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UC Davis EVE161 Lecture 13 by @phylogenomics

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  • 1. Lecture 13: EVE 161:
 Microbial Phylogenomics ! Lecture #13: Era III: Genome Sequencing and Phylogenomic Analysis ! UC Davis, Winter 2014 Instructor: Jonathan Eisen Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !1
  • 2. Where we are going and where we have been • Previous lecture: ! 12: Guest Lecture • Current Lecture: ! 13: Genome Sequencing III • Next Lecture: ! 14: Metagenomics Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !2
  • 3. Phylogenomics I:Major Evolutionary Transitions Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 4. Phylogenomics I:Major Evolutionary Transitions • Analysis of S. pombe genome by Wood et al 2002 • Compared the genomes of eukaryotes to those of prokaryotes • “Are there genes found in all eukaryotes with no obvious homologs in any prokaryote?” Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 5. Evolutionary Model S. pombe Eukaryotes S. cerevisiae Encephalatozoon Archaea Bacteria Worm Fly Humans Dictyostelium Arabidopsis Chlamydomonas Phytophthora Tetrahymena Plasmodium Trypanosoma Euglena Naegleria Trichomonas Giardia Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 6. Eukaryotic Specific Genes • >200 genes found including: – Cytoskeleton components: tubulin, ankyrin, myosin – Protein degradation: ubiquitin, proteases – Chromatin and DNA packaging • Of the 200 many had no known function: could encode novel eukaryotic wide processes Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 7. Multi- vs. Single-Cellular Eukaryotes • Further analysis of S. pombe genome • Compared multi-cellular vs. single-cellular eukaryotes (animals and plants vs. yeast) • “Are there genes in all multi-cellular and not in any singlecellular?” • Found only 3 • Concluded that the genetic basis of multi-cellularity was likely to be gene regulation and not invention of new genes Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 8. Multiple Origins of Multicellularity Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 9. Phylogenomics II:
 Endosymbiont Evolution Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 10. Endosymbiont Evolution • Compared to free-living relatives – – – – Smaller genomes Lower GC content Higher pIs Higher rates of sequence evolution • Baumannia shows ALL of these Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 11. Uses of Whole Genome Trees Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 12. Wolbachia Evolution Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 13. Variation Between Endosymbionts and Free Living • Repair hypothesis ! • Population genetics hypothesis ! Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 14. Variation Between Endosymbionts and Free Living • Repair hypothesis ! • Population genetics hypothesis ! • PopGen explanations favored Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 15. Variation Among Endosymbionts Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 16. Variation Among Endosymbionts MutS MutL + + + + + + + + _ _ _ _ Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 17. Variation Among Endosymbionts • Repair hypothesis ! • Population genetics hypothesis ! Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 18. Variation Among Endosymbionts • Repair hypothesis ! • Population genetics hypothesis ! • Repair explanations favored Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 19. Phylogenomics III:
 Lateral Gene Transfer Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 20. Vertical Evolution From C. Darwin, origin of species, via W. F. Doolittle Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 21. Vertical Inheritance - Binary Bission Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 22. Lateral inheritance I: Competence Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 23. Lateral inheritance II: Conjugation Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 24. Agrobacterium conjugation Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 25. Figure 7.19 - Ab transfer Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 26. Lateral inheritance III: Transduction Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 27. Pathogenicity Island Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 28. Steps in Lateral Gene Transfer (LGT) A B C Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 D
