Applied Microbiology and Biotechnology

, Volume 65, Issue 2, pp 203–210

Phylogenetic analysis based on genome-scale metabolic pathway reaction content

Genomics and Proteomics

DOI: 10.1007/s00253-004-1641-3

Cite this article as:
Hong, S.H., Kim, T.Y. & Lee, S.Y. Appl Microbiol Biotechnol (2004) 65: 203. doi:10.1007/s00253-004-1641-3


Phylogenetic classifications based on single genes such as rRNA genes do not provide a complete and accurate picture of evolution because they do not account for evolutionary leaps caused by gene transfer, duplication, deletion and functional replacement. Here, we present a whole-genome-scale phylogeny based on metabolic pathway reaction content. From the genome sequences of 42 microorganisms, we deduced the metabolic pathway reactions and used the relatedness of these contents to construct a phylogenetic tree that represents the similarity of metabolic profiles (relatedness) as well as the extent of metabolic pathway similarity (evolutionary distance). This method accounts for horizontal gene transfer and specific gene loss by comparison of whole metabolic subpathways, and allows evaluation of evolutionary relatedness and changes in metabolic pathways. Thus, a tree based on metabolic pathway content represents both the evolutionary time scale (changes in genetic content) and the evolutionary process (changes in metabolism).

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  1. 1.Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical & Biomolecular Engineering and BioProcess Engineering Research CenterKorea Advanced Institute of Science and TechnologyDaejeonSouth Korea
  2. 2.Department of Biosystems and Bioinformatics Research CenterKorea Advanced Institute of Science and TechnologyDaejeonSouth Korea