Phylogenomics and the Diversification of Microbes, J. A. Eisen at Genentech 1/27/11
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Phylogenomics and the Diversification of Microbes, J. A. Eisen at Genentech 1/27/11
- 1. Phylogenomics and the Diversity and Diversification of Microbes Jonathan A. Eisen UC Davis Genentech Talk January 27, 2011 Friday, January 28, 2011
- 2. My Obsessions Jonathan A. Eisen UC Davis UCSD Talk January 19, 2011 Friday, January 28, 2011
- 3. Friday, January 28, 2011
- 4. Social Networking in Science HOME PAGE MY TIMES TODAY'S PAPER VIDEO MOST POPULAR TIMES TOPICS Welcome, fcollins Member Center Log Out Sunday, April 1, 2007 Health WORLD 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 & BEHAVIOR Scientist Reveals Secret of the Ocean: It's Him By NICHOLAS WADE Published: April 1, 2007 PRINT nytimes.com/sports Maverick scientist J. Craig Venter has done it again. It was just a few years SINGLE-PAGE ago that Dr. Venter announced that the human genome sequenced by Celera SAVE Genomics was in fact, mostly his own. And now, Venter has revealed a second SHARE twist in his genomic self-examination. Venter was discussing his Global SHARE Ocean Voyage, in which he used his personal yacht to collect ocean water samples 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 sports microbes 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 Final sequence the human genome to study the genomes of the 1000s of ocean Four dwelling 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 athlete latest attack on the standards of science – some of the samples were in fact not from the ocean, but were 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 my genome 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 a hot research topic. So hot that the same people who were involved in the race to sequence the human genome have been involved in this race too. Francis Collins, Venter main competitor and still the Friday, January 28, 2011 director of the National Human Genome Research Institute (NHGRI), recently testified before
- 5. Bacterial evolve Friday, January 28, 2011
- 6. Research Areas Friday, January 28, 2011
- 7. Research Areas Mechanisms of Origin of New Functions Friday, January 28, 2011
- 8. Research Areas Mechanisms of Variation in Origin of New Mechanisms: Functions Patterns, Causes and Effects Friday, January 28, 2011
- 9. Research Areas Mechanisms of Variation in Origin of New Mechanisms: Functions Patterns, Causes and Effects Species Evolution Friday, January 28, 2011
- 10. Research Areas • Study the evolution of function • Make extensive use of genome sequence data • Requires integration of experimental information and genome analysis • Categorize and classify ways that novelty originates (examples) • Duplication and divergence • Recombination • Simple substitutions • Gene transfer Friday, January 28, 2011
- 11. Research Areas • Study the evolution of function • Make extensive use of genome Mechanisms of sequence data Origin of New • Requires integration of Functions experimental information and genome analysis • Categorize and classify ways that novelty originates (examples) • Duplication and divergence • Recombination • Simple substitutions • Gene transfer Friday, January 28, 2011
- 12. Research Areas • Patterns of variation • Within species • Between species • Comparative genomics plays important role • Causes • Variation in RRR • Regulatory complexity • Effects • Differences in evolvability • Ecological niche • Short and long term genome evolution Friday, January 28, 2011
- 13. Research Areas • Patterns of variation • Within species Variation in • Between species Mechanisms: • Comparative genomics plays Patterns, Causes important role and Effects • Causes • Variation in RRR • Regulatory complexity • Effects • Differences in evolvability • Ecological niche • Short and long term genome evolution Friday, January 28, 2011
