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Nucleic Acids Research 2005 33(2):616-621; doi:10.1093/nar/gki181
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Published online 28 January 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Measuring genome conservation across taxa: divided strains and united kingdoms

Victor Kunin, Dag Ahren, Leon Goldovsky, Paul Janssen1 and Christos A. Ouzounis*

Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge CB10 1SD, UK 1 Laboratory of Microbiology, Belgian Nuclear Research Centre SCK/CEN Boeretang 200, B-2400-MOL, Belgium

*To whom correspondence should be addressed. Tel: +44 1223 494653; Fax: +44 1223 494471; Email: ouzounis{at}ebi.ac.uk

Received September 24, 2004. Revised November 23, 2004. Accepted December 20, 2004.

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>.


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