A Phylogeny-Driven Genomic
       Encyclopedia of Bacteria and Archaea



                         Jonathan A. Eisen

    ...
Eisen Lab - Phylogenomics of Novelty


      Origin of New                                               Genome
      Func...
Bacterial evolve




Sunday, April 25, 2010
TIGR            Fleischmann et al.
                         1995
Sunday, April 25, 2010
Microbial genomes




                             From http://genomesonline.org
Sunday, April 25, 2010
Sunday, April 25, 2010
rRNA Tree of Life
                         Bacteria




                                                         Archaea

...
The Tree is not Happy
                         Bacteria




                                                         Archa...
Proteobacteria

2002                     TM6
                         OS-K
                         Acidobacteria
        ...
Proteobacteria

2002                     TM6
                         OS-K
                         Acidobacteria
        ...
Proteobacteria

2002                     TM6
                         OS-K
                         Acidobacteria
        ...
Proteobacteria

2002                     TM6
                         OS-K
                         Acidobacteria
        ...
Proteobacteria

2002                     TM6
                         OS-K
                         Acidobacteria
        ...
Filling in the Genomic Phylogenetic Gaps

     • Common approach within some eukaryotic
       groups

     • Many small p...
Proteobacteria
• NSF-funded             TM6
                         OS-K
                                                ...
The Tree of Life is Still Angry
                         Bacteria




                                                    ...
Major Lineages of Actinobacteria
                                                                       2.5 Actinobacteria...
Microbial genomes 2010- ...




                                  From http://genomesonline.org
Sunday, April 25, 2010
Proteobacteria
                         TM6
                         OS-K
                                                ...
Why Increase Phylogenetic Coverage?

         • Gene discovery
         • Annotation, functional prediction
         • Met...
A Genomic Encyclopedia of Bacteria
                    and Archaea (GEBA)




Sunday, April 25, 2010
GEBA Pilot Project Overview

        • Identify major branches in rRNA tree for
          which no genomes are available
 ...
B:
                                      Ac
                                        tin
                                  ...
GEBA and Openness
 • All data being released as quickly
   as possible with no restrictions to
   IMG-GEBA; Genbank, etc
 ...
Assess Benefits of GEBA

         • All genomes have some value

         • But what, if any, is the benefit of tree-
     ...
GEBA Lesson 1

                         rRNA Tree is Useful for Identifying
                          Phylogenetically Nov...
rRNA Tree of Life
                         Bacteria




                                                         Archaea

...
Sunday, April 25, 2010
Network of Life
                         Bacteria




                                                         Archaea



...
Wh




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


Sunday, April 25, 2010
PD of rRNA, Genome Trees Similar




   From Wu et al. 2009
Sunday, April 25, 2010
Proteobacteria




Sunday, April 25, 2010
GEBA Lesson 2

                         Phylogenetically-guided genome
                           selection improves genom...
Predicting Function

         • Key step in genome projects
         • More accurate predictions help guide
           exp...
Most/All Functional Prediction Improves
            w/ Better Phylogenetic Sampling
           • Better definition of prote...
From Wu et al. 2009.
Sunday, April 25, 2010
GEBA Lesson 3

                         Improves analysis of genome data
                            from uncultured organ...
Metagenomics


                                 shotgun



                                           clone




Sunday, Ap...
Sunday, April 25, 2010
rRNA phylotyping from metagenomics




                           Venter et al., 2004
Sunday, April 25, 2010
Shotgun Sequencing Allows Use of
                  Alternative Anchors (e.g., RecA)




                                  ...
Weighted % of Clones




                                                                                                 ...
Weighted % of Clones




                                                                                                 ...
Binning challenge

      A                                      T
      B                                      U
      C  ...
Binning challenge

      A                                                           T
      B                            ...
Binning challenge

      A                                                         T
      B                              ...
Binning challenge

      A                                                         T
      B                              ...
Al
                                                                              ph
                                      ...
Phylogenetic Binning Using AMPHORA
                                                                             dnaG
     ...
GEBA Phylogenomic Lesson 5

                         We have still only scratched the
                          surface of...
Protein Family Rarefaction Curves

         • Take data set of multiple complete genomes
         • Identify all protein f...
Sunday, April 25, 2010
Sunday, April 25, 2010
Sunday, April 25, 2010
Sunday, April 25, 2010
Sunday, April 25, 2010
Mobile
      Motility
      Element?




