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Genomic Evolvability
                                  and the Origin of Novelty
                                        Jonathan A. Eisen
                                    U. C. Davis Genome Center

                                      ASM General Meeting
                                         Boston, MA
                                         June 4, 2008
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Secret Message Coming …

                                        Jonathan A. Eisen
                                    U. C. Davis Genome Center

                                      ASM General Meeting
                                         Boston, MA
                                         June 4, 2008
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Genomic Evolvability
                                  and the Origin of Novelty
                                            Jonathan A. Eisen
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                                       U. C. Davis Genome Center

                                         ASM General Meeting
                                            Boston, MA
                                            June 4, 2008




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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
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“Nothing in biology makes sense
                                  except in the light of evolution.”

                                     T. H. Dobzhansky (1973)



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Origin of Novelty

                        • How does novelty originate?
                        • What are the constraints on evolvability?
                        • What leads to variation within the genome
                          and within and between species in
                          evolvability

                        • This information helps interpret the past,
                          understand the present and (maybe) predict
                          the future
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Phylogenomic Analysis

                        • Evolutionary reconstructions greatly
                          improve genome analyses
                        • Genome analysis greatly improves
                          evolutionary reconstructions
                        • There is a feedback loop such that these
                          should be integrated


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Phylogenomic Tales

                        • Predicting functions with evolutionary trees
                        • Recently evolved new functions
                        • Uncharacterized genes
                        • Stealing functions
                        • Knowing what we do not know



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Phylogenomics I:

                                  Predicting Functions with
                                     Evolutionary Trees



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SNF2 Family of Proteins (1995)
                        • SNF2 family defined by presence of conserved DNA-
                          dependent ATPase domain                  Bork and Koonin 1993
                        • 100s of proteins
                        • Diversity of functions:
                                  –   transcriptional activation (SNF2)
                                  –   transcriptional repression (MOT1)
                                  –   Recombination (RAD54)                        QuickTimeª and a
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                                  –   post-replication repair (RAD5)
                                  –   chromosome segregation (lodestar)
                                  –   Many with unknown functions
                        • Some species have 15+ representatives


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HEPA._E.c
                                  NPHCG_42
                                  LODE._D.m
                                  MOT1_S.c
                                  SNF2_S.c
                                  STH1_S.c
                                  BRG1_M.m
                                  BRG1_H.s
                                  BRM_H.s
                                  BRM_D.m
                                  SNF2L_H.s
                                  F37A4_C.e
                                  DNRPPX_S.p
                                  NUCP_M.m
                                  NUCP_H.s
                                  RAD26_S.c
                                  ERCC6_H.s
                                  SYGP4_S.c
                                  CHD1_M.m
                                  ETL1_M.m
                                   ISWI_D.m
                                   YB95_S.c
                                   RAD16_S.c
                                   HIP116A_H.s
                                   RAD8_S.p
                                   RAD5_S.c
                                   RAD54_S.c
                                   YB53_S.c
                                   YA19_S.c
                                  LODE
                                  RAD16
                                  RAD54
                                  CSB
                                  ETL1
                                  CHD1
                                  SNF2L
                                  SNF2
                                  Evolution      of the SNF2 Family of Proteins




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SNF2 Tree and F(x) Prediction

                        • Function conserved within but not between
                          subfamilies/orthology groups
                        • Therefore, assignment of genes to
                          subfamilies can be used to predict functions
                          of unknowns
                        • Grouping into subfamilies helps identify
                          motifs conserved within groups
                        • Phylogeny recovers subfamilies better than
                          similarity searches
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From Eisen et al.
                                  1997 Nature
                                  Medicine 3: 1076-10

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Blast Search of H. pylori “MutS”
                                                                                       Score   E
Sequences producing significant alignments:                                           (bits) Value

sp|P73625|MUTS_SYNY3                       DNA   MISMATCH     REPAIR      PROTEIN         117    3e25
                                                                                                  -
sp|P74926|MUTS_THEMA                       DNA   MISMATCH     REPAIR      PROTEIN          69    1e10
                                                                                                  -
sp|P44834|MUTS_HAEIN                       DNA   MISMATCH     REPAIR      PROTEIN          64    3e09
                                                                                                  -
sp|P10339|MUTS_SALTY                       DNA   MISMATCH     REPAIR      PROTEIN          62    2e08
                                                                                                  -
sp|O66652|MUTS_AQUAE                       DNA   MISMATCH     REPAIR      PROTEIN          57    4e07
                                                                                                  -
sp|P23909|MUTS_ECOLI                       DNA   MISMATCH     REPAIR      PROTEIN          57    4e07
                                                                                                  -


                        • Blast search pulls up Syn. sp MutS#2 with much higher p
                          value than other MutS homologs
                        • Based on this TIGR predicted this species had mismatch
                          repair
                        • Assumes functional constancy
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Phylogenetic Tree of MutS Family
                                                                 Aquae
                                                                     Strpy
                                                                         Bacsu
                                                                             Synsp
                                                                               Deira Helpy
                                                    Yeast
                                              Human                              Borbu     Metth
                                              Celeg

                                                                                              mSaco
                                        Yeast
                                      Human                                                     Yeast
                                      Mouse
                                       Arath                                                     Celeg
                                                                                                Human
                                       Arath
                                      Human
                                      Mouse
                                   Spombe                                                        Fly
                                      Yeast                                                     Xenla
                                                                                                Rat
                                                                                                Mouse
                                      Yeast                                                    Human
                                   Spombe                                                       Yeast
                                                                                               Neucr
                                                                                              Arath

                                                  Aquae                            Trepa
                                                  Chltr
                                                   DeiraTheaq
                                                          Thema                  BacsuBorbu              Based on Eisen,
                                                                          SynspStrpy                     1998 Nucl Acids
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                                                                                                         Res 26: 4291-4300.
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                                                                      Neigo
MutS Subfamilies
                                                            M S H 5A q u a e                  M utS 2
                                                                               S trB y c S uns p
                                                                                   p a s y
                                                                                           D e ir a H e lp y
                                                          Ye a s t
                                                   Huma n                                    B orbu          M e tth
                                                   C e le g

                                                                                                          mS a c o
                                  MS H6     Ye a s t
                                          Huma n
                                          Mous e
                                           A ra th
                                                                                                             Ye a s t  MS H4
                                                                                                              C e le g
                                                                                                            Huma n
                                           A ra th
                                           Huma n
               MS H3                    Mous e
                                                                                                               F ly
                                     S pombe
                                        Ye a s t                                                            X e n la
                                                                                                             Rat
                                                                                                             Mous e
                                        Ye a s t                                                            Huma n
                    MS H1            S pombe                                                                Ye a s t
                                                                                                                     MS H2
                                                                                                           Neuc r
                                                                                                          A ra th


