Phylogeny-Driven Genomic Encyclopedia

A Phylogeny-Driven Genomic
Encyclopedia of Bacteria and Archaea

Jonathan A. Eisen

Talk for ASBMB
April 25, 2010
Sunday, April 25, 2010

Eisen Lab - Phylogenomics of Novelty

Origin of New Genome
Functions and Dynamics
Processes
•Evolvability
•New genes •Repair and
•Changes in old genes recombination processes
•Changes in pathways •Intragenomic variation

Species Evolution
•Phylogenetic history
•Vertical vs. horizontal descent
•Needed to track gain/loss of
processes, infer convergence

Bacterial evolve


TIGR Fleischmann et al.
1995

Microbial genomes

From http://genomesonline.org

rRNA Tree of Life
Bacteria

Archaea

Eukaryotes

FIgure from Barton, Eisen et al.
“Evolution”, CSHL Press.
Based on tree from Pace NR, 2003.

The Tree is not Happy
Bacteria

Archaea

Eukaryotes


Proteobacteria

2002 TM6
OS-K
Acidobacteria
• At least 40
Termite Group
OP8
phyla of
Nitrospira
Bacteroides bacteria
Chlorobi
Fibrobacteres
Marine GroupA
WS3
Gemmimonas
Firmicutes
Fusobacteria
Actinobacteria
OP9
Cyanobacteria
Synergistes
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermudesulfobacteria
Thermotogae
OP1 Based on
OP11 Hugenholtz, 2002

Proteobacteria

2002 TM6
OS-K
Acidobacteria
• At least 40
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
Marine GroupA • Genome
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1 Based on

Proteobacteria

2002 TM6
OS-K
Acidobacteria
• At least 40
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
• Some other
Verrucomicrobia
Chlamydia
OP3
phyla are
Planctomycetes
Spriochaetes only sparsely
Coprothmermobacter
OP10
Thermomicrobia
sampled
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1 Based on

Proteobacteria

2002 TM6
OS-K
Acidobacteria
• At least 40
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
• Some other
Verrucomicrobia
Chlamydia
OP3
phyla are
Planctomycetes
Coprothmermobacter
OP10
Thermomicrobia
sampled
Chloroﬂexi
TM7
Deinococcus-Thermus
• Same trend in
Dictyoglomus
Aquiﬁcae
Archaea
Thermotogae
OP1 Based on

Proteobacteria

2002 TM6
OS-K
Acidobacteria
• At least 40
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
• Some other
Verrucomicrobia
Chlamydia
OP3
phyla are
Planctomycetes
Coprothmermobacter
OP10
Thermomicrobia
sampled
Chloroﬂexi
TM7
Deinococcus-Thermus
• Same trend in
Dictyoglomus
Aquiﬁcae
Eukaryotes
Thermotogae
OP1 Based on

Filling in the Genomic Phylogenetic Gaps

• Common approach within some eukaryotic
groups

• Many small projects funded to ﬁll in some
bacterial or archaeal gaps

• Phylogenetic gaps in bacterial and archaeal
projects commonly lamented in literature


Proteobacteria
• NSF-funded TM6
OS-K
• At least 40
Tree of Life Acidobacteria
Termite Group phyla of
OP8
Project Nitrospira
Chlorobi
• A genome Fibrobacteres
WS3
from each of Gemmimonas sequences are
Firmicutes
eight phyla Fusobacteria
mostly from
Actinobacteria
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
• Some other
Verrucomicrobia
Chlamydia
OP3
phyla are only
Planctomycetes
Spriochaetes sparsely
Coprothmermobacter
OP10
Thermomicrobia
sampled
Chloroﬂexi
TM7
Deinococcus-Thermus
• Solution I:
Dictyoglomus
Aquiﬁcae sequence more
Eisen & Ward, PIs Thermudesulfobacteria
Thermotogae
OP1 phyla
OP11


The Tree of Life is Still Angry
Bacteria

Archaea

Eukaryotes


Major Lineages of Actinobacteria
2.5 Actinobacteria
2.5.1 Acidimicrobidae
2.5.1 Acidimicrobidae 2.5.1.1 Unclassified
2.5.1.2 "Microthrixineae
2.5.1.1 Unclassified 2.5.1.3 Acidimicrobineae
2.5.1.3.1 Unclassified
2.5.1.2 "Microthrixineae 2.5.1.3.2 Acidimicrobiaceae
2.5.1.4 BD2-10
2.5.1.3 Acidimicrobineae 2.5.1.5 EB1017
2.5.2 Actinobacteridae
2.5.1.4 BD2-10 2.5.2.1 Unclassified
2.5.2.10 Ellin306/WR160
2.5.1.5 EB1017 2.5.2.11 Ellin5012
2.5.2.12 Ellin5034
2.5.2 Actinobacteridae 2.5.2.13 Frankineae
2.5.2.1 Unclassified 2.5.2.13.2 Acidothermaceae

