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Measuring genome conservation across taxa: divided strains and united kingdoms

Kunin, Victor; Ahrén, Dag LU ; Goldovsky, Leon; Janssen, Paul and Ouzounis, Christos A. (2005) In Nucleic Acids Research 33(2). p.616-621
Abstract
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... (More)
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>. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
genome phylogeny, Comparative genomics, evolution, Bioinformatics
in
Nucleic Acids Research
volume
33
issue
2
pages
616 - 621
publisher
Oxford University Press
external identifiers
  • scopus:13844306368
ISSN
1362-4962
DOI
10.1093/nar/gki181
language
English
LU publication?
yes
id
5dba29ad-5122-42bd-aa2f-c81a3e53d0f9 (old id 756009)
alternative location
http://nar.oxfordjournals.org/cgi/content/full/33/2/616
date added to LUP
2007-12-17 15:01:12
date last changed
2017-06-11 03:34:29
@article{5dba29ad-5122-42bd-aa2f-c81a3e53d0f9,
  abstract     = {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: &lt;http://maine.ebi.ac.uk:8000/cgi-bin/gps/GPS.pl&gt;.},
  author       = {Kunin, Victor and Ahrén, Dag and Goldovsky, Leon and Janssen, Paul and Ouzounis, Christos A.},
  issn         = {1362-4962},
  keyword      = {genome phylogeny,Comparative genomics,evolution,Bioinformatics},
  language     = {eng},
  number       = {2},
  pages        = {616--621},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {Measuring genome conservation across taxa: divided strains and united kingdoms},
  url          = {http://dx.doi.org/10.1093/nar/gki181},
  volume       = {33},
  year         = {2005},
}