                                                        Aquae                               Tre p a
                                                        C h lt r
                                                         D e ir a e a q
                                                                 Th
                                                                                          B a c s u rbu
                                                                                                  Bo
                                                                    Th e m a
                                                                                 S y n sSpt r p y
                                                                      E c o li
                                                                            N e ig o                                     Based on Eisen,
                                                                                                                         1998 Nucl Acids
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Overlaying Functions onto Tree
                                                                                                M utS 2
                                                                              Aquae
                                                             MS H5               S t rB y c S yn s p
                                                                                      pa su
                                                                                              D e ir a H e lp y
                                                               Ye a s t
                                                        Huma n                                  B orbu          M e tth
                                                        C e le g


                                     MS H6                                                                    mS a c o
                                                Ye a s t
                                              Huma n
                                              Mous e
                                               A ra th
                                                                                                                     MS H4
                                                                                                                 Ye a s t
                                                                                                                  C e le g
                                                                                                                 Huma n
                                              A ra th
                                            Huma n
                                  MS H3    Mous e
                                         S pombe                                                                   F ly
                                            Ye a s t                                                            X e n la
                                                                                                                 Rat
                                                                                                                 Mous e
                                            Ye a s t                                                            Huma n
                                  M S H 1 pombe
                                         S                                                                      Ye a s t MS H2
                                                                                                               Neuc r
                                                                                                              A ra th


                                                           Aquae                                Tre p a
                                                           C h lt r
                                                            D e ir a e a q
                                                                   Th
                                                                                              B a c s u rbu
                                                                                                      Bo
                                                                      Th e m a
                                                                                     S y n sSpt r p y                        Based on Eisen,
                                                                          E c o li
                                                                                N e ig o
                                                                                                                             1998 Nucl Acids
                                                                           M utS 1
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Functional Prediction Using Tree
                           M S H 5 - M e io t ic C r o s s in g O v e u t S 2 - U n k n o w n F u n c t io n s
                                                                   M r
                                                                         Aquae
                                                                            S t rB y c S yn s p
                                                                                 pa su
                                                                                         D e ir a H e lp y
                                                              Ye a s t
                                                       Huma n                              B orbu          M e tth
                                                       C e le g

 M S H 6 - N u c le a r                                                                                  mS a c o
 R e p a ir
                         Ye a s t
 O f M is m a t c h e s Huma n                                                                                      M S H 4 - M e io t ic C r o s s in g
                                            Mous e                                                          Y e a sO v e r
                                                                                                                    t
                                             A ra th                                                         C e le g
                                                                                                            Huma n
                          A ra th
M S H 3 - N u c le a r    Huma n
                         Mous e
R e p a ir O f L o o p s o m b e
                     S p                                                                                      F ly
                         Ye a s t                                                                          X e n la
                                                                                                            Rat
                                                                                                            M oM s eH 2 - E u k a r y o t i c N u c l e a r
                                                                                                                 u S
                                          Ye a s t                                                         H u m ai n m a t c h a n d L o o p R e p a i r
                                                                                                               M s
MS H1                                  S pombe                                                              Ye a s t
M it o c h o n d r ia l                                                                                   Neuc r
                                                                                                         A ra th
R e p a ir
                                                       Aquae                               Tre p a
                                                       C h lt r
                                                        D e ir a e a q
                                                               Th
                                                                                         B a c s u rbu
                                                                                                 Bo
                                                                  Th e m a
                                                                                S y n sSpt r p y
                                                                     E c o li                                                    Based on Eisen,
                                                                           N e ig o
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                                            M u t S 1 - B a c t e r ia l M is m a t c h a n d L o o p R e p a ir                 Res 26: 4291-4300.
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Evolutionary Functional Prediction
                                        SpeciesMETHOD EVOLUTION
                                        Duplication?SEQUENCES
                                        5 IDENTIFY HOMOLOGS
                                        4B EXAMPLE A B
                                        3A CALCULATE GENE KNOWN
                                        2CHOOSE GENE(S) OF FUNCTION
                                        1ALIGNINFER LIKELY INTEREST
                                                1ACTUAL
                                                3EXAMPLE
                                        Ambiguous
                                        Duplication
                                        1A
                                        3B
                                        2B
                                        1B
                                        3A
                                        2A
                                        6       2      OVERLAY TREE
                                         (ASSUMED TO BE OFONTO TREE
                                              OF GENE(S) UNKNOWN)
                                               FUNCTIONS INTEREST




                                                                      Based on Eisen,
                                                                      1998 Genome
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                                                                      Res 8: 163-167.
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Phylogenetic Prediction of Function

                        • Many powerful and automated similarity based
                          methods for assigning genes to protein families
                                  – COGs
                                  – PFAM HMM searches
                        • Some limitations of similarity based methods can
                          be overcome by phylogenetic approaches
                        • Automated methods now available
                                  – Sean Eddy
                                  – Steven Brenner
                                  – Kimmen Sjölander
                        • But …
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Phylogenomics II

                                   Recent Evolution




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Recent Functional Changes
                        • Phylogenomic functional prediction may not work
                          well for very newly evolved functions
                        • Can we use understanding of origin of novelty to
                          better understand these cases?
                        • Screen genomes for genes that have changed
                          recently
                                  –   Pseudogenes and gene loss
                                  –   Contingency Loci
                                  –   Acquisition (e.g., LGT)
                                  –   Unusual dS/dN ratios
                                  –   Rapid evolutionary rates
                                  –   Duplication and divergence
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Lineage Specific Gene Family
                                           Expansions
                        • Lineage specific expansions frequently
                          associated with adaptive evolution
                        • Can screen genomes for such expansions by
                          looking for genes more closely related to
                          other genes in the genome than to genes
                          from other species




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Expansion of MCP Family in V. cholerae
                                  NJ

