Special Joint Department of Mathematics /
Quantitative Biology / Gene Expression in Development & Disease Seminar

Note special day!

Tuesday, 16 July 2013 at 11:30 am

Room 1400 Biomedical and Physical Sciences Bldg.

Refreshments at 11:15 am

Speaker:  Bailin Hao, T-Life Research Center and Department of Physics, Fudan University, Shanghai

Title:  Whole-Genome-Based and Alignment-Free Phylogeny of Prokaryotes

Bacteria and Archaea (Prokaryotes) are the most successful creatures on the Earth. Yet our knowledge on this unseen majorty is rather limited. As sequencing prokaryotic genomes becoming cheaper and faster, nearly 3000 genomes have been released and many more are expected. Although the choice of organisms to be sequenced is largely dictated by practical needs, the taxonomic coverage of sequenced genomes is much wider now as compared to 1985, when Carl Woese and coworkers proposed a phylogenetic definition for the major eubacterial divisions using only 400 16S rRNA sequences available then. Due to the extreme diversity of prokaryotic genomes a whole-genome based phylogeny must be alignment-free. On the other hand, prokaryotic taxonomy has reached a high level as witnessed by the completion of the second edition of the Bergey's Manual of Systematic Bacteriology (2001-2012), a grandiose work of more than 8600 pages. Now the faithfulness of a phylogeny may be checked by direct comparison with taxonomy. Our Composition Vector CVTree approach, developed during the last decade, meets many requirements of the genomic era as will be described in this talk. Furthermore, CVTree has very high resolution at the species level and below, a feature greatly surpassing the 16S rRNA analysis. In the long run, CVTRee may become a convenient and effective definitive tool in the hands of microbiologists.

1. J Qi, B Wang, B Hao (2004) Whole genome prokaryote phylogeny without sequence alignment: a K-string composition approach. J MolEvol. 58: 1-11
2. Z Xu, B Hao (2009) CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucl Acids Res. 37 Web Server Issue: W174-w178
3. Q Li, Z Xu, B Hao (2010) Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations. J Biotechn. 149: 115-199
4. B Hao (2011) CVTrees support the Bergey's systematics and provide high resolution at species level and below. The Bulletin of MISMiS, 2 Part2: 189-196
5. G Zuo, Z Xu, B Hao (2013) Shigella species are not strains of Escherichia coli but sister members in the genus Escherichia. Genomics, Proteomics & Bioinformatics, 11: 61-65