Abstract
Evolutionary information was inferred from the topology of metabolic networks corresponding to 17 plant species belonging to major plant lineages Chlorophytes, Bryophytes, Lycophytes and Angiosperms. The plant metabolic networks were built using the substrate-product network modeling based on the metabolic reactions available on the PlantCyc database (version 9.5), from which their local topological properties such as degree, in-degree, out-degree, clustering coefficient, hub-score, authority-score, local efficiency, betweenness and eigencentrality were measured. The topological measurements corresponding to each metabolite within the networks were considered as a set of metabolic characters to compound a feature vector representing each plant. Our results revealed that some local topological characters are able to discern among plant kinships, since similar phylogenies were found when comparing dendrograms obtained by topological metrics to the one obtained by DNA sequences of chloroplast genes. Furthermore, we also found that even a smaller number of metabolic characters is able to separate among major clades with high bootstrap support (BS > 95), while for some suborders a bigger content has been required.
Highlights
Phylogenetic studies of plants were initiated by morphological observations related to their reproductive organs[1]
We considered 17 plants, namely: Brachypodium distachyon (BD), Hordeum vulgare (HV), Oryza sativa japonica (OSJ), Panicum virgatum (PV), Setaria italica (SI), Sorghum bicolor (SB), Zea mays (ZM); Arabidopsis thaliana (AT), Brassica rapa pekinensis (BRP), Carica papaya (CP), Glycine max (GM), Manihot esculenta (ME), Populus trichocarpa (PT), Vitis vinifera (VV); Selaginella moellendorffii (SM); Physcomitrella patens (PP) and Chlamydomonas reinhardtii (CR); whose metabolic pathways, catalytic enzymes and metabolites are available at PlantCyc database[19]
The plant metabolic networks were modeled based on the metabolic reactions corresponding to the 17 plants of the PlantCyc[19]
Summary
These results were supported by both the cophenetic correlation and bootstrap analysis, regarding the phylogenetic distance based on the DNA sequence alignment of chloroplast genes[2], which correctly establish the taxonomy of 17 studied species. One of the main advantages of the proposed method is the possibility to reconstruct phylogenetic trees based on simple topological measures extracted from the metabolic machinery (e.g. a feature vector extracted from the hubs-score), which can be considered as a complementary tool for plant phylogenetic analysis In this manner, different approaches or visions can provide extra information that can be used to corroborate the study of evolution, that apart from being largely studied is not fully understanding yet. These initial hypotheses related to metabolic networks evolution can be tested and possibly extended, but this could open interesting opportunities to implement synthetic biology strategies for plants
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