Phylogenomics Talk at UC Berkeley by J. A. Eisen

Phylogenomics and the Diversity and Diversiﬁcation of Microbes Jonathan A. Eisen UC Davis UC Berkeley Talk February 3, 2011Monday, February 14, 2011

My Obsessions Jonathan A. Eisen UC Davis UC Berkeley Talk February 3, 2011Monday, February 14, 2011

Monday, February 14, 2011

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 humangenome have been involved in this race too. Francis Collins, Venter main competitor and still the Monday, February 14, 2011director of the National Human Genome Research Institute (NHGRI), recently testified before

Bacterial evolveMonday, February 14, 2011

Phylogenomics of NoveltyMonday, February 14, 2011

Phylogenomics of Novelty Mechanisms of Origin of New FunctionsMonday, February 14, 2011

Phylogenomics of Novelty Mechanisms of Variation in Origin of New Mechanisms: Functions Patterns, Causes and EffectsMonday, February 14, 2011

Phylogenomics of Novelty Mechanisms of Variation in Origin of New Mechanisms: Functions Patterns, Causes and Effects Species EvolutionMonday, February 14, 2011

Phylogenomics of Novelty • How does novelty originate? • Major categories of processes • From within • De novo invention • Simple substitutions • Duplication and divergence • Domain shuffling • Small & large rearrangements • Regulatory changes • From outside • Lateral gene transfer • SymbiosesMonday, February 14, 2011

Phylogenomics of Novelty • How does novelty originate? • Major categories of processes Mechanisms of • From within Origin of New • De novo invention Functions • Simple substitutions • Duplication and divergence • Domain shuffling • Small & large rearrangements • Regulatory changes • From outside • Lateral gene transfer • SymbiosesMonday, February 14, 2011

Phylogenomics of Novelty • Patterns of variation • Within species • Between species • Causes • Variation in replication, recombination and repair • Effects • Differences in evolvability • Ecological niche • Short and long term genome evolutionMonday, February 14, 2011

Phylogenomics of Novelty • Patterns of variation • Within species Variation in • Between species Mechanisms: • Causes Patterns, Causes • Variation in replication, and Effects recombination and repair • Effects • Differences in evolvability • Ecological niche • Short and long term genome evolutionMonday, February 14, 2011

Phylogenomics of Novelty • 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 lineagesMonday, February 14, 2011

Phylogenomics of Novelty • 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 EvolutionMonday, February 14, 2011

Phylogenomics of Novelty Variation in Mechanisms of Mechanisms: Origin of New Patterns, Causes Functions and Effects Species EvolutionMonday, February 14, 2011

Phylogenomics of Novelty Variation in Mechanisms of Mechanisms: Origin of New Patterns, Causes Functions and Effects Focus Today on Using Sequence Information for All of This Species EvolutionMonday, February 14, 2011

Why do this? • Discover causes and effects of differences in evolvability • Improve predictions from genome analysis • Guide interpretation of biological dataMonday, February 14, 2011

Outline • Introduction • Phylogenomic Stories – Within genome invention of novelty – Stealing novelty – Communities of microbes – Community service and knowing what we don’t knowMonday, February 14, 2011

Introduction Genome SequencingMonday, February 14, 2011

rRNA Tree of Life FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.Monday, February 14, 2011

Limited Sampling of RRR Studies FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.Monday, February 14, 2011

Limited Sampling of RRR Studies Haloferax Methanococcus Chlorobium Deinococcus Thermotoga FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.Monday, February 14, 2011

UV Survival E.coli vs H.volcanii 1 Ecoli vs. Hvolcanii 0.1 0.01Relative 0.001Survival 0.0001 1E-05 1E-06 1E-07 0 50 100 150 200 250 300 350 400 UV J/m2 E.coli NR10121 mfd- E.coli NR10125 mfd+ TIGR H.volcanii WFD11Monday, February 14, 2011