2.5.2.10 Ellin306/WR160 2.5.2.13.3
2.5.2.13.4
Ellin6090
Frankiaceae

2.5.2.11 Ellin5012 2.5.2.13.5
2.5.2.13.6
Geodermatophilaceae
Microsphaeraceae

2.5.2.12 Ellin5034 2.5.2.13.7
2.5.2.14
Sporichthyaceae
Glycomyces
2.5.2.13 Frankineae 2.5.2.15
2.5.2.15.1
Intrasporangiaceae
Unclassified
2.5.2.14 Glycomyces 2.5.2.15.2
2.5.2.15.3
Dermacoccus
Intrasporangiaceae
2.5.2.15 Intrasporangiaceae 2.5.2.16
2.5.2.17
Kineosporiaceae
Microbacteriaceae
2.5.2.16 Kineosporiaceae 2.5.2.17.1
2.5.2.17.2
Unclassified
Agrococcus
2.5.2.17 Microbacteriaceae 2.5.2.17.3
2.5.2.18
Agromyces
Micrococcaceae
2.5.2.18 Micrococcaceae 2.5.2.19
2.5.2.2
Micromonosporaceae
Actinomyces
2.5.2.19 Micromonosporaceae 2.5.2.20
2.5.2.20.1
Propionibacterineae
Unclassified
2.5.2.2 Actinomyces 2.5.2.20.2
2.5.2.20.3
Kribbella
Nocardioidaceae
2.5.2.20 Propionibacterineae 2.5.2.20.4
2.5.2.21
Propionibacteriaceae
Pseudonocardiaceae
2.5.2.21 Pseudonocardiaceae 2.5.2.22
2.5.2.22.1
Streptomycineae
Unclassified
2.5.2.22 Streptomycineae 2.5.2.22.2
2.5.2.22.3
Kitasatospora
Streptacidiphilus
2.5.2.23 Streptosporangineae 2.5.2.23
2.5.2.23.1
Streptosporangineae
Unclassified
2.5.2.3 Actinomycineae 2.5.2.23.2
2.5.2.23.3
Ellin5129
Nocardiopsaceae
2.5.2.4 Actinosynnemataceae 2.5.2.23.4
2.5.2.23.5
Streptosporangiaceae
Thermomonosporaceae
2.5.2.5 Bifidobacteriaceae 2.5.2.3 Actinomycineae
2.5.2.4 Actinosynnemataceae
2.5.2.6 Brevibacteriaceae 2.5.2.5 Bifidobacteriaceae
2.5.2.6 Brevibacteriaceae
2.5.2.7 Cellulomonadaceae 2.5.2.7 Cellulomonadaceae
2.5.2.8 Corynebacterineae
2.5.2.8 Corynebacterineae 2.5.2.8.1 Unclassified
2.5.2.8.2 Corynebacteriaceae
2.5.2.9 Dermabacteraceae 2.5.2.8.3 Dietziaceae
2.5.2.8.4 Gordoniaceae
2.5.3 Coriobacteridae 2.5.2.8.5 Mycobacteriaceae
2.5.2.8.6 Rhodococcus
2.5.3.1 Unclassified 2.5.2.8.7 Rhodococcus
2.5.2.8.8 Rhodococcus
2.5.3.2 Atopobiales 2.5.2.9 Dermabacteraceae
2.5.3.3 Coriobacteriales 2.5.2.9.2 Brachybacterium
2.5.2.9.3 Dermabacter
2.5.3.4 Eggerthellales 2.5.3 Coriobacteridae
2.5.3.1 Unclassified
2.5.4 OPB41 2.5.3.2 Atopobiales
2.5.3.3 Coriobacteriales
2.5.5 PK1 2.5.3.4 Eggerthellales
2.5.4 OPB41
2.5.6 Rubrobacteridae 2.5.5 PK1
2.5.6 Rubrobacteridae
2.5.6.1 Unclassified 2.5.6.1 Unclassified
2.5.6.2 "Thermoleiphilaceae
2.5.6.2 "Thermoleiphilaceae 2.5.6.2.1 Unclassified
2.5.6.2.2 Conexibacter
2.5.6.3 MC47 2.5.6.2.3 XGE514
2.5.6.3 MC47
2.5.6.4 Rubrobacteraceae 2.5.6.4 Rubrobacteraceae


Microbial genomes 2010- ...

