title: Reconstructing phylogeny from metabolic substrate-product relationships.
abstract: BACKGROUND
  Many approaches utilize metabolic pathway information to reconstruct the phyletic tree of fully sequenced organisms, but how metabolic networks can add information to original genomic annotations has remained open.
  
  
  METHODS
  We translated enzyme reactions assigned in 1075 organisms into substrate-product relationships to represent the metabolic information at a finer resolution than enzymes and compounds. Each organism was represented as a vector of substrate-product relationships and the phyletic tree was reconstructed by a simple hierarchical method. Obtained results were compared with several other approaches that use genome information and network properties.
  
  
  RESULTS
  Phyletic trees without consideration of network properties can already extract organisms in anomalous environments. This efficient method can add insights to traditional genome-based phylogenetic reconstruction.
  
  
  CONCLUSIONS
  Structural relationship among metabolites can highlight parasitic or symbiont species such as spirochaete and clamydia. The method assists understanding of species-environment interaction when used in combination with traditional phylogenetic methods.
authors.affiliation: Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2 Kuang Fu Road, Taiwan. freshrogerchang@gmail.com
authors.forename: Che-Wei
authors.initials: CW
authors.lastname: Chang
authors.forename: Ping-Chiang
authors.initials: PC
authors.lastname: Lyu
authors.forename: Masanori
authors.initials: M
authors.lastname: Arita
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D056890:Eukaryota / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D010802:Phylogeny; D012984:Software