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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]

Coronaviruses including Human SARS-CoV ,[object Object],[object Object],[object Object]

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]

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!

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]

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