- 14. Research Areas • Information needed to distinguish convergence from homology • Allows inference of rates and patterns of change • Allows one to determine if something is a “one time” event or a common theme in many lineages Friday, January 28, 2011
- 15. Research Areas • Information needed to distinguish convergence from homology • Allows inference of rates and patterns of change • Allows one to determine if something is a “one time” event or a common theme in many lineages Species Evolution Friday, January 28, 2011
- 16. Phylogenomics of Novelty Variation in Mechanisms of Mechanisms: Origin of New Patterns, Causes Functions and Effects Species Evolution Friday, January 28, 2011
- 17. Why do this? • Discover causes and effects of differences in evolvability • Improve predictions from genome analysis • Guide interpretation of biological dat Friday, January 28, 2011
- 18. My microbial evolution obsessions • Introduction • Phylogenomic Stories – Within genome invention of novelty – Stealing novelty – Community service Friday, January 28, 2011
- 19. Introduction Genome Sequencing Friday, January 28, 2011
- 20. Fleischmann et al. 1995 Friday, January 28, 2011
- 21. From http://genomesonline.org Friday, January 28, 2011
- 22. Friday, January 28, 2011
- 23. Friday, January 28, 2011
- 24. Friday, January 28, 2011
- 25. Human commensals Friday, January 28, 2011
- 26. From http://genomesonline.org Friday, January 28, 2011
- 27. Phylogenomics of Novelty I Origin of Functions from Within Friday, January 28, 2011
- 28. Origin of New Functions • Many different processes contribute to the origin of novelty • Denovo invention of new genes • Simple substitutions within existing genes • Duplication and divergence • Domain swapping • Genome rearrangements • Regulatory changes Friday, January 28, 2011
- 29. Origin of New Functions • Many different processes contribute to the origin of novelty Mechanisms of • Denovo invention of new Origin of New genes Functions • Simple substitutions within existing genes • Duplication and divergence • Domain swapping • Genome rearrangements • Regulatory changes Friday, January 28, 2011
- 30. Phylogenomics of Novelty Variation in Mechanisms of Mechanisms: Origin of New Patterns, Causes Functions and Effects Species Evolution Friday, January 28, 2011
- 31. Example I: Mutation Rates and Functional Predictions Friday, January 28, 2011
- 32. From Eisen et al. 1997 Nature Medicine 3: 1076-1078. Friday, January 28, 2011
- 33. 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 • Assumes functional constancy Based on Eisen et al. 1997 Nature Medicine 3: 1076-1078. Friday, January 28, 2011
- 34. MutL?? Based on Eisen et al. 1997 Nature Medicine 3: 1076-1078. Friday, January 28, 2011
- 35. 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. Friday, January 28, 2011
- 36. 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 Human MSH3 Mouse Fly Spombe Yeast Xenla Rat Mouse Yeast MSH1 Spombe Human Yeast MSH2 Neucr Arath Aquae Trepa Chltr DeiraTheaq BacsuBorbu Thema SynspStrpy Ecoli Neigo Based on Eisen, 1998 Nucl Acids MutS1 Res 26: 4291-4300. Friday, January 28, 2011
- 37. MutS Subfamilies • MutS1 Bacterial MMR • MSH1 Euk - mitochondrial MMR • MSH2 Euk - all MMR in nucleus • MSH3 Euk - loop MMR in nucleus • MSH6 Euk - base:base MMR in nucleus • MutS2 Bacterial - function unknown • MSH4 Euk - meiotic crossing-over • MSH5 Euk - meiotic crossing-over Friday, January 28, 2011
- 38. Overlaying Functions onto Tree MutS2 Aquae MSH5 Strpy Bacsu Synsp Deira Helpy Yeast Human Borbu Metth Celeg MSH6 mSaco Yeast Human Mouse Arath Yeast MSH4 Celeg Human Arath Human MSH3 Mouse Fly Spombe Yeast Xenla Rat Mouse Yeast Human MSH1 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. Friday, January 28, 2011
- 39. Functional Prediction Using Tree MSH5 - Meiotic Crossing Over MutS2 - Unknown Functions Aquae Strpy Bacsu Synsp Deira Helpy Yeast Human Borbu Metth Celeg MSH6 - Nuclear mSaco Repair Of Mismatches Yeast Human MSH4 - Meiotic Crossing Mouse Yeast Over Arath Celeg Human Arath MSH3 - Nuclear Human Mouse RepairOf Loops Spombe Fly Yeast Xenla Rat Mouse MSH2 - Eukaryotic Nuclear Yeast Human Mismatch and Loop Repair MSH1 Spombe Yeast Mitochondrial Neucr Arath Repair 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. Friday, January 28, 2011
