Towards reconstructing a metabolic tree of life.

Marina Marcet-Houben,Santiago Garcia-Vallve,Pere Puigbò,Antoni Romeu

doi:10.6026/97320630002135

Abstract

Using information from several metabolic databases, we have built our own metabolic database containing 434 pathways and 1157 different enzymes. We have used this information to construct a dendrogram that demonstrates the metabolic similarities between 282 species. The resulting species distribution and the clusters defined in the tree show a certain taxonomic congruence, especially in recent relationships between species. This dendrogram is another representation of the tree of life, based on metabolism that may complement the trees constructed by other methods. For example, the metabolic dissimilarity we demonstrate between Symbiobacterium thermophilum (previously defined as Actinobacteria) and the other Actinobacteria species, and the metabolic similarity between S. thermophilum and Clostridia, combined with other evidence, suggest that S. thermophilum may be re-classified as Firmicutes, Clostridia.

Highlights

For many years phylogenetic trees have been used to study the evolution of organisms
When whole genome sequences of prokaryote organisms became available, everyone hoped that this extended information would help them to build more accurate phylogenies but it was discovered that different genes produced different trees
[8] As it is difficult to align the sequences of two genomes, several methods that use traditional sequence alignment tools have been developed to construct genome trees. [8, 9, 10] These methods involve concatenating the homologous sequences from different gene families to construct a single tree [9, 10, 11] or comparing different trees to create a supertree

Summary

Introduction

For many years phylogenetic trees have been used to study the evolution of organisms. When whole genome sequences of prokaryote organisms became available, everyone hoped that this extended information would help them to build more accurate phylogenies but it was discovered that different genes produced different trees. It was at this point that doubts were raised as to whether a tree structure was the best representation of evolution. If taking a single gene had become insufficient for consistent tree representation, that hundreds of whole genomic sequences are available, new phylogenomic methods are being developed. Two large genomes that are not phylogenetically closely related can have more common genes than a large and a small genome that are closely related. Measures to prevent this must be taken so that the phylogenetic tree does not become biased. [10]

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Conclusion