This document discusses a new whole-genome based method for constructing phylogenetic trees of prokaryotes without sequence alignment. The method involves using the frequency distribution of k-tuples in complete proteomes to define compositional vectors for each species, and calculating distances between vectors to build trees. Tests recovered accepted relationships from rRNA trees and Bergey's Manual. The approach avoids issues with aligning whole genomes and is independent of genome size and gene content.
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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/
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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
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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
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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
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27. Protein Tree for 132 species K=6 16 Archaea (11 genera, 16 species) 110 Bacteria (57 genera, 88 species) 6 Eukaryotes
43. About 70% genes for every species were selected in one bootstrap
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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!
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50. Protein Tree for 132 species (K=5) 16 Archaea (11 genera, 16 species) 110 Bacteria (57 genera, 88 species) 6 Eukaryotes