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Bioinformatics Advance Access published online on May 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth324
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 26, 2003
Revised March 5, 2004
Accepted April 8, 2004

Article

Whole-genome prokaryotic phylogeny

Stefan R. Henz 1, Daniel H. Huson 1*, Alexander F. Auch 1, Kay Nieselt-Struwe 1, Stephan C. Schuster 2

1 Center for Bioinformatics Tübingen (ZBIT), Sand 14, Tübingen, 72076, Germany
2 Max-Planck-Institute for Development Biology, Spemannstrasse 35, Tübingen, 72076, Germany

* To whom correspondence should be addressed. E-mail: huson{at}informatik.uni-tuebingen.de.


  Abstract

Current understanding of the phylogeny of prokaryotes is based on the comparison of the highly conserved small ssu-rRNA subunit and similar regions. Although such molecules have proved to be very useful phylogenetic markers, mutational saturation is a problem, due to their restricted lengths. Now, a growing number of complete prokaryotic genomes are available. This paper addresses the problem of determining a prokaryotic phylogeny utilizing the comparison of complete genomes. We introduce a new strategy, GBDP, "genome blast distance phylogeny", and show that different variants of this approach robustly produce phylogenies that are biologically sound, when applied to 91 prokaryotic genomes. In this approach, first BLAST is used to compare genomes, then a distance matrix is computed, and finally a tree- or network-reconstruction method such as UPGMA, Neighbor-Joining, BioNJ or Neighbor-Net is applied.


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