  • 29. Steps in Lateral Gene Transfer (LGT) A B C 1 D Gene acquires host features Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 30. Steps in Lateral Gene Transfer (LGT) A B C D 2 Transfer 1 Gene acquires host features Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 31. Steps in Lateral Gene Transfer (LGT) A B C 3-5 D Integration, selection, spread 2 Transfer 1 Gene acquires host features Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 32. Steps in Lateral Gene Transfer (LGT) A B C D Amelioration Integration, selection, spread 6 3-5 2 Transfer 1 Gene acquires host features Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 33. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 34. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 35. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 36. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 37. How to Infer Gene Transfers • Unusual distribution patterns ! • Unusual nucleotide composition ! • High sequence similarity to supposedly distantly related species ! • Unusual gene trees ! • Observe transfer events Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 38. Case Study I: Aphids ig. 1 Coloration and carotenoids in the pea aphid. Typical green (A) and red (B) aphid clones, (C) 5AY, a green mutant clone arising from the red clone 5A. (D) rofiles of carotenoids in red (5A, LSR1), mutant redgreen (5AY, two samples), and green (8-10-1, 7-2-1) pea aphid clones. Torulene and a related red compound re restricted to red clones; the mutant 5AY clone lacks these and displays an elevation in their predicted precursor, -carotene. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 39. Case Study I: Aphids Table 1 Genes in the A. pisum genome with closest homology to carotenoid biosynthetic enzymes, including scaffold of origin and matching EST sequences. Similar color indicates that the gene is on the same scaffold. The 3' end of scaffold NW_001925130 overlaps with the 5' end of NW_001923501 for 5400 base pairs, and PCR demonstrated continuity of these scaffolds. Pink row is the gene corresponding to torR and conferring red color (see text). Protein length, amino acids; ESTs are those present in GenBank, mostly from clone LSR1. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 40. Case Study I: Aphids Fig. 2 Phylogenetic relations of inferred carotenoid biosynthetic enzymes from the pea aphid genome. (A) Carotenoid desaturases and (B) carotenoid cyclase– carotenoid synthases. Sequences are from aphids, bacteria, plants, and fungi; no homologs were detectable in other sequenced animal genomes. Bootstrap support greater than 50% is indicated on branches. ! Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 41. Case Study II: GEBA Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 42. Tree of Life Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 43. Genomes Poorly Sampled Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 44. TIGR Tree of Life Project Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 45. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !41
  • 46. Genomes Still Poorly Sampled Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 47. Genomic Encyclopedia of Bacteria & Archaea Wu et al. 2009 Nature 462, 1056-1060 Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 48. Genomic Encyclopedia of Bacteria & Archaea Wu et al. 2009 Nature 462, 1056-1060 Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 49. GEBA Lesson 1: rRNA utility in IDing novel genomes From Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !45
  • 50. GEBA Lesson 2: rRNA Tree is not perfect 16s WGT, 23S Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !46
  • 51. GEBA Lesson 3: Phylogenetic sampling improves 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 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !47