From http://genomesonline.org

Proteobacteria
TM6
OS-K
• At least 100 phyla of
Acidobacteria
Termite Group
OP8
bacteria
Nitrospira
Bacteroides
Chlorobi
• Genome sequences are
Fibrobacteres
Marine GroupA mostly from three phyla
WS3
Gemmimonas
Firmicutes • Most phyla with cultured
Fusobacteria
Actinobacteria species are sparsely
OP9
Cyanobacteria
Synergistes
sampled
Deferribacteres
Chrysiogenetes
NKB19 • Lineages with no cultured
Verrucomicrobia
Chlamydia
OP3
taxa even more poorly
Planctomycetes
Spriochaetes sampled
Coprothmermobacter
OP10
Thermomicrobia
Chloroflexi
• Solution - use tree to really
TM7
Deinococcus-Thermus fill gaps
Dictyoglomus
Aquificae Well sampled phyla
Thermotogae
OP1
OP11


Why Increase Phylogenetic Coverage?

• Gene discovery
• Annotation, functional prediction
• Metagenomic analysis
• Mechanisms of diversiﬁcation
• Species phylogeny and classiﬁcation


A Genomic Encyclopedia of Bacteria
and Archaea (GEBA)


GEBA Pilot Project Overview

• Identify major branches in rRNA tree for
which no genomes are available
• Identify a cultured representative for each
group
• Grow > 200 of these and prep. DNA
• Sequence and ﬁnish 100
• Annotate, analyze, release data
• Assess beneﬁts of tree guided sequencing
• Paper published in Nature Dec. 2009.


B:
Ac
tin
ob
ac
te
B: ria # of Genomes
Am (H

in igh

10
15
20
25
30
35

0
5
an G
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B: B: er )
Ba Aq ob
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e i
B: B: ro cae
D Ch ide
B: efe lo te
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ef ba e
B: e c xi
B: De B rrib ter
Ep lta : D act es
si Pr ei er
lo o n es
n te oc
Pr ob oc
ot a ci
B: e ct
G B: oba eri
am B F ct a
: ir e
B: m Fu mi ria
a
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t c s
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ba ri
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B: loa ona eri
a
B: Pl nae de
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Th c o s

Phyla
er B: to bia
m S m le
y s
B: od piro ce
es c te
T u h
B: he lfo ae s
rm b te
GEBA Pilot Target List

Th o a s
er de cte
m s ri
u a
A: ove lfo
H n bi
A: alo abu a
A: A b la
M rc ac e
A: et ha te
M han eo ria
et g
ha ob lob
ac i
A: no te
m r
A: The icr ia
Th rm obi
er oc a
m oc
op ci
ro
te
i

GEBA and Openness
• All data being released as quickly
as possible with no restrictions to
IMG-GEBA; Genbank, etc
• Data also available in Biotorrents
(http://biotorrents.net)
• Individual genome reports being
published in new Open Access
journal “Standards in Genome
Sciences (SIGS)”
• Main GEBA paper in Nature
freely available and published
using Creative Commons License

Assess Benefits of GEBA

• All genomes have some value

• But what, if any, is the beneﬁt of tree-
guided sequencing over other selection
methods

• Lessons for other large scale microbial
genome projects?


GEBA Lesson 1

rRNA Tree is Useful for Identifying
Phylogenetically Novel Genomes

rRNA Tree topology is not perfect;
Genome-based trees better

Network of Life
Bacteria

Archaea

Eukaryotes


Wh

Whole genome tree
built using
AMPHORA
by Martin Wu and
Dongying Wu


PD of rRNA, Genome Trees Similar

From Wu et al. 2009

Proteobacteria


GEBA Lesson 2

Phylogenetically-guided genome
selection improves genome
annotation


Predicting Function

• Key step in genome projects
• More accurate predictions help guide
experimental and computational analyses
• Many diverse approaches
• Comparative and evolutionary analysis
greatly improves most predictions


Most/All Functional Prediction Improves
w/ Better Phylogenetic Sampling
• Better deﬁnition of protein family sequence
“patterns”
• Conversion of hypothetical into conserved
hypotheticals
• Greatly improves “comparative” and
“evolutionary” based predictions
• Linking distantly related members of protein
families
• Improved non-homology prediction


From Wu et al. 2009.

