Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Eisen Talk for MBL Microbial Diversity Course

3,153 views

Published on

Talk by Jonathan Eisen for MBL Microbial Diversity Course

Published in: Education, Technology
  • Be the first to comment

  • Be the first to like this

Eisen Talk for MBL Microbial Diversity Course

  1. 1. Phylogenomics and theOrigin of Novelty in Microbes Jonathan A. Eisen UC Davis MBL Microbial Diversity Course July 9, 2011
  2. 2. Phylogenomics and theOrigin of Novelty in Microbes Jonathan A. Eisen UC Davis MBL Microbial Diversity Course July 9, 2011
  3. 3. My Obsessions Jonathan A. Eisen UC DavisMBL Microbial Diversity Course July 9, 2011
  4. 4. Social Networking in ScienceHOME PAGE MY TIMES TODAYS PAPER VIDEO MOST POPULAR TIMES TOPICS Welcome, fcollins Member Center Log OutSunday, April 1, 2007 HealthWORLD U.S. N.Y. / REGION BUSINESS TECHNOLOGY SCIENCE HEALTH SPORTS OPINION ARTS STYLE TRAVEL JOBS REAL ESTATE AUTOS FITNESS & NUTRITION HEALTH CARE POLICY MENTAL HEALTH & BEHAVIORScientist Reveals Secret of the Ocean: Its HimBy NICHOLAS WADEPublished: April 1, 2007 PRINT nytimes.com/sportsMaverick scientist J. Craig Venter has done it again. It was just a few years SINGLE-PAGEago that Dr. Venter announced that the human genome sequenced by Celera SAVEGenomics was in fact, mostly his own. And now, Venter has revealed a second SHAREtwist in his genomic self-examination. Venter was discussing his Global SHAREOcean Voyage, in which he used his personal yacht to collect ocean watersamples from around the world. He then used large filtration units to collect How good is your bracket? Compare your tournament picks to choices from members of The New York Times sportsmicrobes from the water samples which were then brought back to his high desk and other players.tech lab in Rockville, MD where he used the same methods that were used to Also in Sports: The Bracket Blog - all the news leading up to the Finalsequence the human genome to study the genomes of the 1000s of ocean Fourdwelling microbes found in each sample. In discussing the sampling methods, Venter let slip his Bats Blog: Spring training updates Play Magazine: How to build a super athletelatest attack on the standards of science – some of the samples were in fact not from the ocean, butwere from microbial habitats in and on his body.“The human microbiome is the next frontier,” Dr. Venter said. “The ocean voyage was just a cover.My main goal has always been to work on the microbes that live in and on people. And now that mygenome is nearly complete, why not use myself as the model for human microbiome studies as well.”It is certainly true that in the last few years, the microbes that live in and on people have become ahot research topic. So hot that the same people who were involved in the race to sequence the human
  5. 5. Bacterial evolve
  6. 6. T. H. Dobzhansky (1973)“Nothing in biology makes senseexcept in the light of evolution.”
  7. 7. Evolutionary Perspective and Comparative Biology• Comparative biology is the analysis of differences and similarities between species.• An evolutionary perspective is useful in such studies because it allows one to focus on how and why similarities and differences came to be.• In other words, biological objects have a history and understanding that history is important
  8. 8. 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
  9. 9. Phylogenomics of Novelty Variation inMechanisms of Mechanisms:Origin of New Patterns, Causes Functions and Effects Species Evolution
  10. 10. rRNA Tree of Life Figure from Barton, Eisen et al. “Evolution”, CSHL Press. 2007.Based on tree from Pace 1997 Science 276:734-740
  11. 11. Limited Sampling of RRR Studies Figure from Barton, Eisen et al. “Evolution”, CSHL Press. 2007. Based on tree from Pace 1997 Science 276:734-740
  12. 12. Limited Sampling of RRR Studies Haloferax MethanococcusChlorobiumDeinococcusThermotoga Figure from Barton, Eisen et al. “Evolution”, CSHL Press. 2007. Based on tree from Pace 1997 Science 276:734-740
  13. 13. Fleischmann et al.1995 Science269:496-512
  14. 14. TIGR Genome Projects MethanococcusChlorobiumDeinococcusThermotoga Figure from Barton, Eisen et al. “Evolution”, CSHL Press. 2007. Based on tree from Pace 1997 Science 276:734-740
  15. 15. Fleischmann et al.1995 Science269:496-512
  16. 16. Whole Genome Shotgun Sequencing
  17. 17. Whole Genome Shotgun Sequencing
  18. 18. Whole Genome Shotgun SequencingWarner Brothers, Inc.