  • 52. GEBA Lesson 4 : Metadata Important Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !48
  • 53. GEBA Lesson 5:Improves discovering new genetic diversity Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !49
  • 54. Protein Family Rarefaction Curves • Take data set of multiple complete genomes • Identify all protein families using MCL • Plot # of genomes vs. # of protein families Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !50
  • 55. Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !51
  • 56. Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !51
  • 57. Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !51
  • 58. Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !51
  • 59. Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !51
  • 60. Synapomorphies exist Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !52
  • 61. Phylogenetic Distribution Novelty: Bacterial Actin Related Protein 87 C. boidinii  gi57157304 S. cerevisiae  gi14318479 L. starkeyi  gi166080363  S. japonicus  gi213407080 ACTIN A. cliftonii  gi14269497 U. pertusa  gi50355609 99 H. sapiens  gi4501889 M. cerebralis  gi46326807 67 C. cinerea  gi169844021 ARP1 N. crassa  gi85101929 100 I. scapularis  gi215507378  100 H. sapiens  gi5031569 51 65 S. japonicus  gi213404844 100 S. cerevisiae  gi6320175 ARP2 D. melanogaster  gi24642545 100 G. gallus  gi45382569 75 C. neoformans  gi58266690 S. cerevisiae  gi6322525 ARP3 100 D. melanogaster  gi17737543 100 H. sapiens  gi5031573  H. ochraceum  gi227395998 BARP S. cerevisiae  gi1008244  P. patens  gi168051992  ARP4 73 99 A. thaliana  gi18394608  94 S. cerevisiae  gi1301932 100 S. japonicus  gi213408393  ARP5 D. discoideum  gi66802418 D. melanogaster  gi17737347 74 S. cerevisiae  gi6323114 97 ARP6 100 D. hansenii gi21851 1921 100 O. sativa  gi182657420  ARP7 A. thaliana gi1841 1737 D. melanogater  gi19920358 100 M. musculus  gi226246593 ARP10 0.5  Haliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla, Victor Kunin See also Guljamow et al. 2007 Current Biology. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 62. GEBA Cyanobacteria A B1 B2 B3 D Paulinella C1 C2 C3 A E Glaucophyte Green Red G Chromalveolates F 0.3 B Shih et al. 2013. PNAS 10.1073/pnas.1217107110 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 Fig. mum noba
  • 63. Haloarchaeal GEBA-like Lynch et al. (2012) PLoS ONE 7(7): e41389. doi:10.1371/journal.pone.0041389 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 64. The Dark Matter of Biology From Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 65. GEBA Uncultured SAR A: Hydrothermal vent B: Gold Mine C: Tropical gyres (Mesopelagic) D: Tropical gyres (Photic zone) OP3 Site Site Site Site OP1 406 OD1 1 Number of SAGs from Candidate Phyla 4 6 1 1 13 - 2 - 2 - Sample collections at 4 additional sites are underway. Phil Hugenholtz !57 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 66. JGI Dark Matter Project brackish/freshwater TG HSM SM GBS GBS HOT OT SAK AK hydrothermal sediment ETL E BACTERIA ARCHAEA UGA recoded for Gly (Gracilibacteria) seawater HGT from Eukaryotes (Nanoarchaea) bioreactor EPR EPR T TA G GOM OM Growing AA chain U oxidoretucase Ribo A P51$ environmental samples (n=9) draft genomes (n=201) W51$*O
  • 67. recognizes UGA G isolation of single cells (n=9,600) SSU rRNA gene based identification (n=2,000) whole genome amplification (n=3,300) U genome sequencing, assembly and QC (n=201) 1 H H 1 1 $,$5 adenine +2+2 +2+2 OH 2+3 Woyke et al. Nature 2013. limiting phosphate, fatty acids, carbon, iron SpotT 1+ 2 1$'+ 51$ SROPHUDVH ı3 ı2 -10 ı1 GTP or GDP +ATP limiting amino acids RelA ppGpp (GTP or GDP) + PPi H DksA Expression of components for stress response O OH +2+2 O O O 1+ 1+ 2+3 2+3 tetrapeptide e- acceptor stringent response (Diapherotrites, Nanoarchaea) H +2+2 O IMP 1 1 O O 1+ ı4 -35 )$,$5 1 guanine O PurP O +2 1 H H H + ȕ ȕ¶ Į7' ? H 1 + 1+2 O Oxidation Archaea PurF PurD 3XU1 PurL/Q PurM PurK PurE 3XU PurB 1+2 1 O Į17' archaeal type purine synthesis (Microgenomates) 1 Eukaryota ADP sigma factor (Diapherotrites, Nanoarchaea) ribosome PRPP Reduction 1$'+ + + H- A U A U G U A A U G A U Ribo 1+ H Korarchaeota Cren Thermoprotei Thaumarchaeota Cren MCG Cren pISA7 Cren C2 Aigarchaeota Nanoarchaea Micrarchaea pMC2A384 (Diapherotrites) DSEG (Aenigmarchaea) Nanohaloarchaea Euryarchaeota :6 OP11 (Microgenomates) OD1 (Parcubacteria) SR1 BH1 TM7 GN02 (Gracilibacteria) Bacteriodetes OP1 (Acetothermia) 'HLQRFRFFXVí7KHUPXV 093í 70 ZB3 )LEUREDFWHUHV TG3 Spirochaetes WWE1 (Cloacamonetes) Proteobacteria )LUPLFXWHV Tenericutes )XVREDFWHULD Chrysiogenetes Chlorobi 6$5 0DULQLPLFURELD
