Talk I gave at the JGI User Meeting 2009.

1. GEBA A genomic encyclopedia of bacteria and archaea Jonathan A. Eisen JGI User Meeting 2009

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

4. rRNA Tree of Life

5. The Tree is not Happy

6. From http://genomesonline.org

14. T. roseum genome

15. The Tree of Life is Still Angry

17. Major Lineages of Actinobacteria

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

22. GEBA Pilot I: Selecting Targets

28. GEBA Pilot II: The Importance of Project Management

30. GEBA Pilot III: Partnership with DSMZ

33. Microorganisms Quantification gel of the genomic DNA isolated from Conexibacter woesei (DSM 14684T) Conexibacter woesei (DSM 14684T) was taken from the German Collection of Microorganisms and Cell Cultures (DSMZ). The genomic DNA was isolated using the Qiagen Genomic 500 DNA Kit (Qiagen 10262). The genomic DNA was 10-250 kb in size as determined by Pulsed Field Gel Electrophoresis (PFGE). The bulk of DNA had a size of 50-250 kb (see attached PFGE image). The DNA concentration is 500 ng/µl as estimated from the gel. Spectrophotometric measurements yielded a DNA concentration of 450 µg/ml; 300 µl of genomic DNA are shipped (150 µg). 1 2 3 4 5 6 7 8 Lane 1: c(  -Marker)= 15 ng Lane 2: c(  -Marker)= 30 ng Lane 3: c(  -Marker)= 50 ng Lane 4: DNA Molecular Weight Marker II (Roche 236250) Lane 5: DSM 13279, Collinsella stercoris Lane 6: DSM 43043, Intrasporangium calvum Lane 7: DSM 18053, Dyadobacter fermentans Lane 8: DSM 20476, Slackia heliotrinireducens Lane 9: DSM 18081, Patulibacter minatonensis Lane 10: DSM 14684, Conexibacter woesei Lane 11: DSM 11002, Dethiosulfovibrio peptidovorans Lane 12: DSM 11551, Halogeometricum borinquense Lane 13: DNA Molecular Weight Marker II (Roche 236250) Lane 14: c(  -Marker)= 125 ng Lane 15: c(  -Marker)= 250 ng Lane 16: c(  -Marker)= 500 ng 9 10 11 12 13 14 15 16

34. GEBA Pilot IV: Sequencing, Annotation, Data Release

36. IMG/GEBA http://img.jgi.doe.gov/cgi-bin/geba/main.cgi

37. Adopt a Microbe

38. GEBA Pilot IV: Assess Benefits of GEBA56 All genomes have some value But what, if any, is the benefit of tree-guided sequencing over other selection methods

44. Genome Number Total Gene Number Number of proteins 0 50000 100000 150000 200000 250000 300000 350000 0 10 20 30 40 50 60 70 80 S. agalactiae Enterobacteriaceae Actinobacteria Bacteria from GEBA project

46. Novelty 3 Diversity within known families

47. Transporter Profiles Sebaldella termitidis ATCC 33386 has 2x number of sugar PTS transporters of any genome

48. Novelty 4 Unusual distribution patterns

49. Shotgun Sequencing Detects More Diversity than PCR-methods

50. First Bacterial Actin Related Protein First found by V. Kunin, Structure Analysis by Patrik D. et al

51. Most Closely Related to ARP8

54. Linking Protein Families Improved

55. Fusion Based Predictions Improved

56. Improving Rosetta Stone Predictions

58. Metagenomic Annotation Improves (Slightly)

59. Compositional Binning Improves (Slightly)

60. Phylogenetic Binning Improves Slightly

61. Value of 100 diverse genomes V: Phylogeny

62. 16s Says Hyphomonas is in Rhodobacteriales Badger et al. 2005

63. WGT Says Its Related to Caulobacterales Badger et al. 2005

66. GEBA - After the Pilot

67. PD of sequenced organisms

68. PD with GEBA

73. 0.1 Acidobacteria Bacteroides Fibrobacteres Gemmimonas Verrucomicrobia Planctomycetes Chloroflexi Tree based on Hugenholtz (2002) with some modifications. Need experimental studies from across the tree too Proteobacteria Chlorobi Firmicutes Fusobacteria Actinobacteria Cyanobacteria Chlamydia Spriochaetes Deinococcus-Thermus Aquificae Thermotogae TM6 OS-K Termite Group OP8 Marine GroupA WS3 OP9 NKB19 OP3 OP10 TM7 OP1 OP11 Nitrospira Synergistes Deferribacteres Thermudesulfobacteria Chrysiogenetes Thermomicrobia Dictyoglomus Coprothmermobacter

75. MICROBES

76. A Happy Tree of Life