  19. 19. Whole Genome Shotgun Sequencing shotgunWarner Brothers, Inc.
  20. 20. Whole Genome Shotgun Sequencing shotgunWarner Brothers, Inc.
  21. 21. Whole Genome Shotgun Sequencing shotgunWarner Brothers, Inc. sequence
  22. 22. Whole Genome Shotgun Sequencing shotgunWarner Brothers, Inc. sequence
  23. 23. Assemble Fragments
  24. 24. Assemble Fragmentssequencer output
  25. 25. Assemble Fragmentssequencer output
  26. 26. Assemble Fragmentssequencer output assemble fragments
  27. 27. Assemble Fragmentssequencer output assemble fragments Closure & Annotation
  28. 28. From http://genomesonline.org
  29. 29. General Steps in Analysis of Complete Genomes• Identification/prediction of genes• Characterization of gene features• Characterization of genome features• Prediction of gene function• Prediction of pathways• Integration with known biological data• Comparative genomics
  30. 30. Genome Sequences Have Revolutionized Microbiology• Predictions of metabolic processes• Better vaccine and drug design• New insights into mechanisms of evolution• Genomes serve as template for functional studies• New enzymes and materials for engineering and synthetic biology
  31. 31. From http://genomesonline.org
  32. 32. Outline• Phylogenomic Tales – Selecting genomes for sequencing – Species evolution – Predicting functions of genes – Uncultured microbes – Searching for novel organisms and genes
  33. 33. Outline• Phylogenomic Tales – Selecting genomes for sequencing – Species evolution – Predicting functions of genes – Uncultured microbes – Searching for novel organisms and genes• All of these going to be told in context of a recent project “A Genomic Encyclopedia of Bacteria and Archaea” (aka GEBA)
  34. 34. GEBA IntroductionKnowing What We Don’t Know
  35. 35. Major Microbial Sequencing Efforts• Coordinated, top-down efforts – Fungal Genome Initiative (Broad/Whitehead) – Gordon and Betty Moore Foundation Marine Microbial Genome Sequencing Project – Sanger Center Pathogen Sequencing Unit – NHGRI Human Gut Microbiome Project – NIH Human Microbiome Program• White paper or grant systems – NIAID Microbial Sequencing Centers – DOE/JGI Community Sequencing Program – DOE/JGI BER Sequencing Program – NSF/USDA Microbial Genome Sequencing• Covers lots of ground and biological diversity
  36. 36. As of 2002
  37. 37. 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
  38. 38. 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 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
  39. 39. 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 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
  40. 40. 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 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
  41. 41. Need for Tree Guidance Well Established• 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
  42. 42. 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: DictyoglomusEisen, Ward, Aquificae Thermudesulfobacteria sequence moreRobb, Nelson, et Thermotogae phyla OP1al OP11
  43. 43. Organisms SelectedPhylum Species selectedChrysiogenes Chrysiogenes arsenatis (GCA)Coprothermobacter Coprothermobacter proteolyticus (GCBP)Dictyoglomi Dictyoglomus thermophilum (GD T )Thermodesulfobacteria Thermodesulfobacterium commune (GTC)Nitrospirae Thermodesulfovibrio yellowstonii (GTY)Thermomicrobia Thermomicrobium roseum (GTR )Deferribacteres Geovibrio thiophilus (GGT)Synergistes Synergistes jonesii (GSJ)
  44. 44. Proteobacteria• NSF-funded TM6 OS-K • At least 40 Tree of Life Acidobacteria Termite Group phyla of bacteria OP8 Project Nitrospira • Genome Bacteroides• A genome Chlorobi Fibrobacteres sequences are Marine GroupA from each of WS3 Gemmimonas mostly from eight phyla Firmicutes Fusobacteria three phyla Actinobacteria OP9 Cyanobacteria • Some other Synergistes Deferribacteres Chrysiogenetes phyla are only NKB19 Verrucomicrobia sparsely Chlamydia OP3 Planctomycetes sampled Spriochaetes Coprothmermobacter • Still highly OP10 Thermomicrobia Chloroflexi biased in terms TM7 Deinococcus-Thermus Dictyoglomus of the tree AquificaeEisen & Ward, PIs Thermudesulfobacteria Thermotogae OP1 OP11
