Reconstructing phylogeny by aligning multiple metabolic pathways using functional module mapping

Reconstructing phylogeny by aligning multiple metabolic pathways using functional module mapping

Huang, Yiran (Guangxi University; South China University of Technology; Guangxi Teachers Education University)
Zhong, Cheng (Guangxi University)
Lin, H.X. (TU Delft Mathematical Physics)
Wang, Jianyi (Guangxi University)
Peng, Yuzhong (Guangxi Teachers Education University)

2018

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 our phylogenetic trees are closer to the classic classifications in comparison to existing classification methods using metabolic pathway data.

Functional module mapping
Metabolic pathway alignment
Phylogenetic tree
Union graph

http://resolver.tudelft.nl/uuid:bb1d09e5-9a11-4db2-9d37-2338778e232e

https://doi.org/10.3390/molecules23020486

1420-3049

Molecules: a journal of synthetic organic and natural product chemistry, 23 (2), 1-16

Institutional Repository

journal article

© 2018 Yiran Huang, Cheng Zhong, H.X. Lin, Jianyi Wang, Yuzhong Peng