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Molecules 2018, 23(2), 486; https://doi.org/10.3390/molecules23020486

Reconstructing Phylogeny by Aligning Multiple Metabolic Pathways Using Functional Module Mapping

1
School of Computer and Electronics and Information, Guangxi Universities Key Laboratory of Parallel and Distributed Computing, Guangxi University, Nanning 530004, China
2
School of Computer Science and Engineering, South China University of Technology, Guangzhou 510006, China
3
Guangxi Colleges and Universities Key Laboratory of Data Science, Guangxi Teachers Education University, Nanning 530001, China
4
Guangdong Key Laboratory of Popular High Performance Computers, Shenzhen Key Laboratory of Service Computing and Applications, Shenzhen 518060, China
5
Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands
6
School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
*
Authors to whom correspondence should be addressed.
Received: 20 January 2018 / Revised: 15 February 2018 / Accepted: 16 February 2018 / Published: 23 February 2018
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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 our phylogenetic trees are closer to the classic classifications in comparison to existing classification methods using metabolic pathway data. View Full-Text
Keywords: metabolic pathway alignment; functional module mapping; phylogenetic tree; union graph metabolic pathway alignment; functional module mapping; phylogenetic tree; union graph
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Huang, Y.; Zhong, C.; Lin, H.X.; Wang, J.; Peng, Y. Reconstructing Phylogeny by Aligning Multiple Metabolic Pathways Using Functional Module Mapping. Molecules 2018, 23, 486.

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