  45. 45. 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
  46. 46. Proteobacteria• NSF-funded TM6 OS-K • At least 40 Tree of Life Acidobacteria Termite Group phyla of bacteria OP8 Project Nitrospira • Genome Bacteroides• A genome Chlorobi Fibrobacteres sequences are Marine GroupA from each of WS3 Gemmimonas mostly from eight phyla Firmicutes Fusobacteria three phyla Actinobacteria OP9 Cyanobacteria • Some other Synergistes Deferribacteres Chrysiogenetes phyla are only NKB19 Verrucomicrobia sparsely Chlamydia OP3 Planctomycetes sampled Spriochaetes Coprothmermobacter • Same trend in OP10 Thermomicrobia Chloroflexi Archaea TM7 Deinococcus-Thermus Dictyoglomus AquificaeEisen & Ward, PIs Thermudesulfobacteria Thermotogae OP1 OP11
  47. 47. Proteobacteria• NSF-funded TM6 OS-K • At least 40 Tree of Life Acidobacteria Termite Group phyla of bacteria OP8 Project Nitrospira • Genome Bacteroides• A genome Chlorobi Fibrobacteres sequences are Marine GroupA from each of WS3 Gemmimonas mostly from eight phyla Firmicutes Fusobacteria three phyla Actinobacteria OP9 Cyanobacteria • Some other Synergistes Deferribacteres Chrysiogenetes phyla are only NKB19 Verrucomicrobia sparsely Chlamydia OP3 Planctomycetes sampled Spriochaetes Coprothmermobacter • Same trend in OP10 Thermomicrobia Chloroflexi Eukaryotes TM7 Deinococcus-Thermus Dictyoglomus AquificaeEisen & Ward, PIs Thermudesulfobacteria Thermotogae OP1 OP11
  48. 48. Proteobacteria• NSF-funded TM6 OS-K • At least 40 Tree of Life Acidobacteria Termite Group phyla of bacteria OP8 Project Nitrospira • Genome Bacteroides• A genome Chlorobi Fibrobacteres sequences are Marine GroupA from each of WS3 Gemmimonas mostly from eight phyla Firmicutes Fusobacteria three phyla Actinobacteria OP9 Cyanobacteria • Some other Synergistes Deferribacteres Chrysiogenetes phyla are only NKB19 Verrucomicrobia sparsely Chlamydia OP3 Planctomycetes sampled Spriochaetes Coprothmermobacter • Same trend in OP10 Thermomicrobia Chloroflexi Viruses TM7 Deinococcus-Thermus Dictyoglomus AquificaeEisen & Ward, PIs Thermudesulfobacteria Thermotogae OP1 OP11
  49. 49. Proteobacteria• GEBA TM6 OS-K • At least 40 Acidobacteria• A genomic Termite Group OP8 phyla of bacteria encyclopedia Nitrospira Bacteroides • Genome Chlorobi of bacteria Fibrobacteres Marine GroupA sequences are and archaea WS3 Gemmimonas mostly from Firmicutes Fusobacteria three phyla Actinobacteria OP9 Cyanobacteria • Some other Synergistes Deferribacteres Chrysiogenetes phyla are only NKB19 Verrucomicrobia sparsely Chlamydia OP3 Planctomycetes sampled Spriochaetes Coprothmermobacter OP10 • Solution: Really Thermomicrobia Chloroflexi Fill in the Tree TM7 Deinococcus-Thermus Dictyoglomus Aquificae ThermudesulfobacteriaEisen & Ward, PIs Thermotogae OP1 OP11
  50. 50. http://www.jgi.doe.gov/programs/GEBA/pilot.html
  51. 51. GEBA Pilot Project: Components• Project overview (Phil Hugenholtz, Nikos Kyrpides, Jonathan Eisen, Eddy Rubin, Jim Bristow)• Project management (David Bruce, Eileen Dalin, Lynne Goodwin)• Culture collection and DNA prep (DSMZ, Hans-Peter Klenk)• Sequencing and closure (Eileen Dalin, Susan Lucas, Alla Lapidus, Mat Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng)• Annotation and data release (Nikos Kyrpides, Victor Markowitz, et al)• Analysis (Dongying Wu, Kostas Mavrommatis, Martin Wu, Victor Kunin, Neil Rawlings, Ian Paulsen, Patrick Chain, Patrik D’Haeseleer, Sean Hooper, Iain Anderson, Amrita Pati, Natalia N. Ivanova, Athanasios Lykidis, Adam Zemla)• Adopt a microbe education project (Cheryl Kerfeld)• Outreach (David Gilbert)• $$$ (DOE, Eddy Rubin, Jim Bristow)
