Reconstruction of phyletic trees by global alignment of multiple metabolic networks.
BACKGROUND
In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information.


RESULTS
We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis.


CONCLUSIONS
We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification.
Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan.
Cheng-Yu
CY
Ma
Shu-Hsi
SH
Lin
Chi-Ching
CC
Lee
Chuan Yi
CY
Tang
Bonnie
B
Berger
Chung-Shou
CS
Liao
D000465:Algorithms; D016000:Cluster Analysis; D005285:Fermentation; D023281:Genomics; D007778:Lactobacillus / Q000145:classification; D045342:Light-Harvesting Protein Complexes / Q000032:analysis; D053858:Metabolic Networks and Pathways; D010788:Photosynthesis; D010802:Phylogeny; D048929:Prochlorococcus / Q000145:classification; D016999:Sulfur-Reducing Bacteria / Q000145:classification; D046940:Synechococcus / Q000145:classification
D045342:Light-Harvesting Protein Complexes