100
65
100
100
75
100
100
51
9973
10097
94100
74
100
87
100
0.5
ACTIN
ARP1
ARP2
ARP3
BARP
ARP4
ARP5
ARP6
ARP7
ARP10
See also Guljamow et al. 2007 Current Biology.
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
GEBA Cyanobacteria
Shih et al. 2013. PNAS 10.1073/pnas.1217107110
light-harvesting strategies. The majority of cyanobacteria absorblight mainly with soluble pigment–protein complexes calledphycobilisomes, in contrast to eukaryotes, which use membrane-bound light-harvesting complexes (LHCs). However, an increasingnumber of transmembrane proteins involved in cyanobacteriallight harvesting are being identified, such as Pcb and IsiA (22, 23).These proteins are analogous in function to eukaryotic LHCs.Because of the growing number of proteins and names, an over-arching nomenclature has been proposed to name this proteinfamily the chlorophyll binding proteins (CBPs), which are char-acterized by six transmembrane helices and the ability to bindchlorophyll (24).With the increase in number and diversity of genomes, we find
that CBPs are widely distributed across the cyanobacterial phy-lum: 67% (84 of 126) of cyanobacterial genomes have, in addi-tion to the phycobilisomes, genes that putatively function asmembrane-bound light-harvesting proteins. In our phylogeneticanalysis, the increase in sequence diversity reveals strong supportfor various subclades that we have provisionally named CBPIV,-V, and -VI (Fig. 3A and SI Appendix, Fig. S5). Although not yetexperimentally demonstrated, members of CBPIV, -V, and -VIare expected to bind chlorophyll because they contain position-ally conserved histidine and glutamine residues that ligate chlo-rophyll in confirmed chlorophyll-binding CBPs (SI Appendix, Fig.S6). Some of these proteins, such as CBPIV, have previously
been annotated as PsbC homologs (25), because all CBP pro-teins are thought to have a common evolutionary origin with thepsbC gene (24). Because of the vast enrichment of cyanobacterialprotein sequences, the increase from two to six known CBPVIsequences augments phylogenetic resolution (bootstrap supportof 85%), allowing us to more confidently assert that there isa separate and distinct CBPVI subfamily. On the basis of ourphylogenetic analysis of the CBP family, and consistent withprevious studies (26), there seems to be a substantial amount ofgene duplication and horizontal gene transfer among CBPIV,-V, and -VI. In some genomes, CBPIV and CBPV are found ina gene cluster with other CBP proteins, including IsiA (Fig. 3C),suggestive of the potential for lateral transfer of gene clustersencoding light-harvesting proteins, as documented in marinecyanobacteria (27). Interestingly, many proteins of the CBPVclade also contain a C-terminal extension (SI Appendix, Fig. S7)with homology to the PsaL subunit of photosystem I (PSI).Notably, two distinct subclades within the CBPV family seem tohave independently lost the PsaL domains, reflecting the mod-ularity of this C-terminal extension. Homology modeling andinsertion of the PsaL-like domain into the PSI structure (Fig. 3Band SI Appendix, Fig. S8) suggests how the CBPV protein couldtheoretically be incorporated as an ancillary light-harvestingpolypeptide into a monomeric, but not trimeric, PSI. Althoughscattered observations of members of these CBP protein clades
0.3
B1
B2
C1
Paulinella
Glaucophyte
GreenRed
Chromalveolates
C2C3
AE
FG
B3D
A
B
Fig. 2. Implications on plastid evolution. (A) Maxi-mum-likelihood phylogenetic tree of plastids and cya-nobacteria, grouped by subclades (Fig. 1). The red dot(bootstrap support = 97%) represents the primaryendosymbiosis event that gave rise to the Arch-aeplastida lineage, made up of Glaucophytes (orange),Rhodophytes (red), Viridiplantae (green), and Chro-maleveolates (brown). The independent primary en-dosymbiosis in the amoeba Paulinella chromatophorais shown in purple. (B) Number of predicted eukary-otic, nuclear genes transferred from a cyanobacterialendosymbiont. Colors correspond to the lineageorganisms as above. Light and dark shades of colorsrepresent before and after adding the CyanoGEBAgenomes, respectively.