  52. 52. rRNA Tree of Life FIgure from Barton, Eisen et al. “Evolution”, CSHL Press.Based on tree from Pace NR, 2003.
  53. 53. B: Ac tin ob ac te B: ria # of Genomes Am (H in igh 10 15 20 25 30 35 0 5 an G a C B: B: er ) Ba Aq ob ct uif ia B: ero ica B: e D Ch ide B: e ef 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 sPhyla 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
  54. 54. GEBA Pilot Project Overview• Identify major branches in rRNA tree for which no genomes are available• Identify those with a cultured representative in DSMZ• DSMZ grew > 200 of these and prepped DNA• Sequence and finish 200+• Annotate, analyze, release data• Assess benefits of tree guided sequencing• 1st paper Wu et al in Nature Dec 2009
  55. 55. 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?
  56. 56. GEBA Phylogenomic Lesson 1 The rRNA Tree of Life is a Useful Tool for Identifying Phylogenetically Novel Genomes
  57. 57. rRNA Tree of LifeBacteria Archaea Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press. 2007. Based on tree from Pace 1997 Science 276:734-740
  58. 58. The Core Gets Small ...
  59. 59. The Pangenome
  60. 60. Islands Among Synteny
  61. 61. Network of LifeBacteria Archaea Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.
  62. 62. T. roseum mobile motility element Wu et al doi:10.1371/journal.pone.0004207
  63. 63. Phylogenetic Distribution Novelty: Bacterial Actin Related Protein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aliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla, Victor KuninWu et al. 2009 Nature 462, 1056-1060 See also Guljamow et al. 2007 Current Biology.
  64. 64. articlesAnalysis of the genome sequence of the¯owering plantThe Arabidopsis Genome Initiative Authorship of this paper should be cited as `The Arabidopsis Genome Iniative. A full list of contributors appears at the end of this paper.......................................................................................................................................................................................................................................................................... . .The ¯owering plant is an important model system for identifying genes and determining their functions.Here we report the analysis of the genomic sequence of . The sequenced regions cover 115.4 megabases of the125-megabase genome and extend into centromeric regions. The evolution of involved a whole-genome duplication,followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral genetransfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000families, similar to the functional diversity of and the other sequenced multicellulareukaryotes. has many families of new proteins but also lacks several common protein families, indicating that the setsof common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the ®rstcomplete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processesin all eukaryotes, identifying a wide range of plant-speci®c gene functions and establishing rapid systematic ways to identifygenes for crop improvement. C. elegans Drosophila Overview of sequencing strategy Arabidopsis thaliana Arabidopsis Arabidopsis
  65. 65. Using the Core
  66. 66. WhWhole genome treebuilt usingAMPHORAby Martin Wu andDongying Wu
  67. 67. GEBA Phylogenomic Lesson 2 rRNA Tree is good but not perfect and better genomic sampling improves phylogenetic inference
  68. 68. 16s Says Hyphomonas is in RhodobacterialesBadger et al.2005
  69. 69. WGT and individual gene trees: Its Related to CaulobacteralesBadger et al.2005
  70. 70. 16s WGT, 23SBadger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.