H. volcanii UV Repair Label 7 - 45J / m2) 0.6 Label5#2 0 J/m2 t0 45 J/m2 t0 45 J/m2 Photoreac. 45 J/m2 Dark 24 Hours 0.4 0.2 0 0 2000 4000 6000 8000 10000 12000 14000 16000 18000 Avg. Mol. Wt.(Base Pairs)Monday, February 14, 2011

Fleischmann et al. 1995Monday, February 14, 2011

Limited Sampling of RRR Studies Haloferax Methanococcus Chlorobium Deinococcus Thermotoga FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.Monday, February 14, 2011

From http://genomesonline.orgMonday, February 14, 2011

Human commensalsMonday, February 14, 2011

From http://genomesonline.orgMonday, February 14, 2011

Phylogenomics of Novelty I Origin of Functions from WithinMonday, February 14, 2011

Phylogenomics of Novelty • How does novelty originate? • Major categories of processes • From within • De novo invention • Simple substitutions • Duplication and divergence • Domain shuffling • Small & large rearrangements • Regulatory changes • From outside • Lateral gene transfer • SymbiosesMonday, February 14, 2011

Phylogenomics of Novelty • How does novelty originate? • Major categories of processes Mechanisms of • From within Origin of New • De novo invention Functions • Simple substitutions • Duplication and divergence • Domain shuffling • Small & large rearrangements • Regulatory changes • From outside • Lateral gene transfer • SymbiosesMonday, February 14, 2011

From Eisen et al. 1997 Nature Medicine 3: 1076-1078.Monday, February 14, 2011

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.Monday, February 14, 2011

Predicting Function • Identification of motifs – Short regions of sequence similarity that are indicative of general activity – e.g., ATP binding • Homology/similarity based methods – Gene sequence is searched against a databases of other sequences – If significant similar genes are found, their functional information is used • Problem – Genes frequently have similarity to hundreds of motifs and multiple genes, not all with the same functionMonday, February 14, 2011

MutL?? Based on Eisen et al. 1997 Nature Medicine 3: 1076-1078.Monday, February 14, 2011

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.Monday, February 14, 2011

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.Monday, February 14, 2011

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 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 interpret these cases? 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 A.fulgidus gi2649548 ** B.subtilis gi2634254 • Screen genomes for genes that have 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 changed recently 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 ** H.pylori gi2313179 H.pylori 99 gi4154599 – Pseudogenes and gene loss ** 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 – Contingency Loci 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 ** P.abyssiPAB1336 – Acquisition (e.g., LGT) ** 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 – Unusual dS/dN ratios ** B.burgdorferi gi2688621 M.tuberculosis gi1666149 V.cholerae VC 0622 – Rapid evolutionary rates – Recent duplicationsMonday, February 14, 2011

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.Monday, February 14, 2011

Conclusions • Enormous variation in processes underlying origin of novelty • See within genomes -> between species • Knowledge about mechanisms and variation helps predictions of function and biology from analysis of sequence dataMonday, February 14, 2011

Phylogenomics of Novelty II Sometimes, it is easier to steal, borrow, or coopt functions rather than evolve them anewMonday, February 14, 2011

Stealing DNAMonday, February 14, 2011

rRNA Tree of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.Monday, February 14, 2011

Perna et al. 2003Monday, February 14, 2011

Network of Life Bacteria Archaea Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.Monday, February 14, 2011

A. thaliana T1E2.8 is a Chloroplast Derived HSP60Monday, February 14, 2011

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.Monday, February 14, 2011

Correlated gain/loss of genes • 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 functionsMonday, February 14, 2011

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)Monday, February 14, 2011

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. )Monday, February 14, 2011

Homologs of Sporulation Genes Wu et al. 2005 PLoS Genetics 1: e65.Monday, February 14, 2011

Carboxydothermus sporulates Wu et al. 2005 PLoS Genetics 1: e65.Monday, February 14, 2011