                                                                                                 V. choleraeVC 12   05
                                                                                                  V. chole raeV C 03 4
                                                                                                                     A1
                                                                                                      V. choleraeVC 97 4A0
                                                                          **                         V. choleraeVC 06 8A0
                                                             *                                            V. chole rae C 25
                                                                                                                        V 08
                                                                                                   V. choleraeV C 82   02
                                                                                                V. chole rae C 90 6
                                                                                                                V A0
                                                                                                              V. chole raeV C 979
                                                                                                                               A0
                                                                                                V. chole rae C 05 6
                                                                                                                V A1
                                                                                                   V. choleraeV C 43   16
                                                                                                       V. chole rae C 61
                                                                                                                      V 21
                                                                                  **                     V. choleraeVC 92 3
                                                                                                                          A0
                                                                   **                               V. choleraeV C 14  05
                                                                                                            V. choleraeVC 68 18
                                                                                                        V. chole raeV C 77 3
                                                                                                                          A0
                                                                                                    V. choleraeV C 13  13
                                                                                                        V. chole raeV C 5918
                                                                                                  V. choleraeV C 13  14
                                                                                                V. chole rae C 26 8
                                                                                                                V A0
                                                      **                                                          V. chole raeV C 65 8
                                                                                                                                   A0
                                                                                                       V. choleraeV C 05 14
                                                  *                                                    V. cholerae 12 98
                                                                                                                     VC
                                                                                                           V. choleraeV C 4812
                                                                                               V. chole raeV C 86 4
                                                                                                                  A0
                                                                                              V. choleraeVC 17 6  A0
                                                             **                                    V chole raeV C 22 0
                                                                                                    .                A0
                                                                                                 V. choleraeVC 89   12
                                                                   **                                   V. choleraeVC 06 9A1
                                                                                                   V. choleraeV C 39   24
                                                                                                          V. choleraeVC 67 19
                                                                                                          V. chole rae C 031
                                                                                                                        V A0
                                                                                                  V. choleraeV C 98  18
                                                                                                           V. chole rae C 663
                                                                                                                         V A0
                                                                                             V. choleraeVC 988   A0
                                                                                               V. chole raeV C 16 02
                                                      *                                        V. chole raeV C 49 04
                                                                                             V. chole rae C 00 8
                                                                                                             V A0
                                                                                              V. choleraeVC 06    14
                                                                                                              V. chole raeV C 35
                                                                                                                               15
                                                                                                 V. choleraeV C 40  08
                                                                                                                     B.subtilis gi2633766
                                                                                                               Synechocystis sp. gi1001299
                                                         *                                     Synechocystis sp. gi1001300
                                                 *                                                             Synechocystis sp. gi1652276
                                                           *                                        Synechocystis sp. gi1652103
                                                                                                 H.pylori gi2313716
                                                                                             ** H.pylori9Cj1190c
                                                                                                  C.jejuni
                                                                                                             9 gi4155097
                                                    **
                                                                                          C.jejuni Cj1110c
                                                                                              A.fulgidus gi2649560
                                                                                              A.fulgidus gi2649548
                                                                                          **       B.subtilis gi2634254
                                                                                              B.subtilis gi2632630
                                                                                               B.subtilis gi2635607
                                                                                               B.subtilis gi2635608
                                                                            **                  B.subtilis gi2635609
                                                                         **    **
                                                                                              B.subtilis gi2635610
                                                                                                        B.subtilis gi2635882
                                                                                            E.coli gi1788195
                                                                            **             E.coli gi2367378
                                                                      *                     E.coli gi1788194
                                                                                                  E.coli gi1787690
                                                                                             V. choleraeV C 092  A1
                                                                                                V. choleraeVC 98   00
                                                                                                E.coli gi1789453
                                                                                                      H.pylori gi2313186
                                                                                                     H.pylori99 gi4154603
                                                                                              **              C.jejuni Cj0144
                                                                                                              C.jejuni Cj1564
                                                                                                         ** C.jejuni Cj0262c
                                                                                **                   C.jejuni Cj1506c
                                                                                                       H.pylori gi2313163
                                                                       *                                H.pylori99 gi4154575
                                                                                                 ** H.pylori gi2313179
                                                                            **
                                                                                               ** H.pylori99 gi4154599
                                                                                                            C.jejuni Cj0019c
                                                                                                                     C.jejuni Cj0951c
                                                                                                               C.jejuni Cj0246c
                                                                                                             B.subtilis gi2633374
                                                                                                                T.maritima TM0014
                                                                                                                      V. choleraeV C 03
                                                                                                                                      14
                                                                                                                   V. chole rae C 08 8
                                                                                                                                V A1
                                                                                                                     T.pallidum gi3322777
                                                                      **                                                          T.pallidum gi3322939
                                                                   **                                                 T.pallidum gi3322938
                                                                                                                        B.burgdorferi gi2688522
                                                                                                                           T.pallidum gi3322296
                                                                                                                     B.burgdorferi gi2688521
                                                    *                                              T.maritima TM0429
                                                                                               ** T.maritima TM0918
                                                                                              ** T.maritima TM0023
                                                       *                                     T.maritima TM1428
                                                                                                 T.maritima TM1143
                                                                                             T.maritima TM1146
                                                                                                  P.abyssi PAB1308
                                                                                        **       P.horikoshii gi3256846
                                                                    **                          P.abyssi PAB1336
                                                                                                P.horikoshii gi3256896
                                                                                          ** P.abyssi PAB2066
                                                      **
                                            **                                       **        P.horikoshii gi3258290
                                                 *                                              P.abyssi PAB1026
                                                                                   **             P.horikoshii gi3256884
                                                                                                      **
                                                                                                                    D.radiodurans DRA00354
                                                                                                                   D.radiodurans DRA0353
                                                                                                                  D.radiodurans DRA0352
                                                                                                                                                         Based on Heidelberg et al.
                                                                **

                                                                                                                                                         2000 Nature 406:477-483.
                                       **                                                                   V. choleraeVC 94 13
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                                                                                           **             P.horikoshii gi3258414                                                are needed to see this picture.




are needed to see this picture.                                                                   B.burgdorferi gi2688621
                                                                                                                 M.tuberculosis gi1666149
                                                                                                                    V. choleraeV C 22
                                                                                                                                    06
Phylogenomics III

                                  Uncharacterized genes




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Non homology functional prediction

                        • Many genes have homologs in other species
                          but no homologs have ever been studied
                          experimentally
                        • Non-homology methods can make
                          functional predictions for these




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Phylogenetic profiling basis

                        • Microbial genes are lost rapidly when not
                          maintained by selection
                        • Genes can be acquired by lateral transfer
                        • Frequently gain and loss occurs for entire
                          pathways/processes
                        • Thus might be able to use correlated
                          presence/absence information to identify
                          genes with similar functions
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Non-Homology Predictions:
                                    Phylogenetic Profiling

                           • Step 1: Search all genes in
                             organisms of interest against all
                             other genomes

                           • Ask: Yes or No, is each gene
                             found in each other species

                           • Cluster genes by distribution
                             patterns (profiles)
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Carboxydothermus hydrogenoformans


   • Isolated from a Russian hotspring
   • Thermophile (grows at 80°C)
   • Anaerobic
   • Grows very efficiently on CO
     (Carbon Monoxide)
   • Produces hydrogen gas
   • Low GC Gram positive
     (Firmicute)
   • Genome Determined (Wu et al.
     2005 PLoS Genetics 1: e65. )
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Homologs of Sporulation Genes




