Measuring genome conservation across taxa: divided strains and united kingdoms.
Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order, average ortholog similarity or gene content. Here, we introduce genome conservation--a novel metric of evolutionary distances between species that simultaneously takes into account, both gene content and sequence similarity at the whole-genome level. Genome conservation represents a robust distance measure, as demonstrated by accurate phylogenetic reconstructions. The genome conservation matrix for all presently sequenced organisms exhibits a remarkable ability to define evolutionary relationships across all taxonomic ranges. An assessment of taxonomic ranks with genome conservation shows that certain ranks are inadequately described and raises the possibility for a more precise and quantitative taxonomy in the future. All phylogenetic reconstructions are available at the genome phylogeny server: <http://maine.ebi.ac.uk:8000/cgi-bin/gps/GPS.pl>.
Kunin
Victor
V
Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.
Ahren
Dag
D
Goldovsky
Leon
L
Janssen
Paul
P
Ouzounis
Christos A
CA
D001419:Bacteria / Q000145:classification / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification / Q000235:genetics