Wu et al. 2005 PLoS Genetics 1: e65.Monday, February 14, 2011

Stealing Organisms (Symbioses)Monday, February 14, 2011

Mutualistic Genome Evolution • Compare and contrast different types of mutualistic symbioses • Diverse hosts, symbionts, biology, ages • Organelles, chemosymbioses, photosynthetic symbioses, nutritional symbioses • What are the rules & patterns?Monday, February 14, 2011

Glassy Winged Sharpshooter • Feeds on xylem sap • Vector for Pierce’s Disease • Potential bioterror agentMonday, February 14, 2011

Sharpshooter Shotgun Sequencing shotgun Collaboration with Nancy Wu et al. 2006 PLoS Biology 4: e188. Moran’s labMonday, February 14, 2011

Higher Evolutionary Rates in Endosymbionts Wu et al. 2006 PLoS Biology 4: e188. Collaboration with Nancy Moran’ s LabMonday, February 14, 2011

Variation in Evolution Rates MutS MutL + + + + + + + + _ _ _ _ Wu et al. 2006 PLoS Biology 4: e188. Collaboration with Nancy Moran’ s LabMonday, February 14, 2011

Polymorphisms in Metapopulation • Data from ~200 hosts – 104 SNPs – 2 indels • PCR surveys show that this is between host variation • Much lower ratio of transitions:transversions than in Blochmannia • Consistent with absence of MMR from BlochmanniaMonday, February 14, 2011

Baumannia is a Vitamin and Cofactor Producing Machine Wu et al. 2006 PLoS Biology 4: e188.Monday, February 14, 2011

No Amino-Acid SynthesisMonday, February 14, 2011

The Uncultured MajorityMonday, February 14, 2011

Great Plate Count Anomaly Culturing Microscope Count CountMonday, February 14, 2011

Great Plate Count Anomaly Culturing Microscope Count <<<< CountMonday, February 14, 2011

Great Plate Count Anomaly DNA Culturing Microscope Count <<<< CountMonday, February 14, 2011

rRNA PCR The Hidden Majority Richness estimates Hugenholtz 2002 Bohannan and Hughes 2003Monday, February 14, 2011

rRNA data increasing exponentially tooMonday, February 14, 2011

Perna et al. 2003Monday, February 14, 2011

Metagenomics shotgun cloneMonday, February 14, 2011

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 analysisMonday, February 14, 2011

Example I: Phylotyping with rRNA and other genesMonday, February 14, 2011

Functional Diversity of Proteorhodopsins? Venter et al., 2004Monday, February 14, 2011

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 m t er ap iaMonday, February 14, 2011 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 of le Sp xi 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

Example II: BinningMonday, February 14, 2011

Metagenomics ChallengeMonday, February 14, 2011

Binning challenge A T B U C V D W E X F Y G ZMonday, February 14, 2011

Binning challenge A T B U C V D W E X F Y G Best binning method: reference genomes ZMonday, February 14, 2011

Binning challenge A T B U C V D W E X F Y G No reference genome? What do you do? ZMonday, February 14, 2011

Binning challenge A T B U C V D W E X F Y G No reference genome? What do you do? Z Phylogeny ....Monday, February 14, 2011

No Amino-Acid SynthesisMonday, February 14, 2011

???????Monday, February 14, 2011

CFB PhylaMonday, February 14, 2011

Sulcia makes amino acids Baumannia makes vitamins and cofactors Wu et al. 2006 PLoS Biology 4: e188.Monday, February 14, 2011

Phylogenomics of Novelty III Knowing What We Don’t KnowMonday, February 14, 2011

Research Topics Variation in Mechanisms of Mechanisms: Origin of New Patterns, Causes Functions and Effects Species EvolutionMonday, February 14, 2011

As of 2002Monday, February 14, 2011

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, 2002Monday, February 14, 2011

