Affordable Access

Publisher Website

Tree of Life Based on Genome Context Networks

Authors
Publisher
Public Library of Science
Publication Date
Volume
3
Issue
10
Identifiers
DOI: 10.1371/journal.pone.0003357
Keywords
  • Research Article
  • Computational Biology/Genomics
  • Computational Biology/Systems Biology
  • Evolutionary Biology/Bioinformatics
  • Evolutionary Biology/Genomics
Disciplines
  • Biology

Abstract

Efforts in phylogenomics have greatly improved our understanding of the backbone tree of life. However, due to the systematic error in sequence data, a sequence-based phylogenomic approach leads to well-resolved but statistically significant incongruence. Thus, independent test of current phylogenetic knowledge is required. Here, we have devised a distance-based strategy to reconstruct a highly resolved backbone tree of life, on the basis of the genome context networks of 195 fully sequenced representative species. Along with strongly supporting the monophylies of three superkingdoms and most taxonomic sub-divisions, the derived tree also suggests some intriguing results, such as high G+C gram positive origin of Bacteria, classification of Symbiobacterium thermophilum and Alcanivorax borkumensis in Firmicutes. Furthermore, simulation analyses indicate that addition of more gene relationships with high accuracy can greatly improve the resolution of the phylogenetic tree. Our results demonstrate the feasibility of the reconstruction of highly resolved phylogenetic tree with extensible gene networks across all three domains of life. This strategy also implies that the relationships between the genes (gene network) can define what kind of species it is.

There are no comments yet on this publication. Be the first to share your thoughts.

Statistics

Seen <100 times
0 Comments

More articles like this

Genome trees and the tree of life

on Trends in Genetics Jan 01, 2002

Genome trees and the tree of life.

on Trends in Genetics September 2002

Genome Networks Root the Tree of Life between Prok...

on Genome Biology and Evolution Jan 01, 2010

New approach for phylogenetic tree recovery based...

on Journal of Computational Biolo... July 2014
More articles like this..