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Whole-Genome Prokaryote Phylogeny without Sequence Alignment Bailin HAO  and  Ji QI T-Life Research Center, Fudan University Shanghai 200433, China Institute of Theoretical Physics, Academia Sinica Beijing 100080, China http://www.itp.ac.cn/~hao/
Classification of Prokaryotes: A Long-Standing Problem ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The SSU rRNA Tree of Life: A big progress in molecular phylogeny of prokaryotes as evidenced by the history of the Bergey’s Manual
Bergey’s Manual Trust: Bergey’s Manual   ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Our Final Result ,[object Object],[object Object],[object Object],[object Object],[object Object]
 
Protein Tree for 145 Organisms From 82 Genera (K=5) 16 Archaea (11 genera, 16 species) 123 Bacteria (65 genera, 98 species) 6  Eukaryotes
 
Complete Bacterial Genomes Appeared since 1995 Early Expectations: ,[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Debate on Lateral Gene Transfer ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],Gene  A A ’ B Gene  B ’ C ? 1st species 2nd species
Our Motivations: ,[object Object],[object Object],[object Object],[object Object],[object Object]
Other Whole-Genome Approaches ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Comparison of Complete Genomes/Proteomes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],} }
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],↑
A Key Improvement: Subtraction of Random Background ,[object Object],[object Object],[object Object],[object Object],[object Object]
Frequency and Probability ,[object Object],[object Object],[object Object],[object Object]
Predicting #(K-strings) from that of  lengths (K-1) and (K-2) strings ,[object Object],[object Object],[object Object]
(K-2)-th Order Markov Model ,[object Object],[object Object]
[object Object],[object Object]
Composition Distance ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Materials: Genomes from NCBI ( ftp.ncbi.nih.gov/genomes/Bacteria/ ) Not the original GenBank files 6 Eucaryote genomes were included for reference Tree construction: Neighbor-Joining in Phylip
Protein Tree for 132 species (K=5) 16 Archaea (11 genera, 16 species) 110 Bacteria (57 genera, 88 species) 6  Eukaryotes
 
Protein Tree for 132 species K=6 16 Archaea (11 genera, 16 species) 110 Bacteria (57 genera, 88 species) 6  Eukaryotes
 
Protein Class vs. Whole Proteome ,[object Object],[object Object]
Genus Tree based on Ribosomal Proteins
A Genus Tree based on Aminoacyl tRNA synthetases
Chloroplast Tree ,[object Object],[object Object],[object Object]
Chloroplast tree
Coronaviruses including Human SARS-CoV ,[object Object],[object Object],[object Object]
Coronavirus tree
Understanding the Subtraction Procedure: Analysis of Extreme Cases in  E. coli ,[object Object],[object Object],[object Object],[object Object]
GKSTL: how 58 reduces to 0.646? ,[object Object],[object Object],[object Object],[object Object],[object Object]
HAMSC: how 1 grows to 197? ,[object Object],[object Object],[object Object],[object Object],[object Object]
6121 Exact Matches of GKSTL In PIR Rel.1.26 with >1.2 Mil  Proteins ,[object Object],[object Object],[object Object]
15 Exact Matches of  HAMSC: In PIR Rel.1.26 with >1.2 Mil Proteins   ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Stable Topology of the Tree ,[object Object],[object Object],[object Object],[object Object]
Statistical Test of the Tree ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
About 70% genes for every species were selected in one bootstrap
“ K-string Picture” of Evolution ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The Problem of Higher Taxa ,[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Conclusion:   The Tree of Life is saved! There is phylogenetic information in the prokaryotic proteomes. Time to work on molecular definition of taxa. Thank you!
 
 
Protein Tree for 132 species (K=5) 16 Archaea (11 genera, 16 species) 110 Bacteria (57 genera, 88 species) 6  Eukaryotes
 
 
A Failed Attempt Using Avoidance Sinatures
 
Comparison with the Bergey’s Manual
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],  Phyla Classes Orders Families Genera Species Strains Archaea 2 7 9 9 9 13 13 Bacteria 9 14 23 28 37 46 57 Total 11 21 32 37 46 59 70
Early expectation from genome data ,[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Subtraction of Random Background ,[object Object],[object Object],[object Object]
What to do next ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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bai2

  • 1. Whole-Genome Prokaryote Phylogeny without Sequence Alignment Bailin HAO and Ji QI T-Life Research Center, Fudan University Shanghai 200433, China Institute of Theoretical Physics, Academia Sinica Beijing 100080, China http://www.itp.ac.cn/~hao/
  • 2.
  • 3. The SSU rRNA Tree of Life: A big progress in molecular phylogeny of prokaryotes as evidenced by the history of the Bergey’s Manual
  • 4.
  • 5.
  • 6.  
  • 7. Protein Tree for 145 Organisms From 82 Genera (K=5) 16 Archaea (11 genera, 16 species) 123 Bacteria (65 genera, 98 species) 6 Eukaryotes
  • 8.  
  • 9.
  • 10.
  • 11.
  • 12.
  • 13.
  • 14.
  • 15.
  • 16.
  • 17.
  • 18.
  • 19.
  • 20.
  • 21.
  • 22.
  • 23.
  • 24. Materials: Genomes from NCBI ( ftp.ncbi.nih.gov/genomes/Bacteria/ ) Not the original GenBank files 6 Eucaryote genomes were included for reference Tree construction: Neighbor-Joining in Phylip
  • 25. Protein Tree for 132 species (K=5) 16 Archaea (11 genera, 16 species) 110 Bacteria (57 genera, 88 species) 6 Eukaryotes
  • 26.  
  • 27. Protein Tree for 132 species K=6 16 Archaea (11 genera, 16 species) 110 Bacteria (57 genera, 88 species) 6 Eukaryotes
  • 28.  
  • 29.
  • 30. Genus Tree based on Ribosomal Proteins
  • 31. A Genus Tree based on Aminoacyl tRNA synthetases
  • 32.
  • 34.
  • 36.
  • 37.
  • 38.
  • 39.
  • 40.
  • 41.
  • 42.
  • 43. About 70% genes for every species were selected in one bootstrap
  • 44.
  • 45.
  • 46.
  • 47. Conclusion: The Tree of Life is saved! There is phylogenetic information in the prokaryotic proteomes. Time to work on molecular definition of taxa. Thank you!
  • 48.  
  • 49.  
  • 50. Protein Tree for 132 species (K=5) 16 Archaea (11 genera, 16 species) 110 Bacteria (57 genera, 88 species) 6 Eukaryotes
  • 51.  
  • 52.  
  • 53. A Failed Attempt Using Avoidance Sinatures
  • 54.  
  • 55. Comparison with the Bergey’s Manual
  • 56.
  • 57.
  • 58.
  • 59.
  • 60.
  • 61.
  • 62.
  • 63.