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
Abstract:
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.
References:
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