  71. 71. Zimmer. New York Times. 2009
  72. 72. GEBA Phylogenomic Lesson 3 Phylogenetics guided genome selection (and phylogenetics in general) improves genome annotation
  73. 73. Predicting Function• Key step in genome projects• More accurate predictions help guide experimental and computational analyses• Many diverse approaches• All improved both by “phylogenomic” type analyses that integrate evolutionary reconstructions and understanding of how new functions evolve
  74. 74. From Eisen etal. 1997 NatureMedicine 3:1076-1078.
  75. 75. Blast Search of H. pylori “MutS”• 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 Based on Eisen• Assumes functional constancy et al. 1997 Nature Medicine 3: 1076-1078.
  76. 76. MutL??From http://asajj.roswellpark.org/huberman/dna_repair/mmr.html
  77. 77. 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 Ecoli Neigo Res 26: 4291-4300.
  78. 78. MutS Subfamilies MSH5 MutS2 Aquae Strpy Bacsu Synsp Deira Helpy Yeast Human Borbu Metth Celeg mSaco MSH6 Yeast Human Mouse Arath Yeast MSH4 Celeg Human Arath HumanMSH3 Mouse Fly Spombe Yeast Xenla Rat Mouse YeastMSH1 Spombe Human Yeast MSH2 Neucr Arath Aquae Trepa Chltr Deira Theaq BacsuBorbu Thema SynspStrpy Ecoli Neigo Based on Eisen, 1998 Nucl Acids MutS1 Res 26: 4291-4300.
  79. 79. Overlaying Functions onto Tree MutS2 MSH5 Aquae Strpy Bacsu Synsp Deira Helpy Yeast Human Borbu Metth Celeg MSH6 mSaco Yeast Human Mouse Arath YeastMSH4 Celeg Human Arath HumanMSH3 Mouse Fly Spombe Yeast Xenla Rat Mouse Yeast HumanMSH1 Spombe Yeast MSH2 Neucr Arath Aquae Trepa Chltr DeiraTheaq BacsuBorbu Thema SynspStrpy Based on Eisen, Ecoli Neigo 1998 Nucl Acids MutS1 Res 26: 4291-4300.
  80. 80. Functional Prediction Using Tree MSH5 - Meiotic Crossing Over MutS2 - Unknown Functions Aquae Strpy Bacsu Synsp Deira Helpy Yeast Human Borbu Metth CelegMSH6 - Nuclear mSacoRepair YeastOf Mismatches Human MSH4 - Meiotic Crossing Mouse Yeast Over Arath Celeg Human ArathMSH3 - Nuclear Human MouseRepairOf Loops Spombe Fly Yeast Xenla Rat Mouse MSH2 - Eukaryotic Nuclear Yeast Human Mismatch and Loop RepairMSH1 Spombe Yeast NeucrMitochondrial ArathRepair Aquae Trepa Chltr DeiraTheaq BacsuBorbu Thema SynspStrpy Ecoli Based on Eisen, Neigo 1998 Nucl Acids MutS1 - Bacterial Mismatch and Loop Repair Res 26: 4291-4300.