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                                                                                   Wu et al. 2005
                                                                                   PLoS
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                                                                                   Genetics 1: e65.
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Carboxydothermus sporulates




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PG Profiling Works Better Using
                                             Orthology




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Phylogenomics IV

                                   Acquiring functions




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Acquiring functions

                        • Sometimes, it is easier to steal, borrow, or
                          coopt functions rather than evolve them
                          anew
                        • Two main pathways for this
                                  – Lateral gene transfer
                                  – Symbioses




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Glassy Winged Sharpshooter

                                                   • Obligate xylem feeder
                                                   • Can transmit Pierce’s
                                                     Disease agent
                                                   • Potential bioterror agent
                                                   • Needs to get amino-
                                                     acids and other nutrients
                                                     from symbionts like
                                                     aphids




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Xylem and Phloem




                                                     From
                                                     Lodish et
                                                     al. 2000


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Sharpshooter Shotgun Sequencing



                                                                shotgun




                                     Collaboration with Nancy
                                                                   Wu et al. 2006 PLoS Biology 4: e188.
                                     Moran’s lab
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1



                                            600,000
                                                                          100,000




                                  500,000
                                                                                                            200,000




                                                  400,000
                                                                300,000




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Baumannia is a Vitamin and
                                  Cofactor Producing Machine




                                                               Wu et al.
                                                               2006
                                                               PLoS
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No Amino-Acid Synthesis




                                                            Wu et al.
                                                            2006
                                                            PLoS
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???????




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Commonly Used Binning Methods
                                       Did not Work Well

                        • Assembly
                                  – Only Baumannia generated good contigs
                        • Depth of coverage
                                  – Everything else 0-1X coverage
                        • Nucleotide composition
                                  – No detectible peaks in any vector we looked at



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Host Sequence?




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CFB Phyla




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                                  Wu et al. 2006 PLoS Biology 4: e188.
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Binning by Phylogeny

                        • Four main “phylotypes”
                                  –   Gamma proteobacteria (Baumannia)
                                  –   Arthropoda (sharpshooter)
                                  –   Bacteroidetes (Sulcia)
                                  –   Alpha-proteobacteria (Wolbachia)




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Binning by Phylogeny

                        • Four main “phylotypes”
                                  –   Gamma proteobacteria (Baumannia)
                                  –   Arthropoda (sharpshooter)
                                  –   Bacteroidetes (Sulcia) - only a.a. genes here
                                  –   Alpha-proteobacteria (Wolbachia)




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Essential Amino Acid Synthesis




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                                                            Biology 4: e188.
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Co-Symbiosis?




                                                  Wu et al.
                                                  2006
                                                  PLoS
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Model for Metagenomics

              A                                            T
              B                                            U
              C                                            V
              D                                            W
              E                                            X
              F                                            Y
              G                                            Z
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Functional Diversity of Proteorhodopsins?




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Phylogenomics V

                                  Knowing What We Do Not Know




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rRNA Tree of Life




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The Tree is not Happy




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As of 2002                         Proteobacteria
                                    TM6
                                    OS-K
                                                           • At least 40
                                   Acidobacteria
                                   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
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                                                             Hugenholtz, 2002
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As of 2002                        Proteobacteria
                                   TM6
                                   OS-K
                                                          • At least 40
                                  Acidobacteria
                                  Termite Group
                                   OP8
                                                            phyla of
                                  Nitrospira
                                  Bacteroides
                                                            bacteria
                                  Chlorobi
                                  Fibrobacteres
                                  Marine GroupA           • Genome
                                   WS3
                                  Gemmimonas
                                  Firmicutes
                                                            sequences are
                                  Fusobacteria
                                  Actinobacteria
                                                            mostly from
                                   OP9
                                  Cyanobacteria             three phyla
                                  Synergistes
                                  Deferribacteres
                                  Chrysiogenetes
                                  NKB19
                                  Verrucomicrobia
                                  Chlamydia
                                   OP3
                                  Planctomycetes
                                  Spriochaetes
                                  Coprothmermobacter
                                  OP10
                                  Thermomicrobia
                                  Chloroflexi
                                   TM7
                                  Deinococcus-Thermus
                                  Dictyoglomus
                                  Aquificae
                                  Thermudesulfobacteria
                                  Thermotogae
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                                  OP11                      Hugenholtz, 2002
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are needed to see this picture.
As of 2002                        Proteobacteria
                                   TM6
                                   OS-K
                                                          • At least 40
                                  Acidobacteria
                                  Termite Group
                                   OP8
                                                            phyla of
                                  Nitrospira
                                  Bacteroides
                                                            bacteria
                                  Chlorobi
                                  Fibrobacteres
                                  Marine GroupA           • Genome
                                   WS3
                                  Gemmimonas
                                  Firmicutes
                                                            sequences are
                                  Fusobacteria
                                  Actinobacteria
                                                            mostly from
                                   OP9
                                  Cyanobacteria             three phyla
                                  Synergistes
                                  Deferribacteres
                                  Chrysiogenetes          • Some other
                                  NKB19
                                  Verrucomicrobia
                                  Chlamydia                 phyla are
                                   OP3
                                  Planctomycetes
                                  Spriochaetes
                                                            only sparsely
                                  Coprothmermobacter
                                  OP10                      sampled
                                  Thermomicrobia
                                  Chloroflexi
                                   TM7
                                  Deinococcus-Thermus
                                  Dictyoglomus
                                  Aquificae
                                  Thermudesulfobacteria
                                  Thermotogae
       QuickTimeª and a
                                   OP1                      Based on
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                                  OP11                      Hugenholtz, 2002
                                                                                         QuickTimeª and a
                                                                               TIFF (Uncompressed) decompressor
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are needed to see this picture.
As of 2002                        Proteobacteria
                                   TM6
                                   OS-K
                                                          • At least 40
                                  Acidobacteria
                                  Termite Group
                                   OP8
                                                            phyla of
                                  Nitrospira
                                  Bacteroides
                                                            bacteria
                                  Chlorobi
                                  Fibrobacteres
                                  Marine GroupA           • Genome
                                   WS3
                                  Gemmimonas
                                  Firmicutes
                                                            sequences are
                                  Fusobacteria
                                  Actinobacteria
                                                            mostly from
                                   OP9
                                  Cyanobacteria             three phyla
                                  Synergistes
                                  Deferribacteres
                                  Chrysiogenetes          • Some other
                                  NKB19
                                  Verrucomicrobia
                                  Chlamydia                 phyla are
                                   OP3
                                  Planctomycetes
                                  Spriochaetes
                                                            only sparsely
                                  Coprothmermobacter
                                  OP10                      sampled
                                  Thermomicrobia
                                  Chloroflexi
                                   TM7                    • Same trend in
                                  Deinococcus-Thermus
                                  Dictyoglomus
                                  Aquificae                 Archaea,
                                  Thermudesulfobacteria

