Whole-genome prokaryotic phylogeny.
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.
Henz
Stefan R
SR
Center for Bioinformatics Tübingen (ZBIT), Sand 14, Tübingen 72076, Germany.
Huson
Daniel H
DH
Auch
Alexander F
AF
Nieselt-Struwe
Kay
K
Schuster
Stephan C
SC
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D004269:DNA, Bacterial / Q000032:analysis; D030541:Databases, Genetic; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D016680:Genome, Bacterial; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid
D004269:DNA, Bacterial