  81. 81. PHYLOGENENETIC PREDICTION OF GENE FUNCTION EXAMPLE A METHOD EXAMPLE B 2A CHOOSE GENE(S) OF INTEREST 5 3A 1 3 4 2B 2 IDENTIFY HOMOLOGS 5 1A 2A 1B 3B 6 ALIGN SEQUENCES 1A 2A 3A 1B 2B 3B 1 2 3 4 5 6 CALCULATE GENE TREE Duplication? 1A 2A 3A 1B 2B 3B 1 2 3 4 5 6 OVERLAY KNOWN FUNCTIONS ONTO TREE Duplication? 2A 3A 1B 2B 3B 1 2 3 4 5 6 1A INFER LIKELY FUNCTION OF GENE(S) OF INTEREST Ambiguous Duplication?Species 1 Species 2 Species 3 1A 1B 2A 2B 3A 3B 1 2 3 4 5 6 ACTUAL EVOLUTION (ASSUMED TO BE UNKNOWN) Based on Eisen, 1998 Genome Duplication Res 8: 163-167.
  82. 82. Evolutionary Rate Variation1 2 4 6 3 5
  83. 83. Phylogenetic Prediction of Function• Greatly improves accuracy of functional predictions compared to similarity alone (e.g., blast)• Many surrogate methods (e.g., COGs)• Automated phylogenetic methods now available – Sean Eddy, Steven Brenner, Kimmen Sjölander, etc.• But …
  84. 84. Example 2: Recent Changes• Phylogenomic functional prediction NJ * ** V.cholerae VC V.cholerae VC 0512 A1034 V.cholerae VC V.cholerae VC V.cholerae VC A0974 A0068 V.cholerae VC0825 0282 may not work well for very newly V.cholerae VCA0906 V.cholerae VC A0979 V.cholerae VCA1056 V.cholerae VC1643 V.cholerae VC 2161 V.cholerae VCA0923 ** ** V.cholerae VC0514 V.cholerae VC1868 V.cholerae VCA0773 V.cholerae VC1313 evolved functions V.cholerae VC1859 V.cholerae VC 1413 V.cholerae VCA0268 V.cholerae VC A0658 ** V.cholerae VC1405 V.cholerae VC 1298 * V.cholerae V.cholerae VCA0864 VC 1248 V.cholerae VCA0176 V.cholerae VCA0220 ** V.cholerae VC1289 V.cholerae VC1069 A ** V.cholerae VC2439• Can use understanding of origin of V.cholerae VC967 1 V.cholerae VCA0031 V.cholerae VC 1898 V.cholerae VCA0663 V.cholerae VC0988 A V.cholerae VC0216 V.cholerae VC0449 * V.cholerae VCA0008 V.cholerae VC1406 V.cholerae VC 1535 novelty to better interpret these cases? V.cholerae VC 0840 B.subtilis gi2633766 Synechocystis sp. gi1001299 Synechocystis sp.gi1001300 * Synechocystis sp. gi1652276 * Synechocystis * H.pylori sp. gi1652103 gi2313716 H.pylori 99 gi4155097 **C.jejuni ** C.jejuniCj1190c Cj1110c A.fulgidus gi2649560 A.fulgidus gi2649548 ** B.subtilis gi2634254• Screen genomes for genes that have B.subtilis gi2632630 B.subtilis gi2635607 B.subtilis gi2635608 B.subtilis ** ** B.subtilis gi2635609 ** gi2635610 B.subtilis E.coli gi2635882 E.coligi1788195 gi2367378 * ** E.coligi1788194 E.coli A1092 gi1787690 V.cholerae VC changed recently V.cholerae VC0098 E.coli gi1789453 H.pylori gi2313186 H.pylori 99 gi4154603 C.jejuni ** C.jejuni Cj0144 Cj1564 C.jejuni ** C.jejuniCj0262c ** Cj1506c H.pylori gi2313163 * H.pylori 99 gi4154575 **H.pylori gi2313179 ** H.pylori 99 gi4154599– Pseudogenes and gene loss ** C.jejuni Cj0019c C.jejuni C.jejuni Cj0951c Cj0246c B.subtilis gi2633374 T.maritima TM0014 V.cholerae VC V.cholerae VC 1403 A1088 T.pallidum gi3322777 T.pallidum ** T.pallidum gi3322939 gi3322938 ** B.burgdorferi gi2688522– Contingency Loci T.pallidum gi3322296 B.burgdorferi * T.maritima gi2688521 TM0429 T.maritima **T.maritima TM0918 ** TM1428 T.maritima TM0023 * T.maritima TM1143 T.maritima TM1146 P.abyssi PAB1308 P.horikoshii gi3256846 ** P.horikoshii P.abyssi PAB1336– Acquisition (e.g., LGT) ** gi3256896 ** **P.abyssi PAB2066 ** P.horikoshii gi3258290 * ** P.abyssi PAB1026 P.horikoshii gi3256884 ** D.radiodurans DRA00354 D.radiodurans DRA0353 ** D.radiodurans ** ** VC DRA0352 V.cholerae 1394 P.abyssi PAB1189 P.horikoshii gi3258414– Unusual dS/dN ratios ** B.burgdorferi gi2688621 M.tuberculosis gi1666149 V.cholerae VC 0622– Rapid evolutionary rates– Recent duplications