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, 2002Monday, February 14, 2011

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, 2002Monday, February 14, 2011

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 Eisen, Ward, Aquiﬁcae Thermudesulfobacteria sequence more Robb, Nelson, et Thermotogae phyla OP1 al OP11Monday, February 14, 2011

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 OP11Monday, February 14, 2011

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 OP11Monday, February 14, 2011

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 OP11Monday, February 14, 2011

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 OP11Monday, February 14, 2011

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 OP11Monday, February 14, 2011

http://www.jgi.doe.gov/programs/GEBA/pilot.htmlMonday, February 14, 2011

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)Monday, February 14, 2011

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 100+ (covering breadth of bacteriałarchaea diversity) • Annotate, analyze, release data • Assess beneﬁts of tree guided sequencing • 1st paper Wu et al in Nature Dec 2009Monday, February 14, 2011

GEBA Phylogenomic Lesson 1 The rRNA Tree of Life is a Useful Tool for Identifying Phylogenetically Novel GenomesMonday, February 14, 2011

Compare PD in Trees From Wu et al. 2009 Nature 462, 1056-1060Monday, February 14, 2011

GEBA Phylogenomic Lesson 2 The rRNA Tree of Life is not perfect ...Monday, February 14, 2011

16s Says Hyphomonas is in Rhodobacteriales Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.Monday, February 14, 2011

WGT and individual gene trees: Its Related to Caulobacterales Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.Monday, February 14, 2011

GEBA Phylogenomic Lesson 3 Phylogeny-driven genome selection helps discover new genetic diversityMonday, February 14, 2011

Network of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.Monday, February 14, 2011

Protein Family Rarefaction Curves • Take data set of multiple complete genomes • Identify all protein families using MCL • Plot # of genomes vs. # of protein familiesMonday, February 14, 2011

Wu et al. 2009 Nature 462, 1056-1060Monday, February 14, 2011

Synapomorphies existWu et al. 2009 Nature 462, 1056-1060Monday, February 14, 2011

+,%-./&#(%)"* !"#$%"&(%)"* ! !Monday, February 14, 2011

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.Monday, February 14, 2011

GEBA Phylogenomic Lesson 4 Phylogeny driven genome selection (and phylogenetics in general) improves genome annotationMonday, February 14, 2011

Most/All Functional Prediction Improves w/ Better Phylogenetic Sampling • 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 Kostas Natalia Thanos Nikos Iain Mavrommatis Ivanova Lykidis Kyrpides AndersonMonday, February 14, 2011

GEBA Phylogenomic Lesson 5 Improves analysis of genome data from uncultured organismsMonday, February 14, 2011

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 m t er ap iaMonday, February 14, 2011 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 of le Sp xi 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

Shotgun Sequencing Allows Use of Other Markers Sargasso Phylotypes 0.5000 0.3750 Cannot be doneWeighted % of Clones 0.2500 without good EFG EFTu HSP70 RecA 0.1250 sampling of genomes RpoB rRNA 0 ia ia ia ria ia ia s ia i FB xi s ia ch s a ta ob te te ar mu ot le er er er er er er er eo te C u ae or ae of t t t t t t ct ic r ac ac ac ac ac ac ac ha Eu The hl or ch ba rm b ob ob b b ob ob C rc hl iro eo eo eo so Fi s- na C e te n tin ry Sp Fu t ot t ot ya cu re ro ro ro Ac pr pr C C oc ap ap np ta lta oc ph m lo Be De si am in Al Ep De G Major Phylogenetic Group Venter et al., Science 304: 66-74. 2004 Monday, February 14, 2011

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 m t er ap iaMonday, February 14, 2011 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 of le Sp xi iro ch Phylogenetic Binning 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 EFG Venter et al., Science 304: 66-74. 2004 EFTu rRNA RecA RpoB HSP70