Sunday, April 25, 2010
Phylogenetic Distribution Novelty:
                  Bacterial Actin Related Protein
                                     ...
rRNA Tree of Life
                         Bacteria




                                                         Archaea

...
Phylogenetic Diversity:
                         Sequenced Bacteria & Archaea




From Wu et al. 2009. http://www.nature.c...
Phylogenetic Diversity with GEBA




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




                         From Wu et al. 2009.
Sunday, April 25, 2010
Phylogenetic Diversity: All




From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html...
Proteobacteria
                         TM6
                         OS-K
                                                ...
Uncultured Lineages:
                         Technical Approaches
         •    Get into culture
         •    Enrichment...
GEBA Phylogenomic Lesson 6

                         Need Experiments from Across the
                                 Tre...
As of 2002               Proteobacteria
                         TM6
                         OS-K                    • At...
As of 2002               Proteobacteria
                         TM6
                         OS-K
                       ...
As of 2002               Proteobacteria
                         TM6
                         OS-K
                       ...
Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project
Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project
Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project
Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project
Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project
Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project
Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project
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Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project

  1. 1. A Phylogeny-Driven Genomic Encyclopedia of Bacteria and Archaea Jonathan A. Eisen Talk for ASBMB April 25, 2010 Sunday, April 25, 2010
  2. 2. Eisen Lab - Phylogenomics of Novelty Origin of New Genome Functions and Dynamics Processes •Evolvability •New genes •Repair and •Changes in old genes recombination processes •Changes in pathways •Intragenomic variation Species Evolution •Phylogenetic history •Vertical vs. horizontal descent •Needed to track gain/loss of processes, infer convergence Sunday, April 25, 2010
  3. 3. Bacterial evolve Sunday, April 25, 2010
  4. 4. TIGR Fleischmann et al. 1995 Sunday, April 25, 2010
  5. 5. Microbial genomes From http://genomesonline.org Sunday, April 25, 2010
  6. 6. Sunday, April 25, 2010
  7. 7. rRNA Tree of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
  8. 8. The Tree is not Happy Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
  9. 9. Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA WS3 Gemmimonas Firmicutes Fusobacteria Actinobacteria OP9 Cyanobacteria Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
  10. 10. Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
  11. 11. Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
  12. 12. Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus • Same trend in Dictyoglomus Aquificae Thermudesulfobacteria Archaea Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
  13. 13. Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus • Same trend in Dictyoglomus Aquificae Thermudesulfobacteria Eukaryotes Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
