Abstract
BackgroundMany 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.MethodsWe 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.ResultsPhyletic 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.ConclusionsStructural 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.
Highlights
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
Molecular biologists constructed phylogenetic trees based on the sequence similarity of small subunit ribosomal RNA [1] or other single genes
Numerous methods have been proposed to reconstruct the phylogenetic trees from whole genome features such as oligonucleotide compositions [2], genome fragment
Summary
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. Molecular biologists constructed phylogenetic trees based on the sequence similarity of small subunit ribosomal RNA [1] or other single genes. The comparative analysis of whole genomes can provide more information to reconstruct the phylogeny than individual genes do. In parallel with genomic comparisons, many studies focused on the similarity of metabolic processes. Zhang et al defined existence/ absence of metabolic pathways and computed the network similarity measure for 47 organisms [8]. Clemente et al used sets of EC numbers to define pathway similarity and compared metabolism of 8 bacteria [9]
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