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                                   OP1
                                                            Eukaryotes
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                                  OP11                      Hugenholtz, 2002
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Proteobacteria
• Eisen-Ward                        TM6                    • At least 40
                                    OS-K
  NSF Tree of                      Acidobacteria
                                   Termite Group             phyla of
                                    OP8
  Life Project                     Nitrospira
                                   Bacteroides
                                                             bacteria
                                   Chlorobi
• A genome                         Fibrobacteres
                                   Marine GroupA           • Genome
                                    WS3
  from each of                     Gemmimonas                sequences are
                                   Firmicutes
  eight phyla                      Fusobacteria              mostly from
                                   Actinobacteria
                                    OP9
                                   Cyanobacteria             three phyla
                                   Synergistes
                                   Deferribacteres
                                   Chrysiogenetes          • Some other
                                   NKB19
                                   Verrucomicrobia
                                   Chlamydia                 phyla are only
                                    OP3
                                   Planctomycetes
                                   Spriochaetes
                                                             sparsely
                                   Coprothmermobacter
                                   OP10                      sampled
                                   Thermomicrobia
Based on                           Chloroflexi
                                    TM7                    • Solution I:
Hugenholtz,                        Deinococcus-Thermus

2002
                                   Dictyoglomus
                                   Aquificae                 sequence more
                                   Thermudesulfobacteria

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                                    OP1
                                                             phyla
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Proteobacteria
• JGI -                                                               TM6                    • At least 40
                                                                      OS-K
  Genomic                                                            Acidobacteria
                                                                     Termite Group             phyla of
                                                                      OP8
  Encyclopedia                                                       Nitrospira
                                                                     Bacteroides
                                                                                               bacteria
  of Bacteria                                                        Chlorobi
                                                                     Fibrobacteres
                                                                                             • Genome
                                                                     Marine GroupA
  and Archaea                                                         WS3
                                                                     Gemmimonas                sequences are
                                                                     Firmicutes
                                                                     Fusobacteria
                                                                     Actinobacteria
                                                                                               mostly from
                                                                      OP9
                                                                     Cyanobacteria             three phyla
                                                                     Synergistes
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                                                                     Deferribacteres
                                                                     Chrysiogenetes          • Some other
                                                                     NKB19
                                                                     Verrucomicrobia
                                                                     Chlamydia                 phyla are only
                                                                      OP3
                                                                     Planctomycetes
                                                                     Spriochaetes
                                                                                               sparsely
                                                                     Coprothmermobacter
                                                                     OP10                      sampled
                                                                     Thermomicrobia
Based on                                                             Chloroflexi
                                                                      TM7                    • Solution II: Fill
Hugenholtz,                                                          Deinococcus-Thermus

2002
                                                                     Dictyoglomus
                                                                     Aquificae                 in Phyla
                                                                     Thermudesulfobacteria
                                                                     Thermotogae
                                                                      OP1
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                                  are needed to see this picture.




       QuickTimeª and a
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are needed to see this picture.
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics
Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics

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Genomic Evolvability and the Origin of Novelty - talk for ASMGM 2008 by @phylogenomics