  14. 14. Filling in the Genomic Phylogenetic Gaps • Common approach within some eukaryotic groups • Many small projects funded to fill in some bacterial or archaeal gaps • Phylogenetic gaps in bacterial and archaeal projects commonly lamented in literature Sunday, April 25, 2010
  15. 15. Proteobacteria • NSF-funded TM6 OS-K • At least 40 Tree of Life Acidobacteria Termite Group phyla of OP8 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 Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are only Planctomycetes Spriochaetes sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus • Solution I: Dictyoglomus Aquificae sequence more Eisen & Ward, PIs Thermudesulfobacteria Thermotogae OP1 phyla OP11 Sunday, April 25, 2010
  16. 16. The Tree of Life is Still Angry Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
  17. 17. Major Lineages of Actinobacteria 2.5 Actinobacteria 2.5.1 Acidimicrobidae 2.5.1 Acidimicrobidae 2.5.1.1 Unclassified 2.5.1.2 "Microthrixineae 2.5.1.1 Unclassified 2.5.1.3 Acidimicrobineae 2.5.1.3.1 Unclassified 2.5.1.2 "Microthrixineae 2.5.1.3.2 Acidimicrobiaceae 2.5.1.4 BD2-10 2.5.1.3 Acidimicrobineae 2.5.1.5 EB1017 2.5.2 Actinobacteridae 2.5.1.4 BD2-10 2.5.2.1 Unclassified 2.5.2.10 Ellin306/WR160 2.5.1.5 EB1017 2.5.2.11 Ellin5012 2.5.2.12 Ellin5034 2.5.2 Actinobacteridae 2.5.2.13 Frankineae 2.5.2.13.1 Unclassified 2.5.2.1 Unclassified 2.5.2.13.2 Acidothermaceae 2.5.2.10 Ellin306/WR160 2.5.2.13.3 2.5.2.13.4 Ellin6090 Frankiaceae 2.5.2.11 Ellin5012 2.5.2.13.5 2.5.2.13.6 Geodermatophilaceae Microsphaeraceae 2.5.2.12 Ellin5034 2.5.2.13.7 2.5.2.14 Sporichthyaceae Glycomyces 2.5.2.13 Frankineae 2.5.2.15 2.5.2.15.1 Intrasporangiaceae Unclassified 2.5.2.14 Glycomyces 2.5.2.15.2 2.5.2.15.3 Dermacoccus Intrasporangiaceae 2.5.2.15 Intrasporangiaceae 2.5.2.16 2.5.2.17 Kineosporiaceae Microbacteriaceae 2.5.2.16 Kineosporiaceae 2.5.2.17.1 2.5.2.17.2 Unclassified Agrococcus 2.5.2.17 Microbacteriaceae 2.5.2.17.3 2.5.2.18 Agromyces Micrococcaceae 2.5.2.18 Micrococcaceae 2.5.2.19 2.5.2.2 Micromonosporaceae Actinomyces 2.5.2.19 Micromonosporaceae 2.5.2.20 2.5.2.20.1 Propionibacterineae Unclassified 2.5.2.2 Actinomyces 2.5.2.20.2 2.5.2.20.3 Kribbella Nocardioidaceae 2.5.2.20 Propionibacterineae 2.5.2.20.4 2.5.2.21 Propionibacteriaceae Pseudonocardiaceae 2.5.2.21 Pseudonocardiaceae 2.5.2.22 2.5.2.22.1 Streptomycineae Unclassified 2.5.2.22 Streptomycineae 2.5.2.22.2 2.5.2.22.3 Kitasatospora Streptacidiphilus 2.5.2.23 Streptosporangineae 2.5.2.23 2.5.2.23.1 Streptosporangineae Unclassified 2.5.2.3 Actinomycineae 2.5.2.23.2 2.5.2.23.3 Ellin5129 Nocardiopsaceae 2.5.2.4 Actinosynnemataceae 2.5.2.23.4 2.5.2.23.5 Streptosporangiaceae Thermomonosporaceae 2.5.2.5 Bifidobacteriaceae 2.5.2.3 Actinomycineae 2.5.2.4 Actinosynnemataceae 2.5.2.6 Brevibacteriaceae 2.5.2.5 Bifidobacteriaceae 2.5.2.6 Brevibacteriaceae 2.5.2.7 Cellulomonadaceae 2.5.2.7 Cellulomonadaceae 2.5.2.8 Corynebacterineae 2.5.2.8 Corynebacterineae 2.5.2.8.1 Unclassified 2.5.2.8.2 Corynebacteriaceae 2.5.2.9 Dermabacteraceae 2.5.2.8.3 Dietziaceae 2.5.2.8.4 Gordoniaceae 2.5.3 Coriobacteridae 2.5.2.8.5 Mycobacteriaceae 2.5.2.8.6 Rhodococcus 2.5.3.1 Unclassified 2.5.2.8.7 Rhodococcus 2.5.2.8.8 Rhodococcus 2.5.3.2 Atopobiales 2.5.2.9 Dermabacteraceae 2.5.2.9.1 Unclassified 2.5.3.3 Coriobacteriales 2.5.2.9.2 Brachybacterium 2.5.2.9.3 Dermabacter 2.5.3.4 Eggerthellales 2.5.3 Coriobacteridae 2.5.3.1 Unclassified 2.5.4 OPB41 2.5.3.2 Atopobiales 2.5.3.3 Coriobacteriales 2.5.5 PK1 2.5.3.4 Eggerthellales 2.5.4 OPB41 2.5.6 Rubrobacteridae 2.5.5 PK1 2.5.6 Rubrobacteridae 2.5.6.1 Unclassified 2.5.6.1 Unclassified 2.5.6.2 "Thermoleiphilaceae 2.5.6.2 "Thermoleiphilaceae 2.5.6.2.1 Unclassified 2.5.6.2.2 Conexibacter 2.5.6.3 MC47 2.5.6.2.3 XGE514 2.5.6.3 MC47 2.5.6.4 Rubrobacteraceae 2.5.6.4 Rubrobacteraceae Sunday, April 25, 2010