Shotgun Sequencing Allows Use of Other Markers Sargasso Phylotypes 0.5000 0.3750 Cannot be doneWeighted % of Clones 0.2500 without good EFG EFTu HSP70 RecA 0.1250 sampling of genomes RpoB rRNA 0 ia ia ia ria ia ia s ia i FB xi s ia ch s a ta ob te te ar mu ot le er er er er er er er eo te C u ae or ae of t t t t t t ct ic r ac ac ac ac ac ac ac ha Eu The hl or ch ba rm b ob ob b b ob ob C rc hl iro eo eo eo so Fi s- na C e te n tin ry Sp Fu t ot t ot ya cu re ro ro ro Ac pr pr C C oc ap ap np ta lta oc ph m lo Be De si am in Al Ep De G Major Phylogenetic Group Venter et al., Science 304: 66-74. 2004 Monday, February 14, 2011

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 m t er ap iaMonday, February 14, 2011 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 improves Ac s tin ob ac t er C ia hl or ob i C GEBA Project FB Major Phylogenetic Group Sargasso Phylotypes C hl or of le Sp xi iro ch ae te Fu so s De ba in ct er oc ia oc cu metagenomic analysis 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

GEBA Cyano Sequencing status (as of 01/14): Awaiting Material 11 Library 12 Production 22 Finishing 5 Grand Total 50 On-going/ Planed Activities: - Building Cyanobacterial Metadatabase (IMG-GOLD) - 10th Cyanobacterial Molecular Biology Workshop, Lake Arrowhead, CA (06/10) --> Cheryl will host: Workshop training as prep for virtual Jamboree 131Monday, February 14, 2011

GEBA RNB Plan: Sequence multiple Root Nodule Bacteria (RNBs) across the planet. Pilot: 100 RNBs. Beta RNB Cupriavidis Burkholderia Goal: • Understand BioGeographical effects on species Alpha RNB Azorhizobium evolution and understand host-specificity. Allorhizobium Bradyrhizobium Mesorhizobium Rationale: Rhizobium Sinorhizobium • N2 fixation by legume pastures and crops provides 65% of Devosia Ochrobactrum the N currently utilized in agricultural production. Phyllobacterium Balneimonas-like • Contributes 25 to 90 million metric tones N pa. • Symbioses save $US 6-10 billion annually on N fertilizer. • Grain and animal production enhanced by fixed nitrogen supplied by the symbiosis. 132 Nikos KyrpidesMonday, February 14, 2011

133Monday, February 14, 2011

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 not happy OP10 Thermomicrobia Chloroﬂexi TM7 Deinococcus-Thermus Dictyoglomus AquiﬁcaeEisen & Ward, PIs Thermudesulfobacteria Thermotogae OP1 OP11Monday, February 14, 2011

Shotgun Sequencing Allows Use of Other Markers Sargasso Phylotypes 0.5000 0.3750 GEBA ProjectWeighted % of Clones 0.2500 improves EFG EFTu HSP70 0.1250 metagenomic analysis, RecA RpoB rRNA but only a little 0 ia ia ia ria ia ia s ia i FB xi s ia ch s a ta ob te te ar mu ot le er er er er er er er eo te C u ae or ae of t t t t t t ct ic r ac ac ac ac ac ac ac ha Eu The hl or ch ba rm b ob ob b b ob ob C rc hl iro eo eo eo so Fi s- na C e te n tin ry Sp Fu t ot t ot ya cu re ro ro ro Ac pr pr C C oc ap ap np ta lta oc ph m lo Be De si am in Al Ep De G Major Phylogenetic Group Venter et al., Science 304: 66-74. 2004 Monday, February 14, 2011

GEBA Future 1 Need to adapt genomic and metagenomic methods to make use of GEBA dataMonday, February 14, 2011