  • 68. Caldithrix GOUTA4 Acidobacteria Elusimicrobia Nitrospirae 49S1 2B Chloroflexi Caldiserica AD3 OP9 (Atribacteria) :36í2 Synergistetes Thermodesulfobacteria Deferribacteres CD12 (Aerophobetes) OP8 (Aminicenantes) AC1 SBR1093 SPAM GAL15 Dictyoglomi EM3 Thermotogae Aquificae GAL35 EM19 (Calescamantes) 2FW6SDí )HUYLGLEDFWHULD
  • 69. Deltaproteobacteria Cyanobacteria :36í2 Actinobacteria Gemmatimonadetes NC10 SC4 WS2 NKB19 (Hydrogenedentes) WYO Armatimonadetes WS4 Planctomycetes Chlamydiae OP3 (Omnitrophica) Lentisphaerae Verrucomicrobia BRC1 Poribacteria WS1 +Gí LD1 GN01 WS3 (Latescibacteria) GN04 + e- donor ADP archaeal toxins (Nanoarchaea) 1+ 2+3 tetrapeptide murein (peptido-glycan) lytic murein transglycosylase Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 70. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 71. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  • 72. GEBA Lesson 6: Improves analysis of metagenomic data Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !61
  • 73. Other Markers Sargasso Phylotypes 0.500 GEBA Project improves metagenomic analysis EFG EFTu HSP70 RecA RpoB rRNA 0.250 0.125 us ar ch ae ot C a re na rc ha eo ta er m er ia ct Th ba Eu cc u in o co ry s- so iro c ha et es ex i Sp hl or ofl C FB C Fu De ap ro t eo ba Be ct ta er pr ia ot eo ba G am ct er m ia ap ro te ob Ep ac si lo te np ria ro te ob De ac lta te pr ria ot eo ba ct C er ya ia no ba ct er ia Fi rm ic ut es Ac tin ob ac te ria C hl or ob i 0.000 Al ph Weighted % of Clones 0.375 Major Phylogenetic Group Venter et Eisen Winter 304: Slides for UC Davis EVE161 Course Taught by Jonathan al., Science2014 66-74. 2004 !62
  • 74. Venter et Eisen Winter 304: Major Phylogenetic Group Slides for UC Davis EVE161 Course Taught by Jonathan al., Science2014 ar ch re n C ot a ae a ot us rm ria s te te ae ry ar ch Eu Th e s- cu oc De in oc ac so b Fu ae ch Sp iro xi or ofl e hl C FB C i or ob hl C ria te ob ac tin Ac es ut ic rm Fi ria ria te ac ob ya n C te ia er ia er ct ba c eo pr ot lta De ct eo ba ro t np si lo ria te 0.375 Ep eo ba ro t ap am m G ba c eo ia er ct ba eo pr ot pr ot ta ph a Be Al Weighted % of Clones Other Markers 0.500 Sargasso Phylotypes But not a lot EFG rRNA 66-74. 2004 EFTu 0.250 0.125 0.000 !63
  • 75. rRNA Tree of Life Bacteria Archaea Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press. 2007. Based on tree from Pace 1997 Science 276:734-740 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !64
  • 76. PD: Genomes
 From Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !65
  • 77. PD: Genomes + GEBA
 From Wu et al. 2009 Nature 462, 1056-1060 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !66
  • 78. PD: Isolates From Wu et al. 2009 Nature 462, Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 1056-1060 !67
  • 79. PD: All From Wu et al. 2009 Nature 462, Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 1056-1060 !68
  • 80. Uncultured Lineages:
 Technical Approaches • Get into culture • Enrichment cultures • If abundant in low diversity ecosystems • Flow sorting • Microbeads • Microfluidic sorting • Single cell amplification Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !69
  • 81. GEBA uncultured SAR A: Hydrothermal vent B: Gold Mine C: Tropical gyres (Mesopelagic) D: Tropical gyres (Photic zone) OP3 Site Site Site Site OP1 406 OD1 1 Number of SAGs from Candidate Phyla 4 6 1 1 13 - 2 - 2 - Sample collections at 4 additional sites are underway. Phil Hugenholtz Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !70

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