TIGR "Tree of Life" Project Slides (from 2004)
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Slides for talk in 2004 on project at TIGR as part of NSF "Tree of Life" program
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TIGR "Tree of Life" Project Slides (from 2004)
- 1. Phylogenomics: A Genome Level Approach to Assembling the Bacterial Branches of the Tree of Life TIGR: Jonathan A. Eisen Naomi Ward Karen E. Nelson Jonathan H. Badger James Sakwa Martin Wu Dongying Wu Kevin Penn COMB: Frank T. Robb Elizabeth M. O’Connor Julie Enticknap Tim Steppe http://www.tigr.org/tol TIGR QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture.
- 2. Background I: rRNA Tree • Phenotype not very useful for bacterial phylogeny QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture. • Most molecular studies based on 16s rRNA sequence analysis • Studies of other genes do not always agree with rRNA, especially for deep branches from Woese 1987 TIGR
- 3. Background II: Most Bacteria Have Never Been Cultured • Microscopic and molecular studies show that <1% of the microbes in most environments have been grown in pure culture • True in terms of #s and phylogenetic diversity • This means we know little about their biology TIGR
- 4. Background III: Genomics Has Revolutionized Bacteriology • • • • Predictions of biology Drug design, vaccine development Functional genomic studies Evolutionary reconstructions – Whole genome phylogeny – Lateral gene transfer – Population genomics TIGR
- 5. Biased Sampling of Bacterial Genomes TIGR Hugenholtz 2002
- 7. TIGR Tree of Life Project • Major goal – Increase phylogenetic diversity of genome sequences • Three sub-goals – Resolve relationships among the phyla – Launch experimental studies of these phyla – Inform environmental studies of uncultured microbes • The Players – TIGR (Jonathan Eisen, Naomi Ward, Karen Nelson et al.) – COMB (Frank Robb et al.) TIGR
- 8. TIGR Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira CFB Chlorobi Fibrobacteres Marine GroupA WS3 Gemmimonas Firmicutes Fusobacteria This project Actinobacteria OP9 Published Cyanobacteria Synergistes In progress Deferribacteres Uncultured lineage Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes 0.1 Coprothermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificacae Tree based on Thermodesulfobacteria Hugenholtz (2002) Thermotogae with some OP1 modifications. OP11
- 9. Genome Sequencing Progress Phylum Sp eciesse lected Libr aries Chry siogenesars tis ena Grow th, DNA iso lation + + Sho tgun Estim ated # of Aut oCover age Gen e Contigs Ann om otated Size (Mb) 4x 2.5 155 + Chry siogenes Cop hermobacter rot Copr otherm cter pro oba teolyticus(CP) + + 8x 1.38 3 + Dicty oglomi Dictyoglomus m hilum(DT) ther op + + 8x 2.0 9 + Thermo ulfobacteria des Therm sulfobacte ode riumcomm (TC) une + + 8x 1.78 26 + Nitrosp irae Therm sulfovib ye ode rio llows ii (TY) ton + + 8x 1.98 27 + Thermomicrobia Therm icro om biumroseum + + 8x 3.4 82 + De ibacteres ferr Se lectingfrom Deferr cter thermohilus, iba p Ge ovib thiop rio hilus, Flexistipessinusara bici Se lectingfrom Sy nergistesjones ii, Am bacter co biense, ino lom Therm anaero vibrio acida inovor m ans, Am inom onas p aucivorans, Dethio sulfovib peptido rio vorans + In prog ress + In prog ress Syn stes ergi TIGR Type Strain or Species Selected When Possible
- 10. Goal I: Relationships Among Phyla TIGR
- 11. Concatenated Alignment ML Tree TIGR
- 13. Green Non Sulfur Bacteria TIGR
- 14. Goal II: Biology of These Phyla TIGR
- 15. QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture. TIGR
- 17. Key Issues in Uncultured Microbes • Questions – 1. Who is out there? – 2. What are they doing? – 3. Need to connect 1 and 2. • Answers – 1. Phylogenetic anchors – 2. Genomics – 3. Linking anchors to genomics contigs TIGR