- 40. Friday, January 28, 2011
- 41. Evolutionary Functional Prediction 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? 1 2 3 4 5 6 1A 2A 3A 1B 2B 3B 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. Friday, January 28, 2011
- 42. Example 2: Recent Changes • Phylogenomic functional prediction NJ * ** V.cholerae0512 VC V.cholerae VCA1034 V.cholerae VC V.cholerae VC V.cholerae VC A0974 A0068 V.cholerae VC 0825 0282 may not work well for very newly V.cholerae VCA0906 V.cholerae VC A0979 V.cholerae VCA1056 V.cholerae VC1643 V.cholerae VC2161 ** V.cholerae VCA0923 ** V.cholerae VC0514 V.cholerae VC 1868 V.cholerae VC A0773 V.cholerae VC1313 evolved functions V.cholerae VC 1859 V.cholerae VC1413 V.cholerae VCA0268 ** V.cholerae VC A0658 V.cholerae VC 1405 * V.cholerae VC1298 V.cholerae VC1248 V.cholerae VCA0864 V.cholerae VCA0176 ** V.cholerae VCA0220 V.cholerae VC 1289 ** V.cholerae VC1069 A V.cholerae VC2439 • Can we use understanding of origin of V.cholerae VC967 1 V.cholerae VC A0031 V.cholerae VC1898 V.cholerae VC A0663 V.cholerae VC0988 A V.cholerae VC0216 * V.cholerae VC0449 V.cholerae VCA0008 V.cholerae VC1406 V.cholerae VC 1535 novelty to better understand these V.cholerae VC0840 B.subtilis gi2633766 Synechocystis sp. gi1001299 * Synechocystis sp.gi1001300 * Synechocystis sp. gi1652276 * Synechocystis sp. gi1652103 H.pylori gi2313716 ** **H.pylori 99 gi4155097 C.jejuni Cj1190c C.jejuni Cj1110c A.fulgidus gi2649560 cases? A.fulgidus gi2649548 ** B.subtilis gi2634254 B.subtilis gi2632630 B.subtilis gi2635607 B.subtilis gi2635608 ** B.subtilis gi2635609 ** ** B.subtilisgi2635882 gi2635610 B.subtilis E.coligi1788195 E.coli gi2367378 * ** E.coligi1788194 E.coli A1092 gi1787690 V.cholerae VC • Screen genomes for genes that have V.cholerae VC 0098 E.coli gi1789453 H.pylori gi2313186 H.pylori 99 gi4154603 ** C.jejuni Cj0144 C.jejuni Cj1564 **C.jejuni C.jejuni Cj0262c Cj1506c ** H.pylori gi2313163 * H.pylori 99 gi4154575 changed recently **H.pylori gi2313179 ** H.pylori 99 gi4154599 ** C.jejuni Cj0019c C.jejuni Cj0951c C.jejuni Cj0246c B.subtilis gi2633374 T.maritima TM0014 V.cholerae VC1403 V.cholerae VCA1088 T.pallidum gi3322777 ** T.pallidum gi3322939 ** T.pallidum gi3322938 – Pseudogenes and gene loss B.burgdorferi gi2688522 T.pallidum gi3322296 B.burgdorferi gi2688521 * T.maritima TM0429 **T.maritima TM0918 * **T.maritima T.maritima TM0023 TM1428 T.maritima TM1143 T.maritima TM1146 P.abyssi PAB1308 P.horikoshii gi3256846 – Contingency Loci ** P.abyssiPAB1336 ** P.horikoshii gi3256896 ** **P.abyssi PAB2066 ** P.horikoshii ** P.abyssi gi3258290 * PAB1026 ** P.horikoshii DRA00354 gi3256884 D.radiodurans D.radiodurans ** D.radioduransDRA0353 ** DRA0352 ** V.cholerae VC 1394 P.abyssi PAB1189 P.horikoshii gi3258414 – Acquisition (e.g., LGT) ** B.burgdorferi gi2688621 M.tuberculosis gi1666149 V.cholerae VC 0622 – Unusual dS/dN ratios – Rapid evolutionary rates Friday, January 28, 2011
- 43. Example II: Duplication Friday, January 28, 2011
- 44. Friday, January 28, 2011
- 45. Expansion of MCP Family in V. cholerae NJ V.cholerae VC0512 V.cholerae VCA1034 V.cholerae VCA0974 V.cholerae VCA0068 ** V.cholerae VC0825 * V.cholerae VC0282 V.cholerae VCA0906 V.cholerae VCA0979 V.cholerae VCA1056 V.cholerae VC1643 V.cholerae VC2161 V.cholerae VCA0923 ** V.cholerae VC0514 ** V.cholerae VC1868 V.cholerae VCA0773 V.cholerae VC1313 V.cholerae VC1859 V.cholerae VC1413 V.cholerae VCA0268 ** V.cholerae VCA0658 V.cholerae VC1405 V.cholerae VC1298 * V.cholerae VC1248 V.cholerae VCA0864 V.cholerae VCA0176 ** V.cholerae VCA0220 V.cholerae VC1289 ** V.cholerae VCA1069 V.cholerae VC2439 V.cholerae VC1967 V.cholerae VCA0031 V.cholerae VC1898 V.cholerae VCA0663 V.cholerae VCA0988 V.cholerae VC0216 * V.cholerae VC0449 