4 of 6 | www.pnas.org/cgi/doi/10.1073/pnas.1217107110 Shih et al.
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Haloarchaeal GEBA-like
Lynch et al. (2012) PLoS ONE 7(7): e41389. doi:10.1371/journal.pone.0041389
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
The Dark Matter of Biology
From Wu et al. 2009 Nature 462, 1056-1060
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014!57
Number of SAGs from Candidate Phyla
OD
1
OP
11
OP
3
SA
R4
06
Site A: Hydrothermal vent 4 1 - -Site B: Gold Mine 6 13 2 -Site C: Tropical gyres (Mesopelagic) - - - 2Site D: Tropical gyres (Photic zone) 1 - - -
Sample collections at 4 additional sites are underway.
Phil Hugenholtz
GEBA Uncultured
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
JGI Dark Matter Project
environmental samples (n=9)
isolation of singlecells (n=9,600)
whole genomeamplification (n=3,300)
SSU rRNA gene based identification
(n=2,000)
genome sequencing, assembly and QC (n=201)
draft genomes(n=201)
SAK
HSM ETLTG
HOT
GOM
GBS
EPR
TAETL T
PR
EBS
AK E
SM G TATTG
OM
OT
seawater brackish/freshwater hydrothermal sediment bioreactor
GN04WS3 (Latescibacteria)GN01
!"#$%&'$LD1
WS1PoribacteriaBRC1
LentisphaeraeVerrucomicrobia
OP3 (Omnitrophica)ChlamydiaePlanctomycetes
NKB19 (Hydrogenedentes)WYOArmatimonadetesWS4
ActinobacteriaGemmatimonadetesNC10SC4WS2
Cyanobacteria()*&2
Deltaproteobacteria
EM19 (Calescamantes)+,-*./'&'012345678#89/,-568/:
GAL35Aquificae
EM3Thermotogae
Dictyoglomi
SPAMGAL15
CD12 (Aerophobetes)OP8 (Aminicenantes)AC1SBR1093
ThermodesulfobacteriaDeferribacteres
Synergistetes
OP9 (Atribacteria)()*&2
CaldisericaAD3
Chloroflexi
AcidobacteriaElusimicrobiaNitrospirae49S1 2B
CaldithrixGOUTA4
*;<%0123=/68>8?8,6@98/:Chlorobi
486?8,A-5BTenericutes4AB@9/,-568/Chrysiogenetes
Proteobacteria
4896@9/,-565BTG3SpirochaetesWWE1 (Cloacamonetes)
C=1ZB3
=D)&'EF58>@,@,,AB&CG56?ABOP1 (Acetothermia)Bacteriodetes
TM7GN02 (Gracilibacteria)
SR1BH1
OD1 (Parcubacteria)
(*1OP11 (Microgenomates)
Euryarchaeota
Micrarchaea
DSEG (Aenigmarchaea)Nanohaloarchaea
Nanoarchaea
Cren MCGThaumarchaeota
Cren C2Aigarchaeota
Cren pISA7
Cren ThermoproteiKorarchaeota
pMC2A384 (Diapherotrites)
BACTERIA ARCHAEA
archaeal toxins (Nanoarchaea)
lytic murein transglycosylase
stringent response (Diapherotrites, Nanoarchaea)
ppGpp
limitingamino acids
SpotT RelA
(GTP or GDP)+ PPi
GTP or GDP+ATP
limitingphosphate,fatty acids,carbon, iron
DksA
Expression of components for stress response
sigma factor (Diapherotrites, Nanoarchaea)
!4
"#$#"%
!2!3 !1
-35 -10
&'()
&*()
+',#-./0123452
oxidoretucase
+ +e- donor e- acceptor
H
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+
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O
Reduction
OxidationH
'Ribo
ADP
'6
O
2H
',)##$#6##$#72#####################',)6+ + -
HGT from Eukaryotes (Nanoarchaea)
Eukaryota
O68*62
OH
'6
*8*63
OO
68*62
'6
*8*63
O
tetra-peptide
O68*62
OH
'6
*8*63
OO
68*62
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*8*63
O
tetra-peptide
murein (peptido-glycan)
archaeal type purine synthesis (Microgenomates)
PurFPurD9:3'PurL/QPurMPurKPurE9:3*PurB
PurP
?
