The reach of the genome signature in prokaryotes

Persistent Link:
http://hdl.handle.net/10150/610373
Title:
The reach of the genome signature in prokaryotes
Author:
van Passel, Mark; Kuramae, Eiko; Luyf, Angela; Bart, Aldert; Boekhout, Teun
Affiliation:
Centraalbureau voor Schimmelcultures (CBS), Uppsalalaan 8, Utrecht, The Netherlands; Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands; Center for Infection and Immunity Amsterdam (CINIMA), Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands; Department of Biochemistry and Molecular Biophysics, University of Arizona, P.O. Box 210088, Tucson, Arizona, USA
Issue Date:
2006
Publisher:
BioMed Central
Citation:
BMC Evolutionary Biology 2006, 6:84 doi:10.1186/1471-2148-6-84
Journal:
BMC Evolutionary Biology
Rights:
© 2006 van Passel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:With the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics. One of these studies suggested good congruence between genome synteny, shared gene content, 16S ribosomal DNA identity, codon usage and the genome signature in prokaryotes. Here we rigorously test the phylogenetic signal of the genome signature, which consists of the genome-specific relative frequencies of dinucleotides, on 334 sequenced prokaryotic genome sequences.RESULTS:Intrageneric comparisons show that in general the genomic dissimilarity scores are higher than in intraspecific comparisons, in accordance with the suggested phylogenetic signal of the genome signature. Exceptions to this trend, (Bartonella spp., Bordetella spp., Salmonella spp. and Yersinia spp.), which have low average intrageneric genomic dissimilarity scores, suggest that members of these genera might be considered the same species. On the other hand, high genomic dissimilarity values for intraspecific analyses suggest that in some cases (e.g.Prochlorococcus marinus, Pseudomonas fluorescens, Buchnera aphidicola and Rhodopseudomonas palustris) different strains from the same species may actually represent different species. Comparing 16S rDNA identity with genomic dissimilarity values corroborates the previously suggested trend in phylogenetic signal, albeit that the dissimilarity values only provide low resolution.CONCLUSION:The genome signature has a distinct phylogenetic signal, independent of individual genetic marker genes. A reliable phylogenetic clustering cannot be based on dissimilarity values alone, as bootstrapping is not possible for this parameter. It can however be used to support or refute a given phylogeny and resulting taxonomy.
EISSN:
1471-2148
DOI:
10.1186/1471-2148-6-84
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2148/6/84

Full metadata record

DC FieldValue Language
dc.contributor.authorvan Passel, Marken
dc.contributor.authorKuramae, Eikoen
dc.contributor.authorLuyf, Angelaen
dc.contributor.authorBart, Alderten
dc.contributor.authorBoekhout, Teunen
dc.date.accessioned2016-05-20T09:05:22Z-
dc.date.available2016-05-20T09:05:22Z-
dc.date.issued2006en
dc.identifier.citationBMC Evolutionary Biology 2006, 6:84 doi:10.1186/1471-2148-6-84en
dc.identifier.doi10.1186/1471-2148-6-84en
dc.identifier.urihttp://hdl.handle.net/10150/610373-
dc.description.abstractBACKGROUND:With the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics. One of these studies suggested good congruence between genome synteny, shared gene content, 16S ribosomal DNA identity, codon usage and the genome signature in prokaryotes. Here we rigorously test the phylogenetic signal of the genome signature, which consists of the genome-specific relative frequencies of dinucleotides, on 334 sequenced prokaryotic genome sequences.RESULTS:Intrageneric comparisons show that in general the genomic dissimilarity scores are higher than in intraspecific comparisons, in accordance with the suggested phylogenetic signal of the genome signature. Exceptions to this trend, (Bartonella spp., Bordetella spp., Salmonella spp. and Yersinia spp.), which have low average intrageneric genomic dissimilarity scores, suggest that members of these genera might be considered the same species. On the other hand, high genomic dissimilarity values for intraspecific analyses suggest that in some cases (e.g.Prochlorococcus marinus, Pseudomonas fluorescens, Buchnera aphidicola and Rhodopseudomonas palustris) different strains from the same species may actually represent different species. Comparing 16S rDNA identity with genomic dissimilarity values corroborates the previously suggested trend in phylogenetic signal, albeit that the dissimilarity values only provide low resolution.CONCLUSION:The genome signature has a distinct phylogenetic signal, independent of individual genetic marker genes. A reliable phylogenetic clustering cannot be based on dissimilarity values alone, as bootstrapping is not possible for this parameter. It can however be used to support or refute a given phylogeny and resulting taxonomy.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2148/6/84en
dc.rights© 2006 van Passel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleThe reach of the genome signature in prokaryotesen
dc.typeArticleen
dc.identifier.eissn1471-2148en
dc.contributor.departmentCentraalbureau voor Schimmelcultures (CBS), Uppsalalaan 8, Utrecht, The Netherlandsen
dc.contributor.departmentBioinformatics Laboratory, Academic Medical Center, University of Amsterdam, the Netherlandsen
dc.contributor.departmentCenter for Infection and Immunity Amsterdam (CINIMA), Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlandsen
dc.contributor.departmentDepartment of Biochemistry and Molecular Biophysics, University of Arizona, P.O. Box 210088, Tucson, Arizona, USAen
dc.identifier.journalBMC Evolutionary Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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