V.cholerae VCA0008 V.cholerae VC1406 V.cholerae VC1535 V.cholerae VC0840 B.subtilis gi2633766 Synechocystis sp. gi1001299 * Synechocystis sp. gi1001300 * Synechocystis sp. gi1652276 * Synechocystis sp. gi1652103 H.pylori gi2313716 H.pylori99 gi4155097 ** C.jejuni Cj1190c ** 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.cholerae VCA1092 V.cholerae VC0098 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.cholerae VC1403 V.cholerae VCA1088 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 * Based on Heidelberg et al. P.abyssi PAB1026 ** P.horikoshii gi3256884 D.radiodurans DRA00354 ** D.radiodurans DRA0353 D.radiodurans DRA0352 2000 Nature 406:477-483. ** ** V.cholerae VC1394 P.abyssi PAB1189 P.horikoshii gi3258414 ** B.burgdorferi gi2688621 M.tuberculosis gi1666149 V.cholerae VC0622 Friday, January 28, 2011
- 46. Tetrahymena Genome Processing • Probably exists as a defense mechanism • Analogous to RIPPING and heterochromatin silencing • Presence of repetitive DNA in MAC but not TEs suggests the mechanism involves targeting foreign DNA • Thus unlike RIPPING ciliate processing does not limit diversification by duplication Eisen et al. 2006. PLoS Biology. Friday, January 28, 2011
- 47. Phylogenomics of Novelty II Sometimes, it is easier to steal, borrow, or coopt functions rather than evolve them anew Friday, January 28, 2011
- 48. Stealing DNA Friday, January 28, 2011
- 49. rRNA Tree of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Friday, January 28, 2011
- 50. Perna et al. 2003 Friday, January 28, 2011
- 51. Network of Life Bacteria Archaea Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Friday, January 28, 2011
- 52. Non homology functional prediction 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 Friday, January 28, 2011
- 53. 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 Friday, January 28, 2011
- 54. 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) Friday, January 28, 2011
- 55. 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. ) Friday, January 28, 2011
- 56. Homologs of Sporulation Genes Wu et al. 2005 PLoS Genetics 1: e65. Friday, January 28, 2011
- 57. Carboxydothermus sporulates Wu et al. 2005 PLoS Genetics 1: e65. Friday, January 28, 2011
- 58. Wu et al. 2005 PLoS Genetics 1: e65. Friday, January 28, 2011
- 59. Stealing Organisms (Symbioses) Friday, January 28, 2011
- 60. Friday, January 28, 2011
- 61. Friday, January 28, 2011
- 62. Glassy Winged Sharpshooter • Feeds on xylem sap • Vector for Pierce’s Disease • Potential bioterror agent Friday, January 28, 2011
- 63. Xylem and Phloem From Lodish et al. 2000 Friday, January 28, 2011
- 64. Sharpshooter Shotgun Sequencing shotgun Collaboration with Nancy Wu et al. 2006 PLoS Biology 4: e188. Moran’s lab Friday, January 28, 2011
- 65. Friday, January 28, 2011
- 66. Friday, January 28, 2011
- 67. Friday, January 28, 2011
- 68. Higher Evolutionary Rates in Endosymbionts Wu et al. 2006 PLoS Biology 4: e188. Collaboration with Nancy Moran’ s Lab Friday, January 28, 2011
- 69. Variation in Evolution Rates MutS MutL + + + + + + + + _ _ _ _ Wu et al. 2006 PLoS Biology 4: e188. Collaboration with Nancy Moran’ s Lab Friday, January 28, 2011
- 70. Baumannia is a Vitamin and Cofactor Producing Machine Wu et al. 2006 PLoS Biology 4: e188. Friday, January 28, 2011
- 71. No Amino-Acid Synthesis Friday, January 28, 2011
- 72. Friday, January 28, 2011
- 73. The Uncultured Majority Friday, January 28, 2011
- 74. Great Plate Count Anomaly Culturing Microscope Count Count Friday, January 28, 2011
- 75. Great Plate Count Anomaly Culturing Microscope Count <<<< Count Friday, January 28, 2011
- 76. Great Plate Count Anomaly DNA Culturing Microscope Count <<<< Count Friday, January 28, 2011
- 77. PCR Saves the Day Friday, January 28, 2011
- 78. rRNA: A Phylogenetic Anchor to Determine Who’s Out There Eisen et al. 1992 Friday, January 28, 2011
- 79. rRNA: A Phylogenetic Anchor to Determine Who’s Out There Eisen et al. 1992 Friday, January 28, 2011