- 18. Phylogenetic Anchors and the Sargasso Sea Shotgun Sequencing Warner Brothers, Inc. sequence TIGR shotgun
- 19. rRNA as a Phylogenetic Anchor TIGR Venter et al., 2004
- 20. Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA) TIGR Venter et al., 2004
- 21. Biased Sampling of Bacterial Genomes Hugenholtz 2002 TIGR
- 22. Our Tree of Life Genomes Allow Anchoring of 100s of clones from Yellowstone Mats QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture. TIGR
- 24. Blast of GYOAP59TF >ORF02612-TG_gtr_857 rho transcription termination factor Rho {Thermomicrobium_roseum_DSM5159} Length = 426 Score = 1177 (419.4 bits), Expect = 2.9e-119, P = 2.9e-119 Identities = 232/232 (100%), Positives = 232/232 (100%) Query: Sbjct: Query: Sbjct: Query: Sbjct: Query: Sbjct: TIGR 1 VAPIGRGQRGLIVSPPKAGKTVLLKHIANGITTNYKDIHLIVLLIGERPEEVTDMRRSVD 60 VAPIGRGQRGLIVSPPKAGKTVLLKHIANGITTNYKDIHLIVLLIGERPEEVTDMRRSVD 191 VAPIGRGQRGLIVSPPKAGKTVLLKHIANGITTNYKDIHLIVLLIGERPEEVTDMRRSVD 250 61 GEVISSTFDEPVEDHIRVAEMTLERAKRLVECGMDVVILLDSITRLARAYNLSVPPSGRT 120 GEVISSTFDEPVEDHIRVAEMTLERAKRLVECGMDVVILLDSITRLARAYNLSVPPSGRT 251 GEVISSTFDEPVEDHIRVAEMTLERAKRLVECGMDVVILLDSITRLARAYNLSVPPSGRT 310 121 LSGGIDPVALYPPKRFFGAARNIEGGGSLTIIATCLVDTGSRMDDVIYEEFKGTGNMELH 180 LSGGIDPVALYPPKRFFGAARNIEGGGSLTIIATCLVDTGSRMDDVIYEEFKGTGNMELH 311 LSGGIDPVALYPPKRFFGAARNIEGGGSLTIIATCLVDTGSRMDDVIYEEFKGTGNMELH 370 181 LDRKLAERRIFPAIDIQRSGTRREELLLDEQTLRQVWTMRRMVSMLGGTDGT 232 LDRKLAERRIFPAIDIQRSGTRREELLLDEQTLRQVWTMRRMVSMLGGTDGT 371 LDRKLAERRIFPAIDIQRSGTRREELLLDEQTLRQVWTMRRMVSMLGGTDGT 422
- 25. Broader Impact • Genome sequence data released to TIGR web site • Genome Users Workshop to be held at TIGR in 2005 • Project used as model for evolution teaching in talks to HHMI, MD Science Teachers Assocation, and Montgomery County high school science teachers • Project promoted to public through radio and print media TIGR
- 26. Training • Student involvement – Kevin Penn, technician at TIGR – Temylope Adeyefa-Olasupo, U. Md Undergrad working at COMB – Rebecca Brocato, high school intern, COMB – Joseph Wister, TIGR Summer Fellow with Karen Nelson – Ryan Corces-Zimmerman, high school intern working at TIGR • Teaching using this project – MBL Molecular Evolution Workshop – MBL Genomics Workshop – Jackson Lab Genomics Workshop TIGR
- 27. Future Issues • New estimates suggests > 100 bacterial phyla • Someone needs to cover Archaeal diversity • Need DNA repository TIGR
Notes de l'éditeur
- Phil Hugenholtz wrote an excellent review paper in Genome Biology tracing which Phyla had genome sequences available. Proteobacteria have the most with Firmicutes next (these are the low GC gram positives like B. subtilis) and Actinobacteria (the high GC gram positives like M. tuberculosis) third.
- In Red are the Phyla of bacteria with cultured species but no genome sequences that we are sequencing as part of a NSF Tree of Life project. NOTE **** In White are the Phyla with no cultured representatives. ALSO NOTE **** This project is contingent upon having a good tree of bacteria.
- Shotgun genome sequencing works by breaking a genome apart into millions of little pieces and then sequencing those pieces randomly
- This is a tree of a rRNA gene that was found on a large DNA fragment isolated from the Monterey Bay. This rRNA gene groups in a tree with genes from members of the gamma Proteobacteria a group that includes E. coli as well as many environmental bacteria. This rRNA phylotype has been found to be a dominant species in many ocean ecosystems. clone from the Sargasso Sea. This shows that this
- Phil Hugenholtz wrote an excellent review paper in Genome Biology tracing which Phyla had genome sequences available. Proteobacteria have the most with Firmicutes next (these are the low GC gram positives like B. subtilis) and Actinobacteria (the high GC gram positives like M. tuberculosis) third.