The Evolution of Microbes and Their Genomes: A Phylogenomic Perspective

1. The Evolution of Microbes and Their Genomes: A Phylogenomic Perspective Jonathan A. Eisen October 3, 2009

2. “Nothing in biology makes sense except in the light of evolution.” T. Dobzhansky (1973)

3. Eisen Lab - Phylogenomics of Novelty Origin of New Functions and Processes Genome Dynamics • Evolvability • Repair and recombination processes • Intragenomic variation • New genes • Changes in old genes • Changes in pathways Species Evolution • Phylogenetic history • Vertical vs. horizontal descent • Needed to track gain/loss of processes, infer convergence

4. 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

5. 56.1 The Global Ecosystem’s Compartments are Connected by the Flow of Elements

6. 26.23 Some Would Call It Hell; These Archaea Call It Home

8. Human commensals

9. Deep Sea Ecosystems

10. Fleischmann et al. 1995

11. shotgun Whole Genome Shotgun Sequencing sequence Warner Brothers, Inc.

12. Assemble Fragments sequencer output Closure &Annotation assemble fragments

13. From http://genomesonline.org

14. 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

15. 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

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19. rRNA Tree of Life

20. The Tree is not Happy

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

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

23. Nitrospira Proteobacteria TM6 As of 2002 OS-K Termite Group OP8 Chlorobi Marine GroupA WS3 Synergistes Firmicutes Deferribacteres Chrysiogenetes Fusobacteria OP9 Actinobacteria Cyanobacteria NKB19 Coprothmermobacter OP3 Thermomicrobia Chlamydia Spriochaetes Dictyoglomus OP10 Thermudesulfobacteria TM7 Deinococcus-Thermus Aquificae OP1 Thermotogae OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Based on Hugenholtz, 2002

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

25. 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

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

27. The Tree of Life is Still Angry

28. Major Lineages of Actinobacteria

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

30. http://www.jgi.doe.gov/programs/GEBA/pilot.html

31. 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

33. Some Lessons From GEBA

34. GEBA Lesson 1 rRNA Tree of Life is a Useful Guide and Genomes Improve Resolution

35. rRNA Tree of Life

38. GEBA Lesson 2 Phylogenetically Guided Selection Can Help Annotate Other Genomes

39. Predicting Function • Identification of motifs • Small sequence elements that code for some general activity (e.g., ATPase) • Homology/similarity based methods • Identify longer stretches of similarity to genes with known function • Evolutionary reconstructions

40. Evolutionary Functional Prediction Based on Eisen, 1998 Genome Res 8: 163-167.

41. E.coli V.cholerae gi1789453 VC 0512 B.subtilis gi2633766 ** Recent Functional Changes NJ * V.cholerae VC A1034 Synechocystis sp. gi1001299 H.pylori gi2313186 H.pylori V.cholerae 99 gi4154603 VC A0974 Synechocystis sp. gi1001300 V.cholerae VC A0068 C.jejuni Cj0144 Synechocystis sp. gi1652276 V.cholerae VC 0825 C.jejuni Cj1564 Synechocystis sp. gi1652103 C.jejuni Cj0262c V.cholerae VC 0282 H.pylori gi2313716 V.cholerae VC A0906 C.jejuni H.pylori Cj1506c 99 gi4155097 V.cholerae VC A0979 C.jejuni H.pylori Cj1190c gi2313163 V.cholerae VC A1056 ** C.jejuni Cj1110c H.pylori 99 gi4154575 ** V.cholerae VC 1643 A.fulgidus gi2649560 H.pylori gi2313179 V.cholerae VC 2161 A.fulgidus gi2649548 H.pylori 99 gi4154599 C.jejuni Cj0019c B.subtilis gi2634254 V.cholerae VC A0923 V.cholerae VC C.jejuni 0514 Cj0951c B.subtilis gi2632630 V.cholerae C.jejuni Cj0246c VC 1868 B.subtilis gi2635607 V.cholerae VC A0773 B.subtilis gi2633374 B.subtilis gi2635608 T.maritima TM0014 V.cholerae VC 1313 B.subtilis gi2635609 ** B.subtilis V.cholerae gi2635610 VC 1859 V.cholerae B.subtilis VC 1413 gi2635882 V.cholerae VC A0268 * T.pallidum gi3322777 E.coli gi1788195 E.coli gi2367378 V.cholerae VC T.pallidum A0658 gi3322939 V.cholerae VC 1405 E.coli gi1788194 T.pallidum gi3322938 V.cholerae VC 1298 E.coli gi1787690 B.burgdorferi gi2688522 V.cholerae VC 1248 ** T.pallidum gi3322296 V.cholerae VC A0864 B.burgdorferi gi2688521 ** T.maritima TM0429 V.cholerae VC A0176 V .cholerae VC A0220 T.maritima TM0918 V.cholerae VC 1289 T.maritima TM0023 V.cholerae VC A1069 T.maritima TM1428 V.cholerae VC 2439 T.maritima TM1143 V.cholerae VC 1967 T.maritima TM1146 P.abyssi PAB1308 V.cholerae VC A0031 V.cholerae VC 1898 P.horikoshii gi3256846 V.cholerae VC A0663 * P.abyssi PAB1336 P.horikoshii gi3256896 V.cholerae VC A0988 P.abyssi PAB2066 V.cholerae VC 0216 V.cholerae VC 0449 P.horikoshii gi3258290 V.cholerae VC A0008 P.abyssi PAB1026 V.cholerae VC 1406 P.horikoshii gi3256884 V.cholerae VC 1535 D.radiodurans DRA00354 V.cholerae VC 0840 D.radiodurans DRA0353 * * D.radiodurans DRA0352 * P.abyssi PAB1189 P.horikoshii gi3258414 ** ** B.burgdorferi gi2688621 M.tuberculosis gi1666149 ** ** ** ** ** * V.cholerae VC A1092 V.cholerae VC 0098 ** ** ** * ** ** ** V.cholerae VC 1403 ** ** V.cholerae VC A1088 * ** ** * ** ** ** ** ** ** * ** ** ** ** ** V.cholerae VC 1394 V.cholerae VC 0622 • Phylogenomic functional prediction may not work well for very newly evolved functions • Screen genomes for genes that have changed recently • Examples: • Acquisition (e.g., LGT) • Unusual dS/dN ratios • Rapid evolutionary rates • Duplication and divergence

42. 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 • Example: correlated presence/absence of genes across species

43. Most/All Functional Prediction Improves w/ Better Phylogenetic Sampling • 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

44. GEBA Lesson 3 Phylogenetically Guided Selection Can Help Study Uncultured Organisms

45. Great Plate Count Anomaly Microscope Culturing Count Count

46. Great Plate Count Anomaly Microscope Culturing Count <<<< Count

47. Great Plate Count Anomaly DNA Microscope Culturing Count <<<< Count

48. PCR Saves the Day

49. Sequencing and uncultured microbes I: rRNA surveys

50. rRNA: A Phylogenetic Anchor to Determine Who’s Out There Biology not similar enough Eisen et al. 1992