  • 1. Genomic Evolvability and the Origin of Novelty Jonathan A. Eisen U. C. Davis Genome Center ASM General Meeting Boston, MA June 4, 2008 QuickTimeª and a QuickTimeª and a TIFF (Uncompressed) decompressor TIFF (LZW) decompressor are needed to see this picture. are needed to see this picture.
  • 2. Secret Message Coming … Jonathan A. Eisen U. C. Davis Genome Center ASM General Meeting Boston, MA June 4, 2008 QuickTimeª and a QuickTimeª and a TIFF (Uncompressed) decompressor TIFF (LZW) decompressor are needed to see this picture. are needed to see this picture.
  • 3. Genomic Evolvability and the Origin of Novelty Jonathan A. Eisen QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. U. C. Davis Genome Center ASM General Meeting Boston, MA June 4, 2008 QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 4. 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 QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. processes, infer convergence QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture.
  • 5. “Nothing in biology makes sense except in the light of evolution.” T. H. Dobzhansky (1973) QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 6. Origin of Novelty • How does novelty originate? • What are the constraints on evolvability? • What leads to variation within the genome and within and between species in evolvability • This information helps interpret the past, understand the present and (maybe) predict the future QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 7. Phylogenomic Analysis • Evolutionary reconstructions greatly improve genome analyses • Genome analysis greatly improves evolutionary reconstructions • There is a feedback loop such that these should be integrated QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 8. Phylogenomic Tales • Predicting functions with evolutionary trees • Recently evolved new functions • Uncharacterized genes • Stealing functions • Knowing what we do not know QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 9. Phylogenomics I: Predicting Functions with Evolutionary Trees QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 10. SNF2 Family of Proteins (1995) • SNF2 family defined by presence of conserved DNA- dependent ATPase domain Bork and Koonin 1993 • 100s of proteins • Diversity of functions: – transcriptional activation (SNF2) – transcriptional repression (MOT1) – Recombination (RAD54) QuickTimeª and a TIFF (LZW) decompressor – transcription-coupled repair (CSB) are needed to see this picture. – post-replication repair (RAD5) – chromosome segregation (lodestar) – Many with unknown functions • Some species have 15+ representatives QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 11. HEPA._E.c NPHCG_42 LODE._D.m MOT1_S.c SNF2_S.c STH1_S.c BRG1_M.m BRG1_H.s BRM_H.s BRM_D.m SNF2L_H.s F37A4_C.e DNRPPX_S.p NUCP_M.m NUCP_H.s RAD26_S.c ERCC6_H.s SYGP4_S.c CHD1_M.m ETL1_M.m ISWI_D.m YB95_S.c RAD16_S.c HIP116A_H.s RAD8_S.p RAD5_S.c RAD54_S.c YB53_S.c YA19_S.c LODE RAD16 RAD54 CSB ETL1 CHD1 SNF2L SNF2 Evolution of the SNF2 Family of Proteins QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 12. SNF2 Tree and F(x) Prediction • Function conserved within but not between subfamilies/orthology groups • Therefore, assignment of genes to subfamilies can be used to predict functions of unknowns • Grouping into subfamilies helps identify motifs conserved within groups • Phylogeny recovers subfamilies better than similarity searches QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 13. From Eisen et al. 1997 Nature Medicine 3: 1076-10 QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 14. Blast Search of H. pylori “MutS” Score E Sequences producing significant alignments: (bits) Value sp|P73625|MUTS_SYNY3 DNA MISMATCH REPAIR PROTEIN 117 3e25 - sp|P74926|MUTS_THEMA DNA MISMATCH REPAIR PROTEIN 69 1e10 - sp|P44834|MUTS_HAEIN DNA MISMATCH REPAIR PROTEIN 64 3e09 - sp|P10339|MUTS_SALTY DNA MISMATCH REPAIR PROTEIN 62 2e08 - sp|O66652|MUTS_AQUAE DNA MISMATCH REPAIR PROTEIN 57 4e07 - sp|P23909|MUTS_ECOLI DNA MISMATCH REPAIR PROTEIN 57 4e07 - • Blast search pulls up Syn. sp MutS#2 with much higher p value than other MutS homologs • Based on this TIGR predicted this species had mismatch repair • Assumes functional constancy QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. Based on Eisen et al. 1997 Nature Medicine 3: 1076-1078. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture.
  • 15. Phylogenetic Tree of MutS Family Aquae Strpy Bacsu Synsp Deira Helpy Yeast Human Borbu Metth Celeg mSaco Yeast Human Yeast Mouse Arath Celeg Human Arath Human Mouse Spombe Fly Yeast Xenla Rat Mouse Yeast Human Spombe Yeast Neucr Arath Aquae Trepa Chltr DeiraTheaq Thema BacsuBorbu Based on Eisen, SynspStrpy 1998 Nucl Acids QuickTimeª and a Ecoli TIFF (LZW) decompressor Res 26: 4291-4300. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture. Neigo
  • 16. MutS Subfamilies M S H 5A q u a e M utS 2 S trB y c S uns p p a s y D e ir a H e lp y Ye a s t Huma n B orbu M e tth C e le g mS a c o MS H6 Ye a s t Huma n Mous e A ra th Ye a s t MS H4 C e le g Huma n A ra th Huma n MS H3 Mous e F ly S pombe Ye a s t X e n la Rat Mous e Ye a s t Huma n MS H1 S pombe Ye a s t MS H2 Neuc r A ra th Aquae Tre p a C h lt r D e ir a e a q Th B a c s u rbu Bo Th e m a S y n sSpt r p y E c o li N e ig o Based on Eisen, 1998 Nucl Acids QuickTimeª and a M utS 1 TIFF (LZW) decompressor Res 26: 4291-4300. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 17. Overlaying Functions onto Tree M utS 2 Aquae MS H5 S t rB y c S yn s p pa su D e ir a H e lp y Ye a s t Huma n B orbu M e tth C e le g MS H6 mS a c o Ye a s t Huma n Mous e A ra th MS H4 Ye a s t C e le g Huma n A ra th Huma n MS H3 Mous e S pombe F ly Ye a s t X e n la Rat Mous e Ye a s t Huma n M S H 1 pombe S Ye a s t MS H2 Neuc r A ra th Aquae Tre p a C h lt r D e ir a e a q Th B a c s u rbu Bo Th e m a S y n sSpt r p y Based on Eisen, E c o li N e ig o 1998 Nucl Acids M utS 1 QuickTimeª and a TIFF (LZW) decompressor Res 26: 4291-4300. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 18. Functional Prediction Using Tree M S H 5 - M e io t ic C r o s s in g O v e u t S 2 - U n k n o w n F u n c t io n s M r Aquae S t rB y c S yn s p pa su D e ir a H e lp y Ye a s t Huma n B orbu M e tth C e le g M S H 6 - N u c le a r mS a c o R e p a ir Ye a s t O f M is m a t c h e s Huma n M S H 4 - M e io t ic C r o s s in g Mous e Y e a sO v e r t A ra th C e le g Huma n A ra th M S H 3 - N u c le a r Huma n Mous e R e p a ir O f L o o p s o m b e S p F ly Ye a s t X e n la Rat M oM s eH 2 - E u k a r y o t i c N u c l e a r u S Ye a s t H u m ai n m a t c h a n d L o o p R e p a i r M s MS H1 S pombe Ye a s t M it o c h o n d r ia l Neuc r A ra th R e p a ir Aquae Tre p a C h lt r D e ir a e a q Th B a c s u rbu Bo Th e m a S y n sSpt r p y E c o li Based on Eisen, N e ig o QuickTimeª and a 1998 Nucl Acids TIFF (LZW) decompressor M u t S 1 - B a c t e r ia l M is m a t c h a n d L o o p R e p a ir Res 26: 4291-4300. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 19. QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 20. Evolutionary Functional Prediction SpeciesMETHOD EVOLUTION Duplication?SEQUENCES 5 IDENTIFY HOMOLOGS 4B EXAMPLE A B 3A CALCULATE GENE KNOWN 2CHOOSE GENE(S) OF FUNCTION 1ALIGNINFER LIKELY INTEREST 1ACTUAL 3EXAMPLE Ambiguous Duplication 1A 3B 2B 1B 3A 2A 6 2 OVERLAY TREE (ASSUMED TO BE OFONTO TREE OF GENE(S) UNKNOWN) FUNCTIONS INTEREST Based on Eisen, 1998 Genome QuickTimeª and a TIFF (LZW) decompressor Res 8: 163-167. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 21. Phylogenetic Prediction of Function • Many powerful and automated similarity based methods for assigning genes to protein families – COGs – PFAM HMM searches • Some limitations of similarity based methods can be overcome by phylogenetic approaches • Automated methods now available – Sean Eddy – Steven Brenner – Kimmen Sjölander • But … QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 22. Phylogenomics II Recent Evolution QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 23. Recent Functional Changes • Phylogenomic functional prediction may not work well for very newly evolved functions • Can we use understanding of origin of novelty to better understand these cases? • Screen genomes for genes that have changed recently – Pseudogenes and gene loss – Contingency Loci – Acquisition (e.g., LGT) – Unusual dS/dN ratios – Rapid evolutionary rates – Duplication and divergence QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 24. Lineage Specific Gene Family Expansions • Lineage specific expansions frequently associated with adaptive evolution • Can screen genomes for such expansions by looking for genes more closely related to other genes in the genome than to genes from other species QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 25. Expansion of MCP Family in V. cholerae NJ V. choleraeVC 12 05 V. chole raeV C 03 4 A1 V. choleraeVC 97 4A0 ** V. choleraeVC 06 8A0 * V. chole rae C 25 V 08 V. choleraeV C 82 02 V. chole rae C 90 6 V A0 V. chole raeV C 979 A0 V. chole rae C 05 6 V A1 V. choleraeV C 43 16 V. chole rae C 61 V 21 ** V. choleraeVC 92 3 A0 ** V. choleraeV C 14 05 V. choleraeVC 68 18 V. chole raeV C 77 3 A0 V. choleraeV C 13 13 V. chole raeV C 5918 V. choleraeV C 13 14 V. chole rae C 26 8 V A0 ** V. chole raeV C 65 8 A0 V. choleraeV C 05 14 * V. cholerae 12 98 VC V. choleraeV C 4812 V. chole raeV C 86 4 A0 V. choleraeVC 17 6 A0 ** V chole raeV C 22 0 . A0 V. choleraeVC 89 12 ** V. choleraeVC 06 9A1 V. choleraeV C 39 24 V. choleraeVC 67 19 V. chole rae C 031 V A0 V. choleraeV C 98 18 V. chole rae C 663 V A0 V. choleraeVC 988 A0 V. chole raeV C 16 02 * V. chole raeV C 49 04 V. chole rae C 00 8 V A0 V. choleraeVC 06 14 V. chole raeV C 35 15 V. choleraeV C 40 08 B.subtilis gi2633766 Synechocystis sp. gi1001299 * Synechocystis sp. gi1001300 * Synechocystis sp. gi1652276 * Synechocystis sp. gi1652103 H.pylori gi2313716 ** H.pylori9Cj1190c C.jejuni 9 gi4155097 ** C.jejuni Cj1110c A.fulgidus gi2649560 A.fulgidus gi2649548 ** B.subtilis gi2634254 B.subtilis gi2632630 B.subtilis gi2635607 B.subtilis gi2635608 ** B.subtilis gi2635609 ** ** B.subtilis gi2635610 B.subtilis gi2635882 E.coli gi1788195 ** E.coli gi2367378 * E.coli gi1788194 E.coli gi1787690 V. choleraeV C 092 A1 V. choleraeVC 98 00 E.coli gi1789453 H.pylori gi2313186 H.pylori99 gi4154603 ** C.jejuni Cj0144 C.jejuni Cj1564 ** C.jejuni Cj0262c ** C.jejuni Cj1506c H.pylori gi2313163 * H.pylori99 gi4154575 ** H.pylori gi2313179 ** ** H.pylori99 gi4154599 C.jejuni Cj0019c C.jejuni Cj0951c C.jejuni Cj0246c B.subtilis gi2633374 T.maritima TM0014 V. choleraeV C 03 14 V. chole rae C 08 8 V A1 T.pallidum gi3322777 ** T.pallidum gi3322939 ** T.pallidum gi3322938 B.burgdorferi gi2688522 T.pallidum gi3322296 B.burgdorferi gi2688521 * T.maritima TM0429 ** T.maritima TM0918 ** T.maritima TM0023 * T.maritima TM1428 T.maritima TM1143 T.maritima TM1146 P.abyssi PAB1308 ** P.horikoshii gi3256846 ** P.abyssi PAB1336 P.horikoshii gi3256896 ** P.abyssi PAB2066 ** ** ** P.horikoshii gi3258290 * P.abyssi PAB1026 ** P.horikoshii gi3256884 ** D.radiodurans DRA00354 D.radiodurans DRA0353 D.radiodurans DRA0352 Based on Heidelberg et al. ** 2000 Nature 406:477-483. ** V. choleraeVC 94 13 QuickTimeª and a P.abyssi PAB1189 TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor ** P.horikoshii gi3258414 are needed to see this picture. are needed to see this picture. B.burgdorferi gi2688621 M.tuberculosis gi1666149 V. choleraeV C 22 06
