Reconstructing Phylogeny by Aligning Multiple Metabolic Pathways Using Functional Module Mapping

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Yiran HuangYuzhong Peng

Abstract

Comparison of metabolic pathways provides a systematic way for understanding the evolutionary and phylogenetic relationships in systems biology. Although a number of phylogenetic methods have been developed, few efforts have been made to provide a unified phylogenetic framework that sufficiently reflects the metabolic features of organisms. In this paper, we propose a phylogenetic framework that characterizes the metabolic features of organisms by aligning multiple metabolic pathways using functional module mapping. Our method transforms the alignment of multiple metabolic pathways into constructing the union graph of pathways, builds mappings between functional modules of pathways in the union graph, and infers phylogenetic relationships among organisms based on module mappings. Experimental results show that the use of functional module mapping enables us to correctly categorize organisms into main categories with specific metabolic characteristics. Traditional genome-based phylogenetic methods can reconstruct phylogenetic relationships, whereas our method can offer in-depth metabolic analysis for phylogenetic reconstruction, which can add insights into traditional phyletic reconstruction. The results also demonstrate that ou...Continue Reading

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Software Mentioned

MWBM
Meta Pathway Hunter ( MPH )
kitsch
MP
MMAL
IsoRankN
Align
TreeView
PHYLIP
COUSINS

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