Archaea
adenine guanine
O
6##'2
+'
'62
'
'
H
H
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'
'
H
HH' '
H
PRPP ;,<*,+
IMP
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GUA *G U
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A
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A UA * U
A * U
Growing AA chain
=+',>?/0@#recognizes
UGA1+',
UGA recoded for Gly (Gracilibacteria)
ribosome
Woyke et al. Nature 2013.
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
A Genomic Encyclopedia of Microbes (GEM)
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
A Genomic Encyclopedia of Microbes (GEM)
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
GEBA Lesson 6: Improves analysis of metagenomic data
!61
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Sargasso Phylotypes
Wei
ghte
d %
of C
lone
s
0.000
0.125
0.250
0.375
0.500
Major Phylogenetic Group
Alphapro
teobacteria
Betap
roteobacteria
Gamm
aproteobacteria
Epsilo
nproteobacteria
Deltapro
teobacteria
Cyanobacteria
Firmicutes
Actinobacteria
Chlorobi
CFB
Chloroflexi
Spirochaetes
Fusobacteria
Deinococcus-Th
ermus
Euryarchaeota
Crenarchaeota
EFGEFTuHSP70RecARpoBrRNA
Other Markers
GEBA Project improves metagenomic analysis
Venter et al., Science 304: 66-74. 2004 !62
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Sargasso Phylotypes
Wei
ghte
d %
of C
lone
s
0.000
0.125
0.250
0.375
0.500
Major Phylogenetic Group
Alphapro
teobacteria
Betap
roteobacteria
Gamm
aproteobacteria
Epsilo
nproteobacteria
Deltapro
teobacteria
Cyanobacteria
Firmicutes
Actinobacteria
Chlorobi
CFB
Chloroflexi
Spirochaetes
Fusobacteria
Deinococcus-Th
ermus
Euryarchaeota
Crenarchaeota
EFG EFTurRNA
But not a lot
Venter et al., Science 304: 66-74. 2004
Other Markers
!63
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rRNA Tree of Life
Figure from Barton, Eisen et al. “Evolution”, CSHL Press. 2007.
Based on tree from Pace 1997 Science 276:734-740
Archaea
Eukaryotes
Bacteria
!64
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
PD: Genomes
From Wu et al. 2009 Nature 462, 1056-1060
!65
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
From Wu et al. 2009 Nature 462, 1056-1060
PD: Genomes + GEBA
!66
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PD: Isolates
From Wu et al. 2009 Nature 462, 1056-1060 !67
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
PD: All
From Wu et al. 2009 Nature 462, 1056-1060 !68
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
Uncultured Lineages:Technical Approaches
• Get into culture
• Enrichment cultures
• If abundant in low diversity ecosystems
• Flow sorting
• Microbeads
• Microfluidic sorting
• Single cell amplification
!69
Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !70
Number of SAGs from Candidate Phyla
OD
1
OP
11
OP
3
SA
R4
06
Site A: Hydrothermal vent 4 1 - -Site B: Gold Mine 6 13 2 -Site C: Tropical gyres (Mesopelagic) - - - 2Site D: Tropical gyres (Photic zone) 1 - - -
Sample collections at 4 additional sites are underway.
Phil Hugenholtz
GEBA uncultured