  • 26. Phylogenomics III Uncharacterized genes QuickTimeª and a QuickTimeª and a TIFF (Uncompressed) decompressor TIFF (LZW) decompressor are needed to see this picture. are needed to see this picture.
  • 27. Non homology functional prediction • Many genes have homologs in other species but no homologs have ever been studied experimentally • Non-homology methods can make functional predictions for these QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 28. Phylogenetic profiling basis • Microbial genes are lost rapidly when not maintained by selection • Genes can be acquired by lateral transfer • Frequently gain and loss occurs for entire pathways/processes • Thus might be able to use correlated presence/absence information to identify genes with similar functions QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 29. Non-Homology Predictions: Phylogenetic Profiling • Step 1: Search all genes in organisms of interest against all other genomes • Ask: Yes or No, is each gene found in each other species • Cluster genes by distribution patterns (profiles) QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 30. Carboxydothermus hydrogenoformans • Isolated from a Russian hotspring • Thermophile (grows at 80°C) • Anaerobic • Grows very efficiently on CO (Carbon Monoxide) • Produces hydrogen gas • Low GC Gram positive (Firmicute) • Genome Determined (Wu et al. 2005 PLoS Genetics 1: e65. ) QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 31. Homologs of Sporulation Genes QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. Wu et al. 2005 PLoS QuickTimeª and a TIFF (LZW) decompressor Genetics 1: e65. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 32. Carboxydothermus sporulates QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. Wu et al. 2005 PLoS Genetics 1: e65. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture.
  • 33. QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. Wu et al. 2005 PLoS Genetics 1: e65. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture.
  • 34. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 35. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 36. PG Profiling Works Better Using Orthology QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 37. Phylogenomics IV Acquiring functions QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 38. Acquiring functions • Sometimes, it is easier to steal, borrow, or coopt functions rather than evolve them anew • Two main pathways for this – Lateral gene transfer – Symbioses QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 39. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 40. Glassy Winged Sharpshooter • Obligate xylem feeder • Can transmit Pierce’s Disease agent • Potential bioterror agent • Needs to get amino- acids and other nutrients from symbionts like aphids QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 41. Xylem and Phloem From Lodish et al. 2000 QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 42. Sharpshooter Shotgun Sequencing shotgun Collaboration with Nancy Wu et al. 2006 PLoS Biology 4: e188. Moran’s lab QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 43. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 44. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 45. 1 600,000 100,000 500,000 200,000 400,000 300,000 QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 46. Baumannia is a Vitamin and Cofactor Producing Machine Wu et al. 2006 PLoS QuickTimeª and a Biology 4: e TIFF (LZW) decompressor . QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 47. No Amino-Acid Synthesis Wu et al. 2006 PLoS QuickTimeª and a Biology 4: e TIFF (LZW) decompressor . QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 48. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 49. ??????? QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 50. Commonly Used Binning Methods Did not Work Well • Assembly – Only Baumannia generated good contigs • Depth of coverage – Everything else 0-1X coverage • Nucleotide composition – No detectible peaks in any vector we looked at QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 51. Host Sequence? QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 52. CFB Phyla QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 53. QuickTimeª and a TIFF (LZW) decompressor Wu et al. 2006 PLoS Biology 4: e188. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 54. Binning by Phylogeny • Four main “phylotypes” – Gamma proteobacteria (Baumannia) – Arthropoda (sharpshooter) – Bacteroidetes (Sulcia) – Alpha-proteobacteria (Wolbachia) QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 55. Binning by Phylogeny • Four main “phylotypes” – Gamma proteobacteria (Baumannia) – Arthropoda (sharpshooter) – Bacteroidetes (Sulcia) - only a.a. genes here – Alpha-proteobacteria (Wolbachia) QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 56. Essential Amino Acid Synthesis QuickTimeª and a Wu et al. 2006 PLoS TIFF (LZW) decompressor Biology 4: e188. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 57. Co-Symbiosis? Wu et al. 2006 PLoS QuickTimeª and a Biology 4: e TIFF (LZW) decompressor . QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 58. Model for Metagenomics A T B U C V D W E X F Y G Z QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 59. Functional Diversity of Proteorhodopsins? QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. Venter et al., 2004 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture.
  • 60. Phylogenomics V Knowing What We Do Not Know QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 61. rRNA Tree of Life QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 62. The Tree is not Happy QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 63. As of 2002 Proteobacteria TM6 OS-K • At least 40 Acidobacteria 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 QuickTimeª and a OP11 TIFF (LZW) decompressor Hugenholtz, 2002 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 64. As of 2002 Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae QuickTimeª and a OP1 Based on TIFF (LZW) decompressor OP11 Hugenholtz, 2002 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 65. As of 2002 Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes • Some other NKB19 Verrucomicrobia Chlamydia phyla are OP3 Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 sampled Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae QuickTimeª and a OP1 Based on TIFF (LZW) decompressor OP11 Hugenholtz, 2002 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 66. As of 2002 Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes • Some other NKB19 Verrucomicrobia Chlamydia phyla are OP3 Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 sampled Thermomicrobia Chloroflexi TM7 • Same trend in Deinococcus-Thermus Dictyoglomus Aquificae Archaea, Thermudesulfobacteria QuickTimeª and a Thermotogae OP1 Eukaryotes Based on TIFF (LZW) decompressor OP11 Hugenholtz, 2002 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.
  • 67. Proteobacteria • Eisen-Ward TM6 • At least 40 OS-K NSF Tree of Acidobacteria Termite Group phyla of OP8 Life Project Nitrospira Bacteroides bacteria Chlorobi • A genome Fibrobacteres Marine GroupA • Genome WS3 from each of Gemmimonas sequences are Firmicutes eight phyla Fusobacteria mostly from Actinobacteria OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes • Some other NKB19 Verrucomicrobia Chlamydia phyla are only OP3 Planctomycetes Spriochaetes sparsely Coprothmermobacter OP10 sampled Thermomicrobia Based on Chloroflexi TM7 • Solution I: Hugenholtz, Deinococcus-Thermus 2002 Dictyoglomus Aquificae sequence more Thermudesulfobacteria QuickTimeª and a Thermotogae OP1 phyla TIFF (LZW) decompressor are needed to see this picture. OP11 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture.
  • 68. Proteobacteria • JGI - TM6 • At least 40 OS-K Genomic Acidobacteria Termite Group phyla of OP8 Encyclopedia Nitrospira Bacteroides bacteria of Bacteria Chlorobi Fibrobacteres • Genome Marine GroupA and Archaea WS3 Gemmimonas sequences are Firmicutes Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria three phyla Synergistes QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. Deferribacteres Chrysiogenetes • Some other NKB19 Verrucomicrobia Chlamydia phyla are only OP3 Planctomycetes Spriochaetes sparsely Coprothmermobacter OP10 sampled Thermomicrobia Based on Chloroflexi TM7 • Solution II: Fill Hugenholtz, Deinococcus-Thermus 2002 Dictyoglomus Aquificae in Phyla Thermudesulfobacteria Thermotogae OP1 QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. OP11 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture.
  • 69. QuickTimeª and a TIFF (LZW) decompressor are needed to see this picture. QuickTimeª and a TIFF (LZW) decompressor QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.