Ways to Make Better Use of GEBA Data • Better phylogenetic methods for short reads • Rebuild protein family models • New phylogenetic markers • Need better phylogenies, including HGT • Improved tools for using distantly related genomes in metagenomic analysisMonday, February 14, 2011

iSEEM ProjectMonday, February 14, 2011

GEBA Future 3 We have still only scratched the surface of microbial diversityMonday, February 14, 2011

rRNA Tree of Life FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.Monday, February 14, 2011

Phylogenetic Diversity: Sequenced Bacteria & ArchaeaFrom Wuet al. 2009Nature462,1056-1060Monday, February 14, 2011

Phylogenetic Diversity with GEBAFrom Wuet al. 2009Nature462,1056-1060Monday, February 14, 2011

Phylogenetic Diversity: Isolates From Wu et al. 2009 Nature 462, 1056-1060Monday, February 14, 2011

Phylogenetic Diversity: All From Wu et al. 2009 Nature 462, 1056-1060Monday, February 14, 2011

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 taxaMonday, February 14, 2011

Uncultured Lineages: Technical Approaches • Get into culture • Enrichment cultures • If abundant in low diversity ecosystems • Flow sorting • Microbeads • Microﬂuidic sorting • Single cell ampliﬁcationMonday, February 14, 2011

GEBA uncultured Number of SAGs from Candidate Phyla 406 1 OD1 OP1 OP3 SAR Site A: Hydrothermal vent 4 1 - - Site B: Gold Mine 6 13 2 - Site C: Tropical gyres (Mesopelagic) - - - 2 Site D: Tropical gyres (Photic zone) 1 - - - Sample collections at 4 additional sites are underway. Phil Hugenholtz 150Monday, February 14, 2011

GEBA Future 2 Need Experiments from Across the Tree of Life tooMonday, February 14, 2011

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, 2002Monday, February 14, 2011

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, 2002Monday, February 14, 2011

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, 2002Monday, February 14, 2011

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 • Same trend in Dictyoglomus Aquiﬁcae Thermudesulfobacteria Eukaryotes Thermotogae OP1 Based on OP11 Hugenholtz, 2002Monday, February 14, 2011

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 • Same trend in Dictyoglomus Aquiﬁcae Thermudesulfobacteria Viruses Thermotogae OP1 Based on OP11 Hugenholtz, 2002Monday, February 14, 2011

Proteobacteria TM6 OS-K Need Acidobacteria Termite Group OP8 experimental Nitrospira Bacteroides Chlorobi studies from Fibrobacteres Marine GroupA WS3 across the tree Gemmimonas Firmicutes too Fusobacteria Actinobacteria OP9 Cyanobacteria Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes 0.1 Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Tree based on Thermudesulfobacteria Thermotogae Hugenholtz (2002) OP1 with some OP11 modifications.Monday, February 14, 2011

Proteobacteria TM6 OS-K Adopt a Acidobacteria Termite Group OP8 Microbe Nitrospira Bacteroides Chlorobi Fibrobacteres Marine GroupA WS3 Gemmimonas Firmicutes Fusobacteria Actinobacteria OP9 Cyanobacteria Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes 0.1 Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Tree based on Thermudesulfobacteria Thermotogae Hugenholtz (2002) OP1 with some OP11 modifications.Monday, February 14, 2011

Conclusion • Phylogenetic sampling of genomes improves our understanding of microbial diversity in many ways • Still need – More biogeography – More phenotypic/experimental data – Deeper phylogenetic samplingMonday, February 14, 2011

MICROBESMonday, February 14, 2011

A Happy Tree of LifeMonday, February 14, 2011

Acknowledgements • GEBA: DOE-JGI • GWSS: Nancy Moran & lab, Dongying Wu • iSEEM: Katie Pollard, Jessica Green, Martin Wu • RecA: Dongying Wu, Craig Venter, Doug Rusch, et al.Monday, February 14, 2011

Phylogenomics Talk at UC Berkeley by J. A. Eisen

by Jonathan Eisen

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