- 80. Uses of rRNA sequences The Hidden Majority Richness estimates Hugenholtz 2002 Bohannan and Hughes 2003 Friday, January 28, 2011
- 81. Friday, January 28, 2011
- 82. rRNA data increasing exponentially too Friday, January 28, 2011
- 83. rRNA phylotyping issues • Massive amounts of data – 1 x 10^6 new partial sequences with new 454 – 2 x 10^6 full length sequences in DB • Alignments of new sequences not always straightforward • Solutions: – Reliance on similarity scores (bad) – High throughput automated phylogenetic tools • STAP • WATERs Friday, January 28, 2011
- 84. rRNA: A Phylogenetic Anchor to Determine Who’s Out There Eisen et al. 1992 Friday, January 28, 2011
- 85. rRNA: A Phylogenetic Anchor to Determine Who’s Out There Eisen et al. 1992 Friday, January 28, 2011
- 86. rRNA: A Phylogenetic Anchor to Determine Who’s Out There Eisen et al. 1992 Friday, January 28, 2011
- 87. rRNA: A Phylogenetic Anchor to Determine Who’s Out There Biology not Eisen et similar enough al. 1992 Friday, January 28, 2011
- 88. Perna et al. 2003 Friday, January 28, 2011
- 89. Metagenomics shotgun clone Friday, January 28, 2011
- 90. Friday, January 28, 2011
- 91. How can we best use metagenomic data? • Many possible uses including: – Improvements on rRNA based phylotyping and species diversity measurements – Adding functional information on top of phylogenetic/species diversity information • Most/all possible uses either require or are improved with phylogenetic analysis Friday, January 28, 2011
- 92. Example I: Phylotyping with rRNA and other genes Friday, January 28, 2011
- 93. 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 ob am ac Friday, January 28, 2011 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 ter n ob ia ac t er Fi ia rm ic u te Ac s tin ob ac t er C ia hl or ob i C FB Major Phylogenetic Group Sargasso Phylotypes C hl or ofl xi e Sp iro ch ae te Fu so s 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 EFG Venter et al., Science 304: 66-74. 2004 EFTu rRNA RecA RpoB HSP70
- 94. Functional Diversity of Proteorhodopsins? Venter et al., 2004 Friday, January 28, 2011
- 95. Example II: Binning Friday, January 28, 2011
- 96. Metagenomics Challenge Friday, January 28, 2011
- 97. Binning challenge A T B U C V D W E X F Y G Z Friday, January 28, 2011
- 98. Binning challenge A T B U C V D W E X F Y G Best binning method: reference genomes Z Friday, January 28, 2011
- 99. Binning challenge A T B U C V D W E X F Y G Best binning method: reference genomes Z Friday, January 28, 2011
- 100. Binning challenge A T B U C V D W E X F Y G No reference genome? What do you do? Z Friday, January 28, 2011
- 101. Binning challenge A T B U C V D W E X F Y G No reference genome? What do you do? Z Phylogeny .... Friday, January 28, 2011
- 102. Friday, January 28, 2011
- 103. No Amino-Acid Synthesis Friday, January 28, 2011
- 104. Friday, January 28, 2011
- 105. ??????? Friday, January 28, 2011
- 106. 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 Friday, January 28, 2011
- 107. CFB Phyla Friday, January 28, 2011
- 108. Binning by Phylogeny • Four main “phylotypes” – Gamma proteobacteria (Baumannia) – Arthropoda (sharpshooter) – Bacteroidetes (Sulcia) – Alpha-proteobacteria (Wolbachia) Friday, January 28, 2011
- 109. Binning by Phylogeny • Four main “phylotypes” – Gamma proteobacteria (Baumannia) – Arthropoda (sharpshooter) – Bacteroidetes (Sulcia) - only a.a. genes here – Alpha-proteobacteria (Wolbachia) Friday, January 28, 2011
- 110. Wu et al. 2006 PLoS Biology 4: e188. Friday, January 28, 2011
- 111. Essential Amino Acid Synthesis Wu et al. 2006 PLoS Biology 4: e188. Friday, January 28, 2011
- 112. Sulcia makes amino acids Baumannia makes vitamins and cofactors Wu et al. 2006 PLoS Biology 4: e188. Friday, January 28, 2011
- 113. Phylogenomics of Novelty III Knowing What We Don’t Know Friday, January 28, 2011
- 114. As of 2002 Friday, January 28, 2011
- 115. 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 Friday, January 28, 2011