Hinweis der Redaktion

  1. Research in my lab focuses on the mechanisms through which novelty (e.g., new functions and new processes) originates in microorganisms. In particular we make use of phylogenomic analysis (combining evolutionary reconstructions with genome sequence analyses) to study these mechanisms. The mechanisms in which I am include those that allow an existing gene to change its function (e.g., gene duplication and divergence; domain swapping) and that allow organisms to acquire functions from other species (e.g., lateral transfer and symbioses). In addition, my work examines how differences in DNA repair, replication, and recombination processes influence the ability of organisms to generate novelty. In my talk I will discuss our recent work in this area, first focusing on model cultured organisms whose genomes we are sequencing or have recently sequenced (e.g., Tetrahymena thermophila, Haloferax volcanii). Then I will discuss how phylogenomic approaches can be used to study the origin of novelty in uncultured species (e.g., symbionts and microbial communities). Finally, I will discuss our plans for future research on the origin of novelty.
  2. Research in my lab focuses on the mechanisms through which novelty (e.g., new functions and new processes) originates in microorganisms. In particular we make use of phylogenomic analysis (combining evolutionary reconstructions with genome sequence analyses) to study these mechanisms. The mechanisms in which I am include those that allow an existing gene to change its function (e.g., gene duplication and divergence; domain swapping) and that allow organisms to acquire functions from other species (e.g., lateral transfer and symbioses). In addition, my work examines how differences in DNA repair, replication, and recombination processes influence the ability of organisms to generate novelty. In my talk I will discuss our recent work in this area, first focusing on model cultured organisms whose genomes we are sequencing or have recently sequenced (e.g., Tetrahymena thermophila, Haloferax volcanii). Then I will discuss how phylogenomic approaches can be used to study the origin of novelty in uncultured species (e.g., symbionts and microbial communities). Finally, I will discuss our plans for future research on the origin of novelty.
  3. Research in my lab focuses on the mechanisms through which novelty (e.g., new functions and new processes) originates in microorganisms. In particular we make use of phylogenomic analysis (combining evolutionary reconstructions with genome sequence analyses) to study these mechanisms. The mechanisms in which I am include those that allow an existing gene to change its function (e.g., gene duplication and divergence; domain swapping) and that allow organisms to acquire functions from other species (e.g., lateral transfer and symbioses). In addition, my work examines how differences in DNA repair, replication, and recombination processes influence the ability of organisms to generate novelty. In my talk I will discuss our recent work in this area, first focusing on model cultured organisms whose genomes we are sequencing or have recently sequenced (e.g., Tetrahymena thermophila, Haloferax volcanii). Then I will discuss how phylogenomic approaches can be used to study the origin of novelty in uncultured species (e.g., symbionts and microbial communities). Finally, I will discuss our plans for future research on the origin of novelty.
  4. My major research interests