GEBA Lesson 3

Improves analysis of genome data
from uncultured organisms


Metagenomics

shotgun

clone


rRNA phylotyping from metagenomics

Venter et al., 2004

Shotgun Sequencing Allows Use of
Alternative Anchors (e.g., RecA)

Venter et al., 2004

Weighted % of Clones

0
0.1250
0.2500
0.3750
0.5000
Al
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FB

Major Phylogenetic Group
Sargasso Phylotypes

C
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Shotgun Sequencing Allows Use of Other Markers

Venter et al., 2004
EFG
EFTu

rRNA
RecA
RpoB
HSP70

Weighted % of Clones

0
0.1250
0.2500
0.3750
0.5000
Al
ph
ap
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Ac s
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without good

C
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Major Phylogenetic Group
Sargasso Phylotypes

C
Cannot be done

hl
or
of
le
Sp xi
iro
c ha
et
Fu es
so
De ba
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oc ia
sampling of genomes

oc
cu
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ar mu
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ae
C ot
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na
rc
ha
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ta
Shotgun Sequencing Allows Use of Other Markers

Venter et al., 2004
EFG
EFTu

rRNA
RecA
RpoB
HSP70

Binning challenge

A T
B U
C V
D W
E X
F Y
G Z

Binning challenge

A T
B U
C V
D W
E X
F Y
G Best binning method: reference genomes Z

Binning challenge

A T
B U
C V
D W
E X
F Y
G No reference genome? What do you do? Z

Binning challenge

A T
B U
C V
D W
E X
F Y
G No reference genome? What do you do? Z
Phylogeny ....

Al
ph
ap
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Be te
ta o ba
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0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
am ro ct
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AMPHORA - each read on its own tree
iro es
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Phylogenetic Binning Using AMPHORA
frr

tsf
pgk

rplL
rplF

rplP

rplT
rplE
infC

rpsI
rplS
rplA
rplB

rplK
rplC

rpsJ
rplN
rplD

rplM

rpsE

rpsS
rpsB

rpsK
rpsC
rpoB

rpsM
pyrG
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dnaG

rpmA

smpB

Phylogenetic Binning Using AMPHORA
dnaG
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frr
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0.6 nusA
pgk
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0.5

0.4
Cannot be done rplA
rplB
rplC
rplD

0.3 without good rplE
rplF
rplK
rplL
0.2

0.1
sampling of genomes rplM
rplN
rplP
rplS
rplT
rpmA
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AMPHORA - each read on its own tree

GEBA Phylogenomic Lesson 5

We have still only scratched the
surface of microbial diversity


Protein Family Rarefaction Curves

• Take data set of multiple complete genomes
• Identify all protein families using MCL
• Plot # of genomes vs. # of protein families


Mobile
Motility
Element?


Phylogenetic Distribution Novelty:
Bacterial Actin Related Protein
2"#3)&4&*&& !"#*)$*),+%
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+/*!

Haliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam
Zemla, Victor Kunin
See also Guljamow et al. 2007 Current Biology.

Phylogenetic Diversity:
Sequenced Bacteria & Archaea

From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html

Phylogenetic Diversity with GEBA


Phylogenetic Diversity: Isolates

From Wu et al. 2009.

Phylogenetic Diversity: All


Proteobacteria
TM6
OS-K
• At least 40 phyla of
Acidobacteria
Termite Group
OP8
bacteria
Nitrospira
Bacteroides
Chlorobi
• Genome sequences are
Fibrobacteres
Marine GroupA mostly from three phyla
WS3
Gemmimonas
Firmicutes • Most phyla with cultured
Fusobacteria
Actinobacteria species are sparsely
OP9
Cyanobacteria
Synergistes
sampled
Deferribacteres
Chrysiogenetes
NKB19 • Lineages with no cultured
Verrucomicrobia
Chlamydia
OP3
taxa even more poorly
Planctomycetes
Spriochaetes sampled
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae Well sampled phyla
Thermotogae Poorly sampled
OP1
OP11
No cultured taxa

Uncultured Lineages:
Technical Approaches
• Get into culture
• Enrichment cultures
• If abundant in low diversity ecosystems
• Flow sorting
• Microbeads
• Microﬂuidic sorting
• Single cell ampliﬁcation


GEBA Phylogenomic Lesson 6

Need Experiments from Across the
Tree of Life too


As of 2002 Proteobacteria
TM6
OS-K • At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
Marine GroupA
WS3
Gemmimonas
Firmicutes
Fusobacteria
Actinobacteria
OP9
Cyanobacteria
Synergistes
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1 Based on

TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
Marine GroupA • Experimental
WS3
Gemmimonas
Firmicutes
studies are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1 Based on

TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
Marine GroupA • Experimental
WS3
Gemmimonas
Firmicutes
studies are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
• Some studies
Verrucomicrobia
Chlamydia
OP3
in other phyla
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1 Based on

Phylogeny-Driven Genomic Encyclopedia

Phylogeny-Driven Genomic Encyclopedia

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