  85. 85. Example 3: Non homology methods• Many genes have homologs in other species but no homologs have ever been studied experimentally• Non-homology methods can make functional predictions for these• Example: phylogenetic profiling (extension of prior work of Koonin, Tatusov, Ragan, et al.)
  86. 86. 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
  87. 87. 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)
  88. 88. 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. )
  89. 89. Homologs of Sporulation Genes Wu et al. 2005 PLoS Genetics 1: e65.
  90. 90. Carboxydothermus sporulates Wu et al. 2005 PLoS Genetics 1: e65.
  91. 91. Wu et al. 2005 PLoS Genetics 1: e65.
  92. 92. PG Profiling Works Better Using Orthology
  93. 93. GEBA Lesson 3: Phylogeny driven genome selection (and phylogenetics) improves genome annotation• Took 56 GEBA genomes and compared results vs. 56 randomly sampled new genomes• Better definition of protein family sequence “patterns”• Greatly improves “comparative” and “evolutionary” based predictions• Conversion of hypothetical into conserved hypotheticals• Linking distantly related members of protein families• Improved non-homology prediction
  94. 94. GEBA Lesson 4: Metadata Important
  95. 95. GEBA Phylogenomic Lesson 5 Phylogeny-driven genome selection helps discover new genetic diversity
  96. 96. Network of LifeBacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.
  97. 97. Protein Family Rarefaction• Take data set of multiple complete genomes• Identify all protein families using MCL• Plot # of genomes vs. # of protein families
  98. 98. Wu et al. 2009 Nature 462, 1056-1060
  99. 99. Wu et al. 2009 Nature 462, 1056-1060
  100. 100. Wu et al. 2009 Nature 462, 1056-1060
  101. 101. Wu et al. 2009 Nature 462, 1056-1060
  102. 102. Wu et al. 2009 Nature 462, 1056-1060
  103. 103. Synapomorphies existWu et al. 2009 Nature 462, 1056-1060
  104. 104. GEBA Phylogenomic Lesson 6 Improves analysis of genome data from uncultured organisms
  105. 105. rRNA Phylotyping • Collect DNA from environment • PCR amplify rRNA genes using broad (so- called universal) primers • Sequence • Align to others • Infer evolutionary tree • Unknowns “identified” by placement on tree • Some use BLAST, but not as good as phylogeny
  106. 106. rRNA PCRThe Hidden Majority Richness estimates Hugenholtz 2002 Bohannan and Hughes 2003
  107. 107. Metagenomics shotgun sequence
  108. 108. Example I:Phylotyping w/ many genes
  109. 109. rRNA Phylotyping in Sargasso Sea Venter et al., Science 304: 66. 2004
  110. 110. Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA) Venter et al., Science 304: 66. 2004

×