  18. 18. Microbial genomes 2010- ... From http://genomesonline.org Sunday, April 25, 2010
  19. 19. Proteobacteria TM6 OS-K • At least 100 phyla of Acidobacteria Termite Group OP8 bacteria Nitrospira Bacteroides Chlorobi • Genome sequences are Fibrobacteres Marine GroupA mostly from three phyla WS3 Gemmimonas Firmicutes • Most phyla with cultured Fusobacteria Actinobacteria species are sparsely OP9 Cyanobacteria Synergistes sampled Deferribacteres Chrysiogenetes NKB19 • Lineages with no cultured Verrucomicrobia Chlamydia OP3 taxa even more poorly Planctomycetes Spriochaetes sampled Coprothmermobacter OP10 Thermomicrobia Chloroflexi • Solution - use tree to really TM7 Deinococcus-Thermus fill gaps Dictyoglomus Aquificae Well sampled phyla Thermudesulfobacteria Thermotogae OP1 OP11 Sunday, April 25, 2010
  20. 20. Why Increase Phylogenetic Coverage? • Gene discovery • Annotation, functional prediction • Metagenomic analysis • Mechanisms of diversification • Species phylogeny and classification Sunday, April 25, 2010
  21. 21. A Genomic Encyclopedia of Bacteria and Archaea (GEBA) Sunday, April 25, 2010
  22. 22. GEBA Pilot Project Overview • Identify major branches in rRNA tree for which no genomes are available • Identify a cultured representative for each group • Grow > 200 of these and prep. DNA • Sequence and finish 100 • Annotate, analyze, release data • Assess benefits of tree guided sequencing • Paper published in Nature Dec. 2009. Sunday, April 25, 2010
  23. 23. B: Ac tin ob ac te B: ria # of Genomes Am (H Sunday, April 25, 2010 in igh 10 15 20 25 30 35 0 5 an G a C B: B: er ) Ba Aq ob ct uif ia e i B: B: ro cae D Ch ide B: efe lo te r s D rri ofl ef ba e B: e c xi B: De B rrib ter Ep lta : D act es si Pr ei er lo o n es n te oc Pr ob oc ot a ci B: e ct G B: oba eri am B F ct a : ir e B: m Fu mi ria a G P so cut em ro ba e t c s B: ma eo te ba ri H tim c a a t B: loa ona eri a B: Pl nae de an r te Th c o s Phyla er B: to bia m S m le y s B: od piro ce es c te T u h B: he lfo ae s rm b te GEBA Pilot Target List Th o a s er de cte m s ri u a A: ove lfo H n bi A: alo abu a A: A b la M rc ac e A: et ha te M han eo ria et g ha ob lob ac i A: no te m r A: The icr ia Th rm obi er oc a m oc op ci ro te i
  24. 24. GEBA and Openness • All data being released as quickly as possible with no restrictions to IMG-GEBA; Genbank, etc • Data also available in Biotorrents (http://biotorrents.net) • Individual genome reports being published in new Open Access journal “Standards in Genome Sciences (SIGS)” • Main GEBA paper in Nature freely available and published using Creative Commons License Sunday, April 25, 2010
  25. 25. Assess Benefits of GEBA • All genomes have some value • But what, if any, is the benefit of tree- guided sequencing over other selection methods • Lessons for other large scale microbial genome projects? Sunday, April 25, 2010
  26. 26. GEBA Lesson 1 rRNA Tree is Useful for Identifying Phylogenetically Novel Genomes rRNA Tree topology is not perfect; Genome-based trees better Sunday, April 25, 2010
  27. 27. rRNA Tree of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
  28. 28. Sunday, April 25, 2010
  29. 29. Network of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
  30. 30. Wh Whole genome tree built using AMPHORA by Martin Wu and Dongying Wu Sunday, April 25, 2010
  31. 31. PD of rRNA, Genome Trees Similar From Wu et al. 2009 Sunday, April 25, 2010
  32. 32. Proteobacteria Sunday, April 25, 2010
  33. 33. GEBA Lesson 2 Phylogenetically-guided genome selection improves genome annotation Sunday, April 25, 2010
  34. 34. Predicting Function • Key step in genome projects • More accurate predictions help guide experimental and computational analyses • Many diverse approaches • Comparative and evolutionary analysis greatly improves most predictions Sunday, April 25, 2010
  35. 35. Most/All Functional Prediction Improves w/ Better Phylogenetic Sampling • Better definition of protein family sequence “patterns” • Conversion of hypothetical into conserved hypotheticals • Greatly improves “comparative” and “evolutionary” based predictions • Linking distantly related members of protein families • Improved non-homology prediction Sunday, April 25, 2010
  36. 36. From Wu et al. 2009. Sunday, April 25, 2010
  37. 37. GEBA Lesson 3 Improves analysis of genome data from uncultured organisms Sunday, April 25, 2010
  38. 38. Metagenomics shotgun clone Sunday, April 25, 2010
  39. 39. Sunday, April 25, 2010
  40. 40. rRNA phylotyping from metagenomics Venter et al., 2004 Sunday, April 25, 2010
  41. 41. Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA) Venter et al., 2004 Sunday, April 25, 2010
  42. 42. Weighted % of Clones 0 0.1250 0.2500 0.3750 0.5000 Al ph ap ro t eo Be b ac ta pr t er ot e ia G Sunday, April 25, 2010 am ob ac m t er ap ia ro Ep te si ob lo ac np t er ro ia De t eo lta b ac pr te ot ria eo b C ac ya t er n ob ia ac t er Fi ia rm ic u te Ac s tin ob ac ter C ia hl or ob i C FB Major Phylogenetic Group Sargasso Phylotypes C hl or of le Sp xi iro c ha et Fu es so De ba in ct er oc ia oc cu s- Eu The ry r ar mu ch s ae C ot re a na rc ha eo ta Shotgun Sequencing Allows Use of Other Markers Venter et al., 2004 EFG EFTu rRNA RecA RpoB HSP70
  43. 43. Weighted % of Clones 0 0.1250 0.2500 0.3750 0.5000 Al ph ap ro t eo Be b ac ta pr t er ot e ia G Sunday, April 25, 2010 am ob ac m t er ap ia ro Ep te si ob lo ac np t er ro ia De t eo lta b ac pr te ot ria eo b C ac ya t er n ob ia ac t er Fi ia rm ic u te Ac s tin ob ac ter C ia hl or ob i without good C FB Major Phylogenetic Group Sargasso Phylotypes C Cannot be done hl or of le Sp xi iro c ha et Fu es so De ba in ct er oc ia sampling of genomes oc cu s- Eu The ry r ar mu ch s ae C ot re a na rc ha eo ta Shotgun Sequencing Allows Use of Other Markers Venter et al., 2004 EFG EFTu rRNA RecA RpoB HSP70
  44. 44. Binning challenge A T B U C V D W E X F Y G Z Sunday, April 25, 2010
  45. 45. Binning challenge A T B U C V D W E X F Y G Best binning method: reference genomes Z Sunday, April 25, 2010
  46. 46. Binning challenge A T B U C V D W E X F Y G No reference genome? What do you do? Z Sunday, April 25, 2010
  47. 47. Binning challenge A T B U C V D W E X F Y G No reference genome? What do you do? Z Phylogeny .... Sunday, April 25, 2010
  48. 48. Al ph ap ro Be te ta o ba G p 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 am ro ct te er m o ia Sunday, April 25, 2010 ap ba ro ct D t er el eo ia ta ba Ep pr ct ot er U si lo eo ia nc ba la np ct ss ro er ifi te ia ed ob Pr ac ot te eo ria ba Cy ct an er ob ia ac Ch te ria la m Ac yd id ia ob e Ba ac te ct ria er Ac oi de tin te ob s ac te ria Aq Pl ui an fic ct om ae yc Sp et AMPHORA - each read on its own tree iro es ch ae Fi te rm s ic ut Ch es lo ro U fle nc xi la Ch ss lo ifi ro ed bi Ba ct er ia Phylogenetic Binning Using AMPHORA frr tsf pgk rplL rplF rplP rplT rplE infC rpsI rplS rplA rplB rplK rplC rpsJ rplN rplD rplM rpsE rpsS rpsB rpsK rpsC rpoB rpsM pyrG nusA dnaG rpmA smpB
  49. 49. Phylogenetic Binning Using AMPHORA dnaG 0.7 frr infC 0.6 nusA pgk pyrG 0.5 0.4 Cannot be done rplA rplB rplC rplD 0.3 without good rplE rplF rplK rplL 0.2 0.1 sampling of genomes rplM rplN rplP rplS rplT rpmA 0 rpoB rpsB es ia s es s ria ia ia bi ia ia om ae e ia ria ria ria xi te te ia er er er er er er fle ro et ut rpsC fic te te te te yd de ae ct ct ct ct ct ct lo yc ro ic ac ac ac ac ui m ch oi ba ba Ch ba ba ba Ba rm rpsE lo Aq ob ob ob ob er la iro eo Ch o eo o eo Fi ed Ch ct an te te te id tin ct rpsI Sp ot ot t Ba Ac ro ro ro ro ifi an Cy Ac Pr pr ss ap p ap np rpsJ Pl ta ta ed la ph m lo el Be nc rpsK si ifi am Al D Ep U ss rpsM G la nc rpsS U smpB tsf AMPHORA - each read on its own tree Sunday, April 25, 2010
  50. 50. GEBA Phylogenomic Lesson 5 We have still only scratched the surface of microbial diversity Sunday, April 25, 2010
  51. 51. Protein Family Rarefaction Curves • Take data set of multiple complete genomes • Identify all protein families using MCL • Plot # of genomes vs. # of protein families Sunday, April 25, 2010
  52. 52. Sunday, April 25, 2010
  53. 53. Sunday, April 25, 2010
  54. 54. Sunday, April 25, 2010
  55. 55. Sunday, April 25, 2010
  56. 56. Sunday, April 25, 2010
  57. 57. Mobile Motility Element? Sunday, April 25, 2010
  58. 58. Phylogenetic Distribution Novelty: Bacterial Actin Related Protein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aliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla, Victor Kunin See also Guljamow et al. 2007 Current Biology. Sunday, April 25, 2010
  59. 59. rRNA Tree of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
  60. 60. Phylogenetic Diversity: Sequenced Bacteria & Archaea From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html Sunday, April 25, 2010
  61. 61. Phylogenetic Diversity with GEBA From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html Sunday, April 25, 2010
  62. 62. Phylogenetic Diversity: Isolates From Wu et al. 2009. Sunday, April 25, 2010
  63. 63. Phylogenetic Diversity: All From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html Sunday, April 25, 2010
  64. 64. Proteobacteria TM6 OS-K • At least 40 phyla of Acidobacteria Termite Group OP8 bacteria Nitrospira Bacteroides Chlorobi • Genome sequences are Fibrobacteres Marine GroupA mostly from three phyla WS3 Gemmimonas Firmicutes • Most phyla with cultured Fusobacteria Actinobacteria species are sparsely OP9 Cyanobacteria Synergistes sampled Deferribacteres Chrysiogenetes NKB19 • Lineages with no cultured Verrucomicrobia Chlamydia OP3 taxa even more poorly Planctomycetes Spriochaetes sampled Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Well sampled phyla Thermudesulfobacteria Thermotogae Poorly sampled OP1 OP11 No cultured taxa Sunday, April 25, 2010
  65. 65. Uncultured Lineages: Technical Approaches • Get into culture • Enrichment cultures • If abundant in low diversity ecosystems • Flow sorting • Microbeads • Microfluidic sorting • Single cell amplification Sunday, April 25, 2010
  66. 66. GEBA Phylogenomic Lesson 6 Need Experiments from Across the Tree of Life too Sunday, April 25, 2010
  67. 67. 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 OP11 Hugenholtz, 2002 Sunday, April 25, 2010
  68. 68. As of 2002 Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Experimental WS3 Gemmimonas Firmicutes studies are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
  69. 69. As of 2002 Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Experimental WS3 Gemmimonas Firmicutes studies are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some studies Verrucomicrobia